Biochemistry Laboratory Course Research Articles

A survey on faculty perspectives on the transition to a biochemistry course-based undergraduate research experience laboratory.

It will always remain a goal of an undergraduate biochemistry laboratory course to engage students hands-on in a wide range of biochemistry laboratory experiences. In 2006, our research group initiated a project for in silico prediction of enzyme function based only on the 3D coordinates of the more than 3800 proteins "of unknown function" in the Protein Data Bank, many of which resulted from the Protein Structure Initiative. Students have used the ProMOL plugin to the PyMOL molecular graphics environment along with BLAST, Pfam, and Dali to predict protein functions. As young scientists, these undergraduate research students wanted to see if their predictions were correct and so they developed an approach for in vitro testing of predicted enzyme function that included literature exploration, selection of a suitable assay and the search for commercially available substrates. Over the past two years, a team of faculty members from seven different campuses (California Polytechnic San Luis Obispo, Hope College, Oral Roberts University, Rochester Institute of Technology, St. Mary's University, Ursinus College, and Purdue University) have transferred this approach to the undergraduate biochemistry teaching laboratory as a Course-based Undergraduate Research Experience. A series of ten course modules and eight instructional videos have been created (www.promol.org/home/basil-modules-1) and the group is now expanding these resources, creating assessments and evaluating how this approach helps student to grow as scientists. The focus of this manuscript will be the logistical implications of this transition on campuses that have different cultures, expectations, schedules, and student populations. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):426-436, 2017.

Introduction of Enzymatic Polymer Degradation to enhance the Undergraduate Polymer Chemistry Curriculum

Changes to the 2015 ACS Guidelines and Evaluation Procedures for Bachelor's Degree Programs included mandatory instruction in polymers and macromolecules for the ACS‐certified degrees. To satisfy this mandate, we have begun developing a series of undergraduate laboratory exercises involving the synthesis, degradation, and characterization of poly(aspartic acid) (PAA). PAA, a biodegradable, water‐soluble synthetic polymer, could potentially replace commonly used poly(acrylic acid), which is a non‐biodegradable polymer that possess environmental risks. In this module of experiments, PAA is prepared in the organic chemistry laboratory course by polymerizing aspartic acid to form poly(succinimide) as an intermediate, which is converted to PAA by base induced ring‐opening. The synthetic PAA, composed of both β‐amide (70%) and α‐amide units (30%), is then transferred to the biochemistry laboratory course for enzymatic biodegradation using two enzymes, PAA hydrolase‐1 (PAAH‐1) and PAA hydrolase‐2 (PAAH‐2). A proposed mechanism suggests that PAAH‐1 hydrolyzes β‐β amide linkages, resulting in oligo (aspartic acid), wherein PAAH‐2 completes the degradation process by cleaving the oligo (aspartic acid) units into monomeric aspartic acid. Current progress on the development of this biochemistry laboratory exercise including overexpression of recombinant PAAH‐1 and PAAH‐2, purification, and characterization will be presented.Support or Funding InformationDUE 1611988

A Process for Defining and Validating Learning Competencies for Course‐based Undergraduate Research Experiences in a Biochemistry Laboratory Course

There is a move in science education to provide students with more Course‐based Undergraduate Research Experiences (CUREs). As CUREs begin to be implemented, their impact on student learning needs to be thoroughly evaluated. Thus far, educational research on CUREs has mainly utilized generalized surveys, rubrics, and perception instruments to assess students' technical performance and laboratory experiences; with a dearth of research focusing on the assessment of the scientific research attributes and behaviors that these courses are expected to develop in students. The goal of this study was to design a process for the development and validation of a taxonomy of scientific research abilities that students could acquire during a novel biochemistry CURE laboratory, where students predict and evaluate hypotheses for the function of proteins that have a known structure, but no confirmed function. Towards this goal, the following research questions were addressed: 1) which scientific research abilities are key to the competent performance of the biochemistry CURE laboratory? and 2) what educational research process could be developed to identify these scientific research abilities to enable the construction of the taxonomy? To address these questions, data was collected at six institutions from instructors who had participated in the development of the lab teaching materials. The study was framed by the Concept‐Reasoning‐Mode of Representation (CRM) model and focused on the scientific reasoning taking place with the various concepts and representations, either presented or generated as part of each lab. The process included the collection of three types of data: content analysis of the lab protocols to identify concepts and representations, a faculty survey to determine how experts reason with the different concepts and representations of relevance to the lab, and faculty interviews to probe deeper into the nature of students' research experiences and abilities that may be encountered during the performance of the laboratory. Analysis of the data allowed for triangulation and identification of items in common across the data sources which, in turn, permitted identification of student competencies acquired from the CUREs. Proposed ability statements were validated by surveying the faculty members about their importance and whether they expected students to acquire such abilities during the lab. The process proved effective for the identification of research abilities that in the future could be used to develop a taxonomy of student learning for biochemistry CURE laboratories. This taxonomy will be used to inform further curriculum development, including student assessment and more carefully targeted teaching and learning activities. Finally, the process shows potential for application to other lab courses across institutions where the goal is to develop students' abilities to think and perform like a research scientist.Support or Funding InformationThis work was funded by the National Science Foundation (NSF) Division of Undergraduate Education (DUE) grant #1503798. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

Design of a robust undergraduate biochemistry laboratory course based on a modified and expanded bovine serum albumin purification scheme

The ASBMB curriculum for an undergraduate degree recommends a set of skills that can be acquired only through laboratory courses and research experience. Based on a modified and expanded purification scheme for BSA, we designed a robust, reproducible, budget‐friendly, safe and inquiry‐based undergraduate biochemistry laboratory course that encompasses a lot of the skill‐sets recommended in the ASBMB curriculum. The purification scheme employed in this work has been reported in a research paper. This work not only modifies certain steps in the scheme, it includes additional steps to enhance student learning and skill acquisition. Salt precipitation, ion exchange and size exclusion chromatography were employed by students to purify BSA from cow plasma. Presence of major contaminants of BSA purification, IgGs and nucleases, were tested in the purified sample by western blotting and DNase I assay respectively. The DNase assay step provides an opportunity for students to learn basic molecular biology techniques such as plasmid isolation and restriction digestion. One major addition to the purification process is the bromocresol green‐BSA complex formation assay to precisely quantitate BSA at each step and generate a purification table. Comparison of sequences and other parameters of albumin proteins from common animals provides a bioinformatics twist to student experience. Abundance of albumin from the plasmas of common animals, cow, pig and chicken, allows for variation in the design of the course, and students can work in groups or individually. The course could be designed as a half‐semester or full‐semester biochemistry laboratory module, and a sample schedule is provided.Support or Funding InformationWelch Foundation Grant # AN‐0008

A multiweek tyrosinase inhibitor synthesis and analysis project: a capstone experiment for the undergraduate biochemistry laboratory course

Drug synthesis and analysis are topics that tend to be of high interest to biochemistry students as many of them have an interest in pursuing careers in healthcare or the pharmaceutical industry. The Biochemistry and Molecular Biology Concept Inventory Project has identified specific foundational and technical skills critical for biochemistry students. Specific foundational skills include experimental design, data analysis, and communication of science. Technical skills include accurate pipetting, solution preparation and proper use of instrumentation. To merge student interest in drug design with these foundational competencies, a multi‐week laboratory exercise where students synthesize, analyze, and test the potency of azostilbenoid tyrosinase inhibitors was designed and carried out over multiple years at two primarily undergraduate institutions. This project is a capstone experiment as it draws on content and techniques from other chemistry courses as well as biochemistry. This presentation will outline experimental design, results, practical considerations, and student learning outcomes of this novel drug synthesis and analysis experiment for the biochemistry laboratory.

Bring Your Own Device: A Digital Notebook for Undergraduate Biochemistry Laboratory Using a Free, Cross-Platform Application

The majority of undergraduates own a smartphone, yet fewer than half view it as a valuable learning technology. Consequently, a digital laboratory notebook (DLN) was developed for an upper-division undergraduate biochemistry laboratory course using the free mobile application Evernote. The cloud-based DLN capitalized on the unique features of smartphones (i.e., photo uploading, audio capture, dictation) and could also be accessed from any Internet-connected device (i.e., tablet, laptop, desktop). This cross-platform flexibility enabled a “Bring Your Own Device” philosophy in the course, leveraging the educational power of students’ personal devices. The DLN served as a secure data management system, where any file could be attached, edited, and analyzed. The DLN also accommodated freehand drawing. A postsemester survey indicated that the cloud connectivity of the DLN facilitated greater collaboration between students and enhanced the quality of their communication with the instructor compared with traditi...

Synchrotron-based macromolecular crystallography module for an undergraduate biochemistry laboratory course.

This paper describes the introduction of synchrotron-based macromolecular crystallography (MX) into an undergraduate laboratory class. An introductory 2week experimental module on MX, consisting of four laboratory sessions and two classroom lectures, was incorporated into a senior-level biochemistry class focused on a survey of biochemical techniques, including the experimental characterization of proteins. Students purified recombinant protein samples, set up crystallization plates and flash-cooled crystals for shipping to a synchrotron. Students then collected X-ray diffraction data sets from their crystals via the remote interface of the Molecular Biology Consortium beamline (4.2.2) at the Advanced Light Source in Berkeley, CA, USA. Processed diffraction data sets were transferred back to the laboratory and used in conjunction with partial protein models provided to the students for refinement and model building. The laboratory component was supplemented by up to 2 h of lectures by faculty with expertise in MX. This module can be easily adapted for implementation into other similar undergraduate classes, assuming the availability of local crystallographic expertise and access to remote data collection at a synchrotron source.

Use of mushroom tyrosinase to introduce michaelis-menten enzyme kinetics to biochemistry students.

An inexpensive enzyme kinetics laboratory exercise for undergraduate biochemistry students is described utilizing tyrosinase from white button mushrooms. The exercise can be completed in one or two three-hour lab sessions. The optimal amounts of enzyme, substrate (catechol), and inhibitor (kojic acid) are first determined, and then kinetic data is collected in the absence and presence of the inhibitor. A Microsoft Excel template is used to plot the data and to fit the Michaelis-Menten equation to the data to determine the kinetic parameters Vmax and Km . The exercise is designed to clarify and reinforce concepts covered in an accompanying biochemistry lecture course. It has been used with positive results in an upper-level biochemistry laboratory course for junior/senior students majoring in chemistry or biology. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):270-276, 2017.

Partial Purification of Hen Egg White Lysozyme: A Short Laboratory Exercise

This laboratory exercise was developed as part of a protein purification and enzymology module for the Biochemistry Laboratory Course at Lane College, a small, historically black college. The overall learning objective of the module is to demonstrate the basic principles of buffer preparation and protein techniques, including protein purification, separation, quantification, and determination of enzyme activity. The objective for the exercise described here is to demonstrate the basic principles of protein purification, including separation of proteins by precipitation with salt or organic compounds. This approach engages the students in a research‐like setting, where they learn that protein purification is not straightforward, often requiring trial and error. While many procedures for the purification of lysozyme laboratory exercise have been described elsewhere, they are not suitable for the limitations of a short laboratory class time of one hour and fifty minutes. This protocol for partial purification of hen egg white lysozyme can be completed within one hour using relatively inexpensive reagents and equipment. The students first dilute the egg white 0.05 M NaCl. Next, they adjust the pH of the mixture using acetic acid, and complete the precipitation by diluting the mixture with ethanol. The students then separate the supernatant from the precipitate either by centrifugation in a benchtop microcentrifuge or by filtration through Whatman paper. The students are encouraged to modify the procedure to determine which method works best. In subsequent laboratory exercises, the students then analyze the degree of purification through comparison of their supernatants with hen egg white by quantification of protein concentration with the Bradford Assay, SDS‐PAGE and lysozyme activity assays using standard protocols.Support or Funding InformationLane College Division of Natural and Physical Sciences and Mathematics

Transforming an Undergraduate Biochemistry Laboratory Courses: Do the Pros Outweigh the Cons?

Recommendations from a number of different agencies (ASBMB, NSF, HHMI, AAAS) have urged undergraduate laboratory courses to adopt a more research‐like curriculum. Often a justification is made that these courses potentially represent the only research experience an undergraduate might have at their institution, valid only for institutions or programs that do not have a mandatory capstone research requirement. Whereas this pedagogical approach is relatively simple for a two‐semester laboratory course, making this transformation in a one semester course requires much greater thought and planning. We have just completed a six year transformation of our upper level one semester biochemistry lab course from a traditional methods and techniques format to one in which the students are involved in an inquiry‐guided research project for three quarters of the semester. This presentation will focus on the pros and cons as well as the challenges of carrying out this transformation.

Student-Led Development of an Interactive and Free Biochemical Methods eBook

An approach to create an interactive and inexpensive electronic book (eBook) for an undergraduate biochemistry laboratory course is presented. This approach featured the involvement of an undergraduate student in the lead role of designing and developing the eBook using Apple’s iBooks Author application. The eBook, entitled Introduction to Biochemical Methods, contains original, interactive course content, including laboratory protocols, lecture slides, images, videos, figures, and quizzes. Access to the book content was expanded through the creation of a Web-based version of the book. User access analytics on both the eBook and the Web site, along with student survey data related to the usage of and attitudes toward the eBook, also are presented. Although the Introduction to Biochemical Methods eBook was developed specifically for use in a particular course, adaptation of its content for use in other classrooms is invited, and educators are encouraged to adopt a similar approach (i.e., involving their students) in developing eBooks for courses at their learning institutions. The immersive nature of the design and development process provided significant learning experiences for the student who led the development of the eBook.

Team-Based Learning, Faculty Research, and Grant Writing Bring Significant Learning Experiences to an Undergraduate Biochemistry Laboratory Course

This biochemistry laboratory course was designed to provide significant learning experiences to expose students to different ways of succeeding as scientists in academia and foster development and improvement of their potential and competency as the next generation of investigators. To meet these goals, the laboratory course employs three different practices that support an ‘Integrated Course Design’ approach: (1) incorporating basic laboratory techniques with faculty research projects, (2) promoting team-based learning, and (3) developing, de novo, a mini-NIH grant proposal that serves as a capstone project. On course evaluations, students give the biochemistry laboratory course the highest ratings for course and teaching effectiveness, and these ratings are a higher percentage overall compared to similar chemistry laboratory courses offered in the program. Students also state that the practices of the laboratory course went beyond their prior experiences in traditional lab courses. They have reported th...

A Two-Week Guided Inquiry Protein Separation and Detection Experiment for Undergraduate Biochemistry

A laboratory experiment for teaching protein separation and detection in an undergraduate biochemistry laboratory course is described. This experiment, performed in two, 4 h laboratory periods, incorporates guided inquiry principles to introduce students to the concepts behind and difficulties of protein purification. After using size-exclusion chromatography to separate a mixture of proteins, students utilize a colorimetric enzymatic assay and an immunoassay to determine the location of individual mixture components. Students proceed to determine the molecular weight of each protein using gel electrophoresis and generated mass spectrometric data. Completing this experiment provides students with an opportunity to expediently separate proteins while learning about protein characterization.

Guided inquiry in a biochemistry laboratory course improves experimental design ability

Many biochemistry laboratory courses expose students to laboratory techniques through pre-determined experiments in which students follow stepwise protocols provided by the instructor. This approach fails to provide students with sufficient opportunities to practice experimental design and critical thinking. Ten inquiry modules were created for a one-semester undergraduate biochemistry laboratory course; these are freely available on the project website. A slightly modified version of the Experimental Design Ability Test (EDAT) was used to assess the impact of inquiry-based learning on student experimental design ability in four experimental (inquiry) and four control (cookbook) sections. EDAT is a published tool that has been validated for use in undergraduate populations. The results, measured by pre- and post-tests, showed a significant positive impact on the experimental design ability of students in sections that employed the inquiry approach, when compared to those in control sections that employed the cookbook approach. A follow-up conversation with students in a sequel course suggested that the inquiry-based approach also benefited students by promoting self-directed learning.

A biochemistry laboratory course designed to enhance students autonomy

INTRODUCTION: Laboratory sessions are responsible for promoting instrumentation skills desirable in biochemistry and biochemistry related careers. They are traditionally based on experimental protocols that lead to the expected results, and students usually have not autonomy to plan and execute their experiments. GOALS: This work aimed to enhance a traditional biochemistry lab course, applying pre-lab quizzes on protein biochemistry and lab techniques in order to have students better prepared to plan, execute and interpret experiments. This approach also aims to bring the laboratory sessions into an inquiry-based environment capable to improve students’ independent capabilities in 2 autonomy domains: learning and communication. MATERIAL AND METHODS: Online quizzes are delivered one week before each laboratory session, containing questions regarding the experimental techniques and theoretical basis related to them. Laboratory activities are presented in an inquiry-based approach where the first class of each activity is dedicated to plan experiments in order to answer the research questions presented by instructors. Activities are also organized in order to enhance students’ autonomy. The first activity is the simplest and more instructor-controlled and the last one is the most complex and less driven, transferring gradually to students the responsibility for their decisions in laboratory, supporting students’ autonomy. RESULTS: Online quizzes allowed instructors to identify students’ difficulties and to timely intervene. Scientific reports presented by students at the end of each activity showed that they performed better on less driven activities in which autonomy support were more complex than in the instructor controlled activities. CONCLUSIONS: Scientific reports analysis reveals students capabilities related to different scopes of autonomy, such as: discuss different strategies; find multiple solutions to solve problems; make their own experiment hypothesis and look for literature to support data found. Thus, this approach may have positively supported students’ autonomy, encouraging them to think by themselves and to take decisions concerning their experiments.

Known structure, unknown function: An inquiry-based undergraduate biochemistry laboratory course.

Undergraduate biochemistry laboratory courses often do not provide students with an authentic research experience, particularly when the express purpose of the laboratory is purely instructional. However, an instructional laboratory course that is inquiry‐ and research‐based could simultaneously impart scientific knowledge and foster a student's research expertise and confidence. We have developed a year‐long undergraduate biochemistry laboratory curriculum wherein students determine, via experiment and computation, the function of a protein of known three‐dimensional structure. The first half of the course is inquiry‐based and modular in design; students learn general biochemical techniques while gaining preparation for research experiments in the second semester. Having learned standard biochemical methods in the first semester, students independently pursue their own (original) research projects in the second semester. This new curriculum has yielded an improvement in student performance and confidence as assessed by various metrics. To disseminate teaching resources to students and instructors alike, a freely accessible Biochemistry Laboratory Education resource is available at http://biochemlab.org. © 2015 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 43(4):245–262, 2015.

An RNA Research‐based Advanced Biochemistry Laboratory Course: Design, Implementation, and Outcomes

Inquiry‐based experiments are traditionally used in biochemistry laboratory courses to teach students a variety of biochemical concepts and techniques. These laboratory experiments are often completed in multi‐week modules, with each module focusing on specific student learning outcomes. In this context, students often struggle to make connections between modules. Integration of an authentic research experience into these courses allows students to master specific learning outcomes in the broader context of a course‐long research project. A three‐credit research‐based advanced biochemistry laboratory course was designed and implemented at Fort Lewis College. The course goals were to introduce students to modern nucleic acid biochemistry techniques and improve their abilities to communicate complex biochemical topics in written and oral form. In this course, students explored the structure and function of the human t‐cell leukemia virus (HTLV) frameshift site RNAs. Teams of three to four students worked on three related research projects throughout the semester. The first part of the course introduced students to the background of the research topic and basic principles of molecular cloning, in vitro transcription, and RNA purification. Students designed RNA constructs to answer specific questions related to their research topic. These RNAs would ultimately be in vitro transcribed, purified, and used in experiments. Students regularly submitted formal research reports and gave oral presentations on their work. Progress towards achievement of course learning goals was monitored with formative and summative assessments. Students made substantial progress towards achievement of these goals and anonymous post‐semester feedback was overwhelming positive.

Utilizing Ligation Independent Cloning in an Undergraduate Biochemistry Laboratory Course

As a continuation of the transformation of our laboratory course to a more research focused experience we tested whether the Ligation Independent Cloning (LIC) technique would be suitable for students with little to no prior experience in molecular biology methodologies. To produce an expression system for for E. coli alkaline phosphatase (PhoA) we cloned its gene into the pETHSUL vector kindly donated by Dr. Patrick Loll. The construct expresses a fusion protein where a His‐tagged SUMO protein is fused to PhoA. The sumo moiety can be proteolytically released from PhoA following affinity column purification. We compare the ease of building the pETHSUL‐PhoA construct and enzyme activity data for the purified enzyme with an expression system developed previously in our class using a classical double restriction enzyme sub‐cloning into a pET29a vector that incorporates a His‐tag at the C‐terminus of PhoA.

Fluorescence quantum yield measurements of fluorescent proteins: a laboratory experiment for a biochemistry or molecular biophysics laboratory course.

Fluorescent proteins are commonly used in cell biology to assess where proteins are within a cell as a function of time and provide insight into intracellular protein function. However, the usefulness of a fluorescent protein depends directly on the quantum yield. The quantum yield relates the efficiency at which a fluorescent molecule converts absorbed photons into emitted photons and it is necessary to know for assessing what fluorescent protein is the most appropriate for a particular application. In this work, we have designed an upper-level, biochemistry laboratory experiment where students measure the fluorescence quantum yields of fluorescent proteins relative to a standard organic dye. Four fluorescent protein variants, enhanced cyan fluorescent protein (ECFP), enhanced green fluorescent protein (EGFP), mCitrine, and mCherry, were used, however the methods described are useful for the characterization of any fluorescent protein or could be expanded to fluorescent quantum yield measurements of organic dye molecules. The laboratory is designed as a guided inquiry project and takes two, 4 hr laboratory periods. During the first day students design the experiment by selecting the excitation wavelength, choosing the standard, and determining the concentration needed for the quantum yield experiment that takes place in the second laboratory period. Overall, this laboratory provides students with a guided inquiry learning experience and introduces concepts of fluorescence biophysics into a biochemistry laboratory curriculum.

Evolution of an undergraduate biochemistry laboratory course (618.15)

Undergraduate laboratory courses represent interactive learning in its purest form, where direct observation provides a mechanism by which students can begin to appreciate the ways in which scientific research is carried out. Designing an effective laboratory course can be a herculean task and often takes into account several important factors: the number of semesters the course will span, whether there is a departmental mandate for subjects to be taught, and importantly whether there is an existing class that can be modified or a course that must be started from scratch. Advocates of research‐like courses cite favorable post‐transformation student assessments as justification for supporting these curricular changes while lacking comparable pre‐transformation evaluations. A unique aspect of the pedagogical approach in this course has been the accumulation of long term pre‐transformation assessments which we can directly relate to the post‐transformation evaluations. In this presentation we outline the rationale behind the de novo development of a one‐semester undergraduate biochemistry laboratory course and its evolution from a traditional “methods and techniques” based course to a more research oriented experience. The motivation to make these changes was not based upon our highly favorable attitudinal assessments; rather they were brought about by the desire to better prepare students who are currently engaged in laboratory research or will begin doing so upon completion of our course.