Biochemistry Instructors Research Articles

How Do Instructors Explain The Mechanism by which ATP Drives Unfavorable Processes?

Concerns regarding students' difficulties with the concept of energy date back to the 1970s. They become particularly apparent for systems involving adenosine triphosphate (ATP), which plays a central role in maintaining the nonequilibrium state of biological systems and in driving energetically unfavorable processes. One of the most well-documented misconceptions related to ATP is the idea that breaking bonds releases energy, when the opposite is true. This misconception is often attributed to language used in biology referring to the "high-energy bonds" in ATP. We interviewed chemistry, biology, and biochemistry instructors to learn how they think about and teach the mechanism(s) by which ATP is used as an energy source in biological systems. Across 15 interviews, we found that instructors relied primarily on two mechanisms to explain the role of ATP: 1) energy release, focused on ATP hydrolysis and bond energies; and/or 2) energy transfer, focused on phosphorylation and common intermediates. Many instructors shared negative and uncomfortable experiences related to teaching ATP and energy release. Based on these findings, we suggest instructional strategies that: 1) aim to ease the concerns expressed by introductory biology instructors, and 2) emphasize the role of ATP so as to support students' understanding of molecular mechanisms.

Using PyMOL to Understand Why COVID-19 Vaccines Save Lives.

Chemistry and biochemistry instructors must help students to develop the ability to visualize and manipulate 3D biomolecular structures and critically analyze them and their relationship to their functions. To do this, representative systems must be strategically selected to stimulate students' motivation. Since the World Health Organization declared a global pandemic caused by a new beta-coronavirus, called SARS-CoV-2 in early 2020, huge efforts are being taken by researchers to learn in depth how this virus works and a lot of scientific results are continuously reported. Many of them focus on the structural features of the viral spike glycoprotein and their relation with the vaccine development. This paper presents a series of workouts that deep into the structural characteristics of the spike protein S SARS-CoV-2 virus and the structural features involved in its infection process, using free online resources such as the PDB and the computer program PyMOL. This type of activity is intended to engage structural biology students in examining these macromolecules and others to help establish procedures for controlling COVID-19 and other future infectious diseases. PyMOL session files and student activities are provided.

Toward a Validated Metabolic Systems Thinking Framework

Several recently reported research projects describe or measure student reasoning about biochemical pathway dynamics and regulation (BPDR). In this growing literature, a variety of approaches are taken to assess conceptual understanding in this area. While some studies have qualitatively investigated student misconceptions that arise in the context of research interviews, others have used test instruments constructed by biochemistry instructors to evaluate student learning quantitatively in the context of biochemistry course exams. In all cases, the focus has been on explicit biochemistry content with less emphasis on underlying general conceptual challenges. For both instructional and research purposes, a BPDR assessment framework based on underlying latent variables particularly informed by research in systems thinking is desirable.This project builds on the insights offered by the work cited above but takes a different approach to assess BPDR reasoning by considering the problem from the perspective of domain‐general conceptual challenges in systems thinking. Drawing on systems thinking research in the learning sciences and a variety of science education research fields, a preliminary Metabolic Systems Thinking Framework (MSTF) is proposed. This framework includes five factors – organizational levels, direct relationships, indirect relationships, parallel processes, and autoregulation. These factors are proposed to represent independent conceptual factors that influence reasoning in the context of BPDR problems.The sufficiency of the MSTF as a tool to assess student reasoning for BPDR is being evaluated through think‐aloud interviews with problems related to reasoning about glycolysis. Data from interviews with undergraduate biochemistry students has yielded evidence for the necessity of each of these factors, but whether they are jointly sufficient in this regard is currently being explored further. Additionally, a survey instrument is currently in development to establish the construct validity of the MSTF. This instrument includes multi‐item subscales for each of the factors of the MSTF. The instrument will be administered to undergraduate students enrolled in a biochemistry course covering metabolic pathways in spring 2022. Psychometric properties of the instrument will be determined to establish instrument reliability followed by confirmatory factor analysis to assess the construct validity of each factor.

Comparing the Impacts of Evidence‐Based Pedagogies in Undergraduate Biochemistry: Lessons from Productive Failure, Worked Examples Plus Practice, and Guided Inquiry

The physical basis of noncovalent interactions (PBI) represents a foundational concept in biochemistry education that students consistently struggle to grasp. Due to the difficulty of PBI, there is a need to determine the optimal instructional approach for presenting the concept in a classroom setting. Three evidence‐based pedagogies have been proposed to enhance student learning compared to traditional lecture‐based lessons: productive failure, worked examples plus practice, and guided inquiry. The productive failure approach is based upon achieving a desirable level of difficulty and preparing students for future learning. Students first attempt to solve problems independently and afterward receive direct instruction on the correct procedures and concepts to solve the problems correctly. The worked examples plus practice approach is based upon reducing cognitive load. Students first receive instruction on how to solve a problem correctly. Then they attempt to solve similar problems independently. The guided inquiry approach is less well‐defined but generally involves instructors continuously and actively supporting students during problem solving. These approaches have never been directly compared. We investigated the impact of productive failure, worked examples plus practice, and two forms of guided inquiry: scaffolded and unscaffolded guidance on student learning of PBI. We collected data from 123 students in Fall 2018 and 66 students in Spring 2019. Students took a basic knowledge pre‐test, and we then randomly assigned them to one of the four experimental conditions. After the lesson, they took a basic knowledge posttest and completed a series of near and far transfer constructed‐response problems. Near transfer problems are problems that resemble the problems used during instruction, while far transfer problems draw upon the same knowledge learned in the lesson but are presented in a different context. After analytically coding and scoring student responses, we found no significant effect of instruction type on basic knowledge change, indicating that students learned basic aspects of PBI in all conditions. We found that unscaffolded guidance was not sufficient for near transfer problem‐solving. Students in all other instruction types performed better on near transfer problems than students in unscaffolded guidance. For far‐transfer problem solving, we found no significant difference between productive failure and scaffolded guidance. These findings suggest important implications for optimizing student learning of PBI in undergraduate biochemistry. Biochemistry instructors need to offer more than unscaffolded guidance to maximize student learning of PBI, and productive failure or scaffolded guidance may facilitate the knowledge transfer indicative of deeper conceptual understanding.Support or Funding InformationThis material is based upon work supported by the National Science Foundation under Grant No. DRL1350345. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

BiochemAR: An Augmented Reality Educational Tool for Teaching Macromolecular Structure and Function

Using 2-dimensional (2D) images in order to teach about 3-dimensional (3D) molecules can limit the ability of students to grasp key visuospatial elements of 3D macromolecular structures, including depth perception and a sense of scale. The lack of simple, accessible, and easy-to-use teaching tools for visualizing and interacting with (i.e., rotating, translating, zooming) 3D virtual representations of macromolecular structure also continues to be a limitation for biochemistry instructors interested in incorporating more 3D visualizations in their classrooms. To address this current gap in available instructional tools, a novel app utilizing augmented reality (AR) technology to visualize macromolecular structures is described. The app allows users to easily visualize and manipulate the 3D structure of the potassium channel and is accompanied by a set of curricular materials to facilitate app implementation during a discussion on membrane transport. The app is free to download on both iOS and Android systems, is suitable for use on mobile and tablet systems, and is aimed for target audiences ranging from introductory to advanced undergraduate levels.

PyMOL as an Instructional Tool To Represent and Manipulate the Myoglobin/Hemoglobin Protein System

A goal for biochemistry instructors is to support their students’ ability to critically analyze protein structure and its relationship to function. To do this, biochemistry instructors strategicall...

Biochemistry instructors’ use of intentions for student learning to evaluate and select external representations of protein translation

Instructors draw on their intentions for student learning in the enactment of curriculum, particularly in the selection and presentation of external representation of scientific phenomena. These representations both create opportunities for students to experience non-experiential biochemical phenomena, such as protein translation, and constrain the possibilities for student learning based on the limited number of features depicted and the visual cues used to draw viewers attention to those features. In this study, we explore biochemistry instructors’ intentions for student learning about protein translation and how those intentions influence their selection of external representations for instruction. A series of instructor interviews were used to identify information that students need to know in order to develop a biochemically accurate understanding of protein translation. We refer to this information as the “critical features” of protein translation. Two dominant themes of critical features were identified: (1) components/structures of protein translation and (2) interactions/chemistry of protein translation. Three general components (the ribosome, the mRNA, and the tRNA) and two primary interactions (base pairing and peptide bond formation) were described by all instructors. Instructors tended to favor simpler, stylized representations that closely aligned with their stated critical features of translation for instructional purposes.

A Competency‐Based Approach to Developing Biomolecular Visual Literacy

When you show a visual representation of a biomolecule, do your students “see” what you “see”? Are they able to interpret the model correctly and draw appropriate conclusions about the structure and atomic/molecular interactions? Do they grasp that cartoon and space‐filling models represent the same protein? Biochemistry instructors use visual representations of biomolecules to teach many concepts, yet there are few tools and frameworks to assess whether students can interpret these models. The BioMolViz.org group is a team of educators developing these tools. Over four years, we have identified a set of overarching themes that encompass biomolecular visualization skills with teachable objectives. We define proficiency levels for the objectives, describe student competency within the objective at the novice (first year) and amateur (junior/senior year) levels, and link these competencies with assessment questions. For example, the objective: “students will describe the significance of the monomer unit location within the three‐dimensional structure of a polymer” can be applied throughout the student's academic career. Novice students would be expected to identify the termini of a biological polymer, while more advanced students would catalog interactions of monomers that stabilize the macromolecule. Here, we present our current efforts on this Biomolecular Visualization Framework, including the results from four National Science Foundation‐funded 2018 workshops and our diversity SACNAS/ABRCMS outreach efforts. We propose targeted visual literacy development will enable students to understand the structure and associated function of biomolecules. The BioMolViz.org website makes resources widely available to help instructors facilitate this growth.Support or Funding InformationThis work was supported by the National Science Foundation under award numbers DUE‐1022793, ‐1323414, ‐1503811 and IUSE‐1712268. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the National Science Foundation.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

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.

Biochemistry instructors' perceptions of analogies and their classroom use

Biochemistry education relies heavily on students' abilities to conceptualize abstract cellular and molecular processes, mechanisms, and components. From a constructivist standpoint, students build their understandings of these abstract processes by connecting, expanding, or revising their prior conceptions and experiences. As such, biochemistry instructors often use analogies to teach difficult or hard-to-visualize topics to their classes by relating these target concepts to more commonplace analogs with which their students may already be familiar. For example, the binding of an enzyme to its substrate is often compared to a lock and a key; and ATP is frequently referred to as a cellular energy currency in discussions of metabolism and reaction coupling. Although the use of analogies in biochemistry classrooms is fairly common, the specific ways biochemistry instructors use analogies differ from instructor to instructor and class to class. In this article, we discuss biochemistry instructors' perceptions of the use of analogies in their classroom instruction. Specifically, we discuss (1) biochemistry instructors' objectives for using analogies, (2) their perceptions of the potential disadvantages associated with analogy use, (3) the sources of the analogies they use in their classes, and (4) the ways they perceive that analogies should be presented in class to promote student learning of biochemical concepts.

What do biochemistry students pay attention to in external representations of protein translation? The case of the Shine–Dalgarno sequence

Biochemistry instructors often use external representations—ranging from static diagrams to dynamic animations and from simplistic, stylized illustrations to more complex, realistic presentations—to help their students visualize abstract cellular and molecular processes, mechanisms, and components. However, relatively little is known about how students use and interpret external representations in biochemistry courses. In the current study, variation theory was used to explore the potential for student learning about protein translation from a stylized, dynamic animation. The results of this study indicate that students learned from this animation, in that they noticed many critical features of the animation and integrated those features into their understandings of protein translation. However, many students also focused on a particular feature of the animation, the Shine–Dalgarno sequence, that their instructors did not feel was critical to promote an overall understanding of this metabolic process. Student attention was focused on this feature because of the design of the animation, which cued students to notice this feature by significantly varying the appearance of the Shine–Dalgarno sequence.

Biochemistry Instructors’ Views toward Developing and Assessing Visual Literacy in Their Courses

Biochemistry instructors are inundated with various representations from which to choose to depict biochemical phenomena. Because of the immense amount of visual know-how needed to be an expert biochemist in the 21st century, there have been calls for instructors to develop biochemistry students’ visual literacy. However, visual literacy has multiple aspects, and determining which area to develop can be quite daunting. Therefore, the goals of this study were to determine what visual literacy skills biochemistry instructors deem to be most important and how instructors develop and assess visual literacy skills in their biochemistry courses. In order to address these goals, a needs assessment was administered to a national sample of biochemistry faculty at four-year colleges and universities. Based on the results of the survey, a cluster analysis was conducted to group instructors into categories based on how they intended to develop visual literacy in their courses. A misalignment was found between the visual literacy skills that were most important and how instructors developed visual literacy. In addition, the majority of instructors assumed these skills on assessments rather than explicitly testing them. Implications focus on the need for better measures to assess visual literacy skills directly.

Results of a National Survey of Biochemistry Instructors To Determine the Prevalence and Types of Representations Used during Instruction and Assessment

Chemists and chemistry educators have long sought meaningful ways to visualize fundamentally abstract components, such as atoms and molecules, of their trade. As technology has improved, computer-based visualization methods have infused both research and education in chemistry. Biochemistry, in particular, has become highly dependent on ways that large molecular systems can be represented, and how to best focus attention on the most critical aspects of the molecular system. To better understand the current state of educational efforts related to visual literacy, a needs assessment was developed and administered to a national sample of biochemistry instructors at four-year institutions (N = 536) to determine the types of representations used during biochemistry course instruction and assessment. Cluster analysis was conducted on the responses to determine similar usage of representations in both instruction and assessment. A significant difference was determined between the types of representations used by instructors teaching a biochemistry survey course and a yearlong course. Implications of how these findings can influence biochemistry instruction and assessment are discussed.

Probing and improving student's understanding of protein α‐helix structure using targeted assessment and classroom interventions in collaboration with a faculty community of practice

The increasing availability of concept inventories and other assessment tools in the molecular life sciences provides instructors with myriad avenues to probe student understanding. For example, although molecular visualization is central to the study of biochemistry, a growing body of evidence suggests that students have substantial limitations in their ability to recognize and interpret basic features of biological macromolecules. In this study, a pre/posttest administered to students at diverse institutions nationwide revealed a robust incorrect idea about the location of the amino acid side chains in the protein α-helix structure. Because this incorrect idea was present even after a semester of biochemistry instruction at a range of institutions, an intervention was necessary. A community of expert biochemistry instructors collaborated to design two active learning classroom activities that systematically examine α-helix structure and function. Several participating faculty used one or both of the activities in their classrooms and some improvement of student understanding of this concept was observed. This study provides a model of how a community of instructors can work together using assessment data to inform targeted changes in instruction with the goal of improving student understanding of fundamental concepts.

“Big-Picture” Worksheets To Help Students Learn and Understand the Pentose Phosphate Pathway and the Calvin Cycle

Two worksheets designed to help biochemistry instructors teach the pentose phosphate pathway and the Calvin cycle are presented. The worksheets avoid excessive detail, but portray the pathways in such a manner that the fates of all molecules involved are depicted; this format allows students to follow the interconversions without having to wonder where a particular intermediate originated or what final compound it is destined to become. When combined with knowledge of the structures of some basic monosaccharides and of key enzymatic steps (e.g., transketolase and transaldolase), the use of these worksheets can help students learn and understand the pathways rather than superficially memorize them.

Probing and improving students’ understanding of protein alpha helix structure using targeted assessment and classroom interventions

Molecular visualization is central to the study of biochemistry. Fundamental skills in this area are often taught in introductory biology and chemistry courses. As biochemistry instructors, we hope that students are able to apply visualization skills learned in earlier coursework to advanced coursework including biochemistry, yet many of us know from experience that this is not always the case. A pre/post‐test we developed revealed a robust incorrect idea about the location of the amino acid side chains in the protein alpha helix structure (1,2). Since this incorrect idea was present even after a semester of instruction in biochemistry at a range of institutions, an intervention was necessary. We worked collaboratively with a community of twenty expert biochemistry instructors to design two active learning classroom activities that examine alpha helix structure more systematically. Several of these faculty used one or both of the activities in their classrooms. Through this process we were able to use assessment data to make targeted changes in teaching. Student responses to the activities revealed further issues related to molecular visualization and students’ ability to properly interpret space‐filling molecular diagrams.

Uncovering students' incorrect ideas about foundational concepts for biochemistry

This paper presents preliminary data on how an assessment instrument with a unique structure can be used to identify common incorrect ideas from prior coursework at the beginning of a biochemistry course, and to determine whether these ideas have changed by the end of the course. The twenty-one multiple-choice items address seven different concepts, with a parallel structure for distractors across each set of items to capture consistent incorrect responses. For the current study, the instrument was administered as a pre-test and post-test in majors level biochemistry courses, and the results from two different groups are presented. These results indicated that students performed better on the post-test, resulting in positive mean gain scores for each concept. The structure of the instrument allows data analysis that helped uncover persistent incorrect ideas for some of the concepts, including bond energy and protein alpha helix structure, even after a semester of instruction in biochemistry. The persistent incorrect idea for the protein alpha helix structure uncovered by this assessment has not been reported before in the literature. These results confirm the need to use a robust diagnostic instrument to assess students’ understanding of basic concepts at the beginning of the semester, but also stress the need to assess students near the end of the course to gain insight on the effectiveness of instruction. Since each group of students is different, biochemistry instructors are encouraged to use the instrument to identify problems with their own students’ incoming ideas rather than rely on published results to inform instruction. In addition to providing assistance for instructors of biochemistry in planning targeted instructional interventions, we anticipate that data collected from this instrument can also be used to identify potential modifications for prerequisite courses.

Book Review of Foundations in Biochemistry

Foundations in Biochemistry by Jenny Loertscher and Vicky Minderhout is a workbook designed to accompany an instructor’s chosen biochemistry textbook. The book is based on the process-oriented, guided-inquiry learning (POGIL) approach to teaching. Loertscher and Minderhout have successfully used a “lectureless” POGIL approach to teaching biochemistry. This workbook allows biochemistry instructors to incorporate the POGIL approach, in whole or in part, into their classrooms. Instructors who would like their students to engage the material and think about the bigger picture will find Foundations in Biochemistry by Loertscher and Minderhout to be a valuable addition to their biochemistry classroom.

Introducing proteomics in the undergraduate curriculum: A simple 2D gel electrophoresis exercise with serum proteins

Two-dimensional gel electrophoresis (2DGE) remains an important tool in the study of biological systems by proteomics. While the use of 2DGE is commonplace in research publications, there are few instructional laboratories that address the use of 2DGE for analyzing complex protein samples. One reason for this lack is the fact that the preparation of samples for 2DGE is a complex and difficult process that can commonly yield gels of poor quality and resolution. In this experiment, we use a serum-based sample to mitigate many of the sample preparation issues that occur in cell-based sample preparations and incorporate a protein precipitation method that was developed to address the problem of high-abundance proteins and dynamic range in serum proteomics research. By focusing on 2DGE apart from many other facets of proteomic experimental design, students have the opportunity to gain fruitful experience in the use of this workhorse proteomics technique. This simplified focus also makes this exercise accessible to biochemistry instructors who are not active in proteomics; the requisite techniques may require some new equipment (i.e. an isoelectric focusing apparatus), but this exercise focuses on using familiar techniques (primarily electrophoresis) to cross the threshold of a new field, proteomics.

Assessment of the Effectiveness of Structure Exploration Tools in Biochemistry Education

Most biochemistry instructors strive to illustrate complex biomacromolecular structures by both static images and interactive computer graphics. Most textbooks come with elaborate tutorials on CD or websites. Other biochemistry educators have written tutorials for stand‐alone graphics viewers such as Rasmol, Deep View, or kinemages, or for browser‐based viewers such as Jmol. Recent attempts to incorporate virtual reality games into structure exploration also seem promising. A clear measure of the educational effectiveness of these computer‐based renderings, however, will require new assessment tools that will have to account for a variety of factors including learning of content, development of spatial abilities, and effect on student attitudes and motivation levels. This presentation will consider possible approaches to developing such assessment instruments.