Upper-division Biochemistry Research Articles

Pivoting Back to the In-Person Capstone Biochemistry Lab: Lessons Learned from the COVID-19 Online Modality to Improve the Course-based Undergraduate Research Experience.

The restructuring of an upper division biochemistry lab capstone course intended for biochemistry students with a range of laboratory experience was explored. A goal of the course was to give students practice with necessary skills needed for an entry level general position in biotechnology. The immediate impact of the online capstone course mandated by the COVID-19 pandemic limited students on learning essential hands-on research skills but evolved during the transition back to in-person instruction to include more elements of in-person practice. This article highlights the restructuring of the online remote course back to an in-person CURE capstone lab, which includes changes in the way information was disseminated and modifications in student assessments. This article documents how course evolution resulted in a shift in pedagogical strategies that also resulted in building a community of biochemistry learners.

Mind the Gap: Investigating Disaggregated Student Performance in an Upper-Division Biochemistry Course Following Team-Based Learning.

Team-based learning (TBL) is a highly intense active learning pedagogy that uses a cycle of preclass preparation, formative assessment for readiness, mini-lectures, and complex team exercises. Consistent with the literature on active learning, prior research on TBL consistently shows its benefits for student outcomes as compared with previous lecture. However, little work has examined student outcomes disaggregated by demographic variable. We analyzed assessment and student demographic data (i.e., binary gender, racial/ethnic group, generational status) in three semesters of TBL in an upper-division biochemistry course to understand the degree to which performance could be predicted by student demographics. We use theoretical and empirical research from social psychology to hypothesize that the intense interpersonal interactions of TBL could activate psychological threats, the effects of which would be measurable as differences in student performance that correlate with demographic variables. Our regression analysis did not support this hypothesis. This null result invites a deeper discussion on how we measure the potential effects of active learning on student outcomes, particularly given how important it is to account for intersectional and invisible identities.

Made for students, by students: Integrating former-student voices into a de-densified biochemistry laboratory.

The COVID-19 pandemic emphasized the importance of peer communication networks for student outcomes. Herein, we describe the use of supplemental instructional videos created by former students and integrated into electronic lab notebooks, to restore the lost community-learning component using student voices in a de-densified upper-division biochemistry laboratory.

Encouraging Biochemistry Students’ Metacognition: Reflecting on How Another Student Might Not Carefully Reflect

Many studies in science education research have found metacognition to be beneficial for undergraduate STEM students. Students do not necessarily know how to employ their metacognition without some training or prompting, and undergraduate chemistry instructors do not always have the capacity to instruct their students on metacognition. Thus, it would be beneficial for instructors and students if metacognition development could be implicitly incorporated into typical classroom activities. In this study, 25 undergraduate students in an upper-division biochemistry course were interviewed via a think-aloud protocol. In the interviews, they were asked to solve two open-ended buffer problems. Before answering the second buffer problem, the students were asked questions designed to target their metacognition. The interview transcripts were qualitatively analyzed through a codebook thematic analysis, with deductive and inductive coding, to understand the types of metacognitive knowledge and metacognitive skills these students demonstrated while solving the buffer problems. The transcripts were also analyzed to understand how these metacognitive prompts may have changed students’ metacognitive approaches to solving the problems. Overall, 20 of the 25 students demonstrated some type of metacognition in response to the metacognitive prompts that they had not demonstrated in the first buffer problem. We discuss how asking students to think how an “unreflective” student would answer a question can prompt students to metacognitively evaluate their thought processes.

Combined Guided and Open Inquiry Project for an Upper Division Biochemistry Lab: Sugar Content, Enzymatic Properties of Lactase, and the Spoiling Process in Milk

Guided inquiry is the practice of allowing students to come to their own conclusions about a set of data instead of verifying a known result using a given experimental procedure. Open inquiry takes...

Using NMR Spectroscopy To Measure Protein Binding Capacity on Gold Nanoparticles.

A simple one-dimensional 1H NMR experiment that quantifies protein bound to gold nanoparticles has been developed for upper-division biochemistry and physical chemistry students. This laboratory experiment teaches the basics of NMR techniques, which is a highly effective tool in protein studies and supports students to understand the concepts of NMR spectroscopy and nanoparticle-protein interactions. Understanding the interactions of gold nanoparticles (AuNPs) with biological macromolecules is becoming increasingly important as interest in the clinical use of nanoparticles has been on the rise. Applications in drug delivery, biosensing, diagnostics, and enhanced imaging are all tangible possibilities with a better understanding of AuNP-protein interactions. The ability to use AuNPs as biosensors for drug delivery methods in cellular uptake is dependent on the amount of protein that is able to bind to the surface of the nanoparticle. This laboratory experiment solidifies concepts such as quantitative NMR spectroscopy while reinforcing precision laboratory titrations. Students learn how 1H proton NMR spectra can be used to measure free protein in solution and protein bound to AuNPs. A simple formula is used to determine the binding capacity of the nanoparticle. This analysis helps students to understand the impact of nanoparticle-protein interactions, and it allows them to conceptualize macromolecular binding using NMR spectroscopy.

Liposome permeability probed by laser light scattering.

We have developed a laboratory project in which students prepare liposomes, expose them to hyperosmotic and hypoosmotic solutions, and follow the resulting shrinking and swelling (respectively) with laser light scattering. Each light intensity transient can be fit to an exponential decline or rise, with the decay constant (k) and the amplitude (ΔVmax ) being indirectly related to the kinetics and thermodynamics (respectively) of transmembrane osmotic flux. Students vary the experimental system by changing the types and concentrations of osmolytes such as alcohols, amides, and salts. Students then compare how these changes alter the rate and extent of osmotic flux. This upper division biochemistry laboratory project is a challenging and rewarding one that exposes students to a biomolecule (lipid) and a spectroscopic technique (laser spectroscopy) that are not commonly used in the undergraduate laboratory setting. © 2019 International Union of Biochemistry and Molecular Biology, 47(3):239-246, 2019.

Highly effective active learning in a one-year biochemistry series with limited resources.

We investigate the effectiveness of an active learning curriculum designed for an upper division Biochemistry series at a large, public research university. The goal was to determine how effective this format was when compared to a parallel conventional course, and to see if the active learning series can be run with limited resources (one instructor, one teaching assistant). The study involved 160 students in the first quarter and 92 students in the second quarter. The active learning curriculum consists of learning goals for each chapter, online quizzes, in-class questions targeting the problematic areas, small group (3-4 students) discussions during class in which students presented their assumptions and arguments in support of their responses to online and in-class questions, and two-stage exams involving the ability to "re-answer" as a group following a discussion). The in-class questions involved the use of a student response system (i > clicker) (multiple choice) and short answer formats. Students in the active learning course and a control, conventional lecture course, took identical midterms and finals for the first, and second quarters. We found that students enrolled in the active learning curriculum had consistently better performance, with statistically significant higher scores on all tests for both quarters. The effect sizes of the improvements are medium to large and are independent of prior GPA and grades in prerequisites. This model curriculum redesign offers promise for improved student learning with less monetary investment than a flipped course model relying on, for example, an extensive collection of instructor-produced videos. © 2018 International Union of Biochemistry and Molecular Biology, 47(1):7-15, 2018.

Enzyme Kinetics Experiment with the Multienzyme Complex Viscozyme L and Two Substrates for the Accurate Determination of Michaelian Parameters

A laboratory experiment in which students study the kinetics of the Viscozyme-L-catalyzed hydrolysis of cellulose and starch comparatively was designed for an upper-division biochemistry laboratory. The main objective of this experiment was to provide an opportunity to perform enhanced enzyme kinetics data analysis using appropriate informatics and statistical tools. By fitting the Michaelis–Menten, Lineweaver–Burk, Eadie–Hofstee, and Hanes equations to the experimental data, students explore the strengths and weaknesses of each plot and determine whether the two Viscozyme-L-catalyzed reactions obey Michaelis–Menten kinetics. Comparing the values of the Michaelian constants (vmax and KM) and the efficiencies obtained for each enzyme-catalyzed reaction allows advanced undergraduates to determine if the differences between these parameters are statistically significant.

Evaluating the Quick Fix: Weight Loss Drugs and Cellular Respiration

One key to student success in introductory and cell biology courses is a foundational knowledge of cellular respiration. This is a content area in which students often harbor misconceptions that make cellular respiration particularly challenging to teach. Conventional approaches presenting cellular respiration as a complex series of isolated steps creates a situation where students tend to memorize the steps but fail to appreciate the bigger picture of how cells transform and utilize energy. Instructors frequently struggle to find ways to motivate students and encourage deeper learning. The learning goals of this cellular respiration lesson are to understand energy transfer in a biological system, develop data analysis skills, practice hypothesis generation, and appreciate the importance of cellular respiration in everyday life.<strong> </strong>These goals are achieved by using a case study as the focal point. The case-based lesson is supported with student-centered instructional strategies, such as individual and group activity sheets, in-class group discussions and debate, and in-class clicker questions. This lesson has been implemented at two institutions in large enrollment introductory biology courses and in a smaller upper-division biochemistry course.

Purification and Electrophoretic Characterization of Lactate Dehydrogenase from Mammalian Blood: A Different Twist on a Classic Experiment

A multiweek protein purification suite, suitable for upper-division biochemistry or biotechnology undergraduate students, is described. Students work in small teams to isolate the enzyme lactate dehydrogenase (LDH) from a nontraditional tissue source, mammalian blood, using a sequence of three column chromatographic procedures: ion-exchange, size exclusion, and affinity chromatography. Protein and enzyme activity elution profiles are determined by graphical analysis of assay data collected using rapid microplate spectrophotometric assays. Students perform quantitative assays on LDH pools and use these data to build a purification table for use in evaluating the protocol. The protocol typically generates final overall fold-purifications from 1500 to 2500 and activity recoveries of 45–60%. Electrophoretic separations in both denaturing and native-gel format are analyzed both visually and by use of commercial digital analysis software to assess the isoenzyme pattern of isolated LDH and to further evaluate the purification. Assessment of student work revealed a high level of achievement of course learning goals that include development of critical thinking skills required to (1) critically evaluate an experimental protocol and (2) draw conclusions based on a variety of forms of experimental data.

The Alcohol Dehydrogenase Kinetics Laboratory: Enhanced Data Analysis and Student-Designed Mini-Projects

A highly instructive, wide-ranging laboratory project in which students study the effects of various parameters on the enzymatic activity of alcohol dehydrogenase has been adapted for the upper-division biochemistry and physical biochemistry laboratory. Our two main goals were to provide enhanced data analysis, featuring nonlinear regression, and also to give students experience in experimental design. Students use appropriate kinetic and thermodynamic equations to fit their data from Michaelis–Menten plots, enzyme activity pH profiles, inhibitor and denaturant concentration profiles, and temperature-dependence plots. Experiments at the end of this project are designed and implemented by student pairs, thus preparing them for independent research.

Correlation, necessity, and sufficiency: Common errors in the scientific reasoning of undergraduate students for interpreting experiments.

Gaining an understanding of how science works is central to an undergraduate education in biology and biochemistry. The reasoning required to design or interpret experiments that ask specific questions does not come naturally, and is an essential part of the science process skills that must be learned for an understanding of how scientists conduct research. Gaps in these reasoning skills make it difficult for students to become proficient in reading primary scientific literature. In this study, we assessed the ability of students in an upper-division biochemistry laboratory class to use the concepts of correlation, necessity, and sufficiency in interpreting experiments presented in a format and context that is similar to what they would encounter when reading a journal article. The students were assessed before and after completion of a laboratory module where necessary vs. sufficient reasoning was used to design and interpret experiments. The assessment identified two types of errors that were commonly committed by students when interpreting experimental data. When presented with an experiment that only establishes a correlation between a potential intermediate and a known effect, students frequently interpreted the intermediate as being sufficient (causative) for the effect. Also, when presented with an experiment that tests only necessity for an intermediate, they frequently made unsupported conclusions about sufficiency, and vice versa. Completion of the laboratory module and instruction in necessary vs. sufficient reasoning showed some promise for addressing these common errors.

Myoglobin structure and function: A multiweek biochemistry laboratory project.

We have developed a multiweek laboratory project in which students isolate myoglobin and characterize its structure, function, and redox state. The important laboratory techniques covered in this project include size-exclusion chromatography, electrophoresis, spectrophotometric titration, and FTIR spectroscopy. Regarding protein structure, students work with computer modeling and visualization of myoglobin and its homologues, after which they spectroscopically characterize its thermal denaturation. Students also study protein function (ligand binding equilibrium) and are instructed on topics in data analysis (calibration curves, nonlinear vs. linear regression). This upper division biochemistry laboratory project is a challenging and rewarding one that not only exposes students to a wide variety of important biochemical laboratory techniques but also ties those techniques together to work with a single readily available and easily characterized protein, myoglobin.

Identification and Analysis of Bioactive Components of Fruit and Vegetable Products

Many small-molecule antioxidants found in whole fruits and vegetables are analyzed and identified in this laboratory module for upper-division biochemistry courses. During this experiment, students develop their knowledge of the bioactivity of fruit and vegetable products while learning techniques to identify vitamins and nutritionally derived secondary metabolites. Students first develop skills by analyzing well-studied fruit and vegetable juice products prior to development of a multicomponent fruit and vegetable superjuice displaying maximal antioxidant capacity. Antioxidant capacity is measured using ascorbic acid standardized ferric reducing antioxidant power (FRAP) assay, and both aqueous and lipophilic small molecules are identified using reverse-phase, high-performance liquid chromatography. Final analyses include correlation of whole fruit and vegetable products with antioxidant capacity and vitamin content using basic statistical analysis, and identification and characterization of antioxidant c...

An Introduction to Passive Ion Transport across Model Lipid Membranes for Undergraduate Students: Proton Permeation Measurements in Liposomes

In an upper-division biochemistry laboratory experiment, students use a variety of experimental techniques and apply several biochemical and biophysical concepts to measure and interpret proton permeation rates across model membranes. Model membranes in the form of liposomes are prepared from lipids by the extrusion method. The liposomes encapsulate the membrane-impermeable fluorescent pH-indicator pyranine, which facilitates pH detection in their aqueous interior. Rates of proton permeation across the lipid membrane in response to acidification of the external volume are measured by fluorescence spectroscopy. Data analysis introduces students to flux calculations and illustrates the concept that concentration differences are the driving force of diffusion processes such as passive ion transport across membranes. Students are given the task of formulating and then testing a hypothesis regarding the effects of bilayer thickness, liposome radius, magnitude of pH difference across the bilayer, and the presence of potential uncouplers on experimentally observable permeation rates.

Teaching Upper-Division Biochemistry Students the Role of Noncovalent Interactions and Ligand Structure in DNA Binding

The experiment described here uses the binding of cyanine dyes to DNA as a model system for demonstrating the role that both ligand structure and noncovalent interactions play in DNA binding. Upper-division biochemistry laboratory students observe changes in absorbance and fluorescence spectra when small molecules bind either in the minor groove of DNA or by intercalation. Students specifically note that ligand charge, substituents, and flexibility greatly influence binding mode. Based on these observations, students then determine the binding mode of an unknown small molecule. This experiment also fosters independent thought and problem-solving abilities. Students must self-direct binding-mode identification of their unknown without any guidance from the instructor. After completing this experiment, students demonstrate a clear understanding of the factors that influence DNA binding.

Detergent‐based isolation of yeast membrane rafts

Lipid rafts have been implicated in numerous cellular processes including cell signaling, endocytosis, and even viral infection. Isolation of these lipid rafts often involves detergent treatment of the membrane to dissolve nonraft components followed by separation of raft regions in a density gradient. We present here an inquiry-based lab series using these techniques to isolate membrane rafts from yeast cells designed for the upper division biochemistry or cell biology course laboratory. The co-localization of a common raft-associated protein with lipid rafts is then followed. This lab series involves undergraduate cell biology or biochemistry students in each step of the scientific process from experimental design to dissemination of their results. Additionally, this lab series reinforces concepts in membrane structure while exposing undergraduates to common techniques in cell biology and biochemistry.

Commentary: Teaching cognitive skills in the biochemistry classroom-A community effort

Commentary: Teaching cognitive skills in the biochemistry classroom-A community effort

Active Learning of Biochemistry Made Easy (for the Teacher)

This active learning pedagogical technique aims to improve students' learning in a two-semester, upper-division biochemistry course sequence in which vast majority of students enrolled will continue on to medical or graduate schools. Instead of lecturing, Instructor moves to side of room, thereby becoming the guide on side. Students take turns being Leader (DL, instructor for day) and administer an oral quiz that requires answering questions of DL's own devising. The remaining students, knowing they must learn assigned material in advance, come prepared for every class. They prepare by creating written work abstracting most important things they have learned on given topic. Students use their prior writing and learning to answer questions asked by Discussion Leader; they also annotate these abstracts as they learn more during class. At end of each class, annotated writing is turned in to Instructor for grading: that grade combi...