Articles

A Curriculum Skills Matrix for Development and Assessment ofUndergraduate Biochemistry and Molecular BiologyLaboratory Programs

Received for publication, September 27, 2002, and in revised form, June 23, 2003

Benjamin Caldwell*, Christopher Rohlman‡, and Marilee Benore-Parsons§¶

From the *Department of Chemistry, Missouri Western State College, St. Joseph, Missouri 64507; ‡ChemistryDepartment, Albion College, Albion, Michigan 49224; and the §Department of Natural Sciences, University ofMichigan at Dearborn, Dearborn, Michigan 48128

We have designed a skills matrix to be used for developing and assessing undergraduate biochemistry andmolecular biology laboratory curricula. We prepared the skills matrix for the Project Kaleidoscope SummerInstitute workshop in Snowbird, Utah (July 2001) to help current and developing undergraduate biochem-istry and molecular biology program designers to determine which laboratory techniques, skills, andtheories to include in a 4-year plan. The skills matrix can be used to evaluate and assess the types oflaboratory skills as well as the level at which they are taught in biochemistry and molecular biologycurricula. The matrix can foster better communication between faculty in chemistry, biology, math, andphysics as they share curricular information. As an example of utility of the skills matrix, we used it to surveyseveral commonly used biochemistry laboratory manuals to evaluate the skills covered in each text.

Keywords: Matrix, assessment, undergraduate, biochemistry, laboratory, skills.

Developing an appropriate undergraduate program inbiochemistry and molecular biology (BMB)1 is a challeng-ing and ever-changing venture. Program curricula must bediligently and rigorously adjusted to reflect the rapidchanges and advances in research, technology, method-ology, software, and internet resources used by the disci-pline. New strategies and requirements for assessmentmake it critical to have available tested methods of eval-uating programs and student learning.

A solid BMB program must be built out of core coursesoffered by biology, chemistry, math, and physics depart-ments. Due to the truly interdisciplinary nature of BMBprograms, faculty communication, “ownership” issues,student needs, and campus limitations often dictate, or atleast have an impact on, curriculum design and implemen-tation. Luckily, there can be significant flexibility in thenumber and types of courses offered as long as certainguidelines are maintained. Guidelines to help direct pro-gram development and assessment are provided by orga-nizations such as the American Association for Biochem-istry and Molecular Biology (ASBMB), the AmericanChemical Society (ACS) and the International Union of

Biochemisty and Molecular Biology [1–3]. Thus, the devel-opment of a BMB program course curriculum, theory, andknowledge is relatively straightforward. However, it is often amore difficult task to plan and develop laboratory strategiesand mechanisms to teach students specific techniques andpromote laboratory problem-solving skills. Several issuesrelated to laboratory curricula must be considered.

A plan should begin with a statement of the program’sgoals and objectives. It is impossible to teach all the skillsand theories applicable to all of biochemistry and molec-ular biology in a standard one- or two-semester BMBlaboratory sequence [4]; however, programs can selectparticular areas in which they excel, incorporate depart-mental strengths, and choose experiences best suited fortheir student population. For example, many midwesternU. S. schools with strong agriculture departments featureexperiments on plant biochemistry. In contrast, programsaffiliated with medical schools are more likely to includelaboratories relating to human disease. Building on localstudent needs and faculty expertise is vital to the designand implementation of a strong and sustainable BMBcurriculum.

Faculty must determine what basic skills and experi-ences students should learn in core biology and chemistrycourses. The laboratory curriculum should then build onand enhance those goals. If there are curricular gaps in theoverall program, such as student research experience,experiments can be developed or added to satisfy thoseneeds. This requires open communication between chem-ists and biologists, working together toward a common

¶ To whom correspondence should be addressed. E-mail:mparsons@umich.edu or caldwell@mwsc.edu.

The authors are not associated with any of the laboratory textssurveyed in this article and do not endorse one text over any ofthe others.

1 The abbreviations used are: BMB, biochemistry and molec-ular biology; ASBMB, American Association for Biochemistry andMolecular Biology; ACS, American Chemical Society; PKAL, Pro-ject Kaleidoscope.

© 2004 by The International Union of Biochemistry and Molecular Biology BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATIONPrinted in U.S.A. Vol. 32, No. 1, pp. 11–16, 2004

This paper is available on line at http://www.bambed.org 11

TABLE IBiochemistry and molecular biology laboratory assessment matrix

BMB skills

When skill is learned and level Type

Lower level courses Upper level BMB coursesQuantitative Qualitative

Theory Usage Proficiency Theory Usage Competence Theory Usage Competence

Lab techniquesAcid/Base chemistryAffinity techniquesAmino acid analysisBlots-NorthernBlots-SouthernBlots-WesterncDNACentrifugation-high-speedCentrifugation separation and pptCentrifugation-ultraspeedCharacterization of carbohydratesCharacterization of lipidsCharacterization of proteinsChromatography-affinityChromatography-ion exchangeChromatography-size exclusionCloning and selectionDialysis and desaltingDNA arrayDNA digestsElectrophoresis-DNA, RNA, agaroseElectrophoresis-proteins, PAGEEnzyme kineticsFluorescence/fluorimetryGene expression/transcriptionHPLCIRLigand-binding, ELISAMembranesNMRPCRPipetting-gilson, rainin stylePipetting-traditionalProtein synthesisPurification of bacterial DNAPurification of carbohydratesPurification of eukaryotic DNAPurification of lipidsPurification of proteinsPurification of RNARadioisotopesRe-Dox, electron transferReagents and solutionsRecombinant DNASequence determination-DNASequence determination-peptidesSite directed-mutagenesisSmall molecule characterizationSpectroscopy-spec 21Spectroscopy-UV/VisSterile techniques-growing bacteriaSterile techniques-solutions & platesSubcellular fractionationGroup workMolecular modelingData analysisComputational chemistryMass spec

Knowledge acquisitionLiterature searchesNCBI databasesAnalytical vs preparative scale

Experimental designPerform work from handoutsPerform work using literaturePerform work using kitsDesign appropriate controlsDesign and prepare experimentsSafety issues

12 BAMBED, Vol. 32, No. 1, pp. 11–16, 2004

goal. Lack of such cooperation is a common complaint atconferences such as the Project Kaleidoscope (PKAL)(www.pkal.org/) workshops, as well as at national profes-sional society meetings. Departments must share re-sources and responsibility for course objectives and goals,as well as the benefits of an interdisciplinary program suchas biochemistry and molecular biology.

Finally, there are larger issues that also need to beaddressed. How does the overall curriculum fit into thecampus’ goals or strategic plans? What are the ultimategoals of students graduating from this program? Aca-demic departments may have different goals, such asencouraging graduate study and research, workforce de-velopment for local or regional industries, professionaltraining in the medical sciences, or preparation of kinder-garten-12th grade educators. In some cases, several ofthese goals may be incorporated into the same curriculum.Additionally, recent developments in biotechnology areforcing many administrators to view biotechnology trainingprograms as lucrative ventures. Some administrators viewbiotechnology-related programs as signature programs forattracting talented students and funding from outsidesources. The strengths or weaknesses of the campus inresearch and teaching are also critical to the success ofBMB programs from an education and funding standpoint.

Guidelines from the ASBMB and ACS for undergraduateprograms include discussions about laboratory coursesand problem solving skills [1, 2, 4–6]. In addition to spe-cific skills and techniques, BMB curricula should includelaboratory experiences that

• Incorporate learning of basic theory and laboratoryskills;

• Allow development of critical thinking skills so thatstudents can design appropriate protocols to solvenew problems;

• Reinforce observation and data-recording skills;• Include opportunities to communicate results in writ-

ten and oral form.

Several other factors should also be considered. Labo-ratory courses should consistently integrate new knowl-edge and reinforce skills that students already possess.

BMB programs should emphasize both quantitative andqualitative aspects of purification and characterization ofbiomolecules. Experiments should incorporate skill build-ing and should model discovery-based research ap-proaches in the curriculum, wherever possible, particularlyif student research experience is limited or not available

THE BMB SKILLS MATRIX

Because teaching research and laboratory techniquesand developing problem solving skills are critical to stu-dent development, these elements became areas of focusat the 2001 PKAL workshop. Before coming to the work-shop, we created a matrix of skills we believed biochem-istry students should have. As part of the workshop, weasked participants which laboratory skills or techniquesthey felt should be included in a one-semester introductorybiochemistry laboratory course. We designed the BMBskills matrix to include a comprehensive list of laboratoryskills, organized into categories according to techniquesand theory, so it contains elements that are unlikely to beincluded by every program. Bell et al. [4, 6] have suggesteda list of topics that students in an ideal undergraduatebiochemistry or molecular life science program wouldneed in order to be well educated in the discipline, and theASBMB Education and Professional Development Com-mittee recently published recommendations. (More re-cently, Boyer [7] offered an examination of the topics thatought to be covered specifically in the laboratory curriculaof BMB programs, which will be a focus of the educationsatellite meeting at the 2004 ASBMB meeting.) During thePKAL workshop, participants reviewed Bell’s list of topicsand commented on the appropriateness of specific labo-ratory topics and whether they could ever truly beachieved. The responses from workshop attendees wereadded to the list of laboratory skills and techniques theauthors had already assigned to the initial matrix, and thefinal result is the skills matrix presented here (Table I).Users can reconstruct the skills matrix in a variety of ways,adapting the published format to meet local needs. Thematrix file can be accessed online and downloaded as anExcel or portable document file (PDF), and adjusted ac-cording to user needs and goals [8].

TABLE I—continued

BMB skills

When skill is learned and level Type

Lower level courses Upper level BMB coursesQuantitative Qualitative

Theory Usage Proficiency Theory Usage Competence Theory Usage Competence

Writing a grant proposalData keeping

Notebooks (legal)ElectronicSpreadsheeShare dataStatistics

Communicating resultsLab reportJournal-style articlePosterDept, local or national conference

Types of experimentsSkill buildingDiscoveryResearch

13

TABLE IIComparison of BMB skills and commercial text books

BMB skillsBMB commercial texts

Boyer [11] Switzer & Garrity [12] Ninfa & Ballou [13] O’Farrel & Ranello [14]

Laboratory techniquesAcid/Base chemistry X X XAffinity techniques X

aX X

Amino acid analysis X XBlots-NorthernBlots-SouthernBlots-Western X X XCentrifugation-high-speed X X XCentrifugation separation and ppt X X X XCentrifugation-ultraspeed XCharacterization of carbohydrates X XCharacterization of lipids X XCharacterization of proteins X X X XChromatography-affinity X X X XChromatography-ion exchange X X XChromatography-size exclusion X X XCloning and selection X X XDialysis and desalting X XDNA arrayDNA digests X X X XElectrophoresis-DNA, RNA, agarose X X XElectrophoresis-proteins, PAGE X X X XEnzyme kinetics X X X XFluorescence/fluorimetry X XIRLigand-binding, ELISA X X XMembranes XNMRPCR X X XPipetting-micropettes X X XPipetting-traditional X XPurification of bacterial DNA X X XPurification of carbohydratesPurification of eukaryotic DNAPurification of lipids X XPurification of proteins X X X XRadioisotopes X XRe-Dox, electron transfer X XReagents and solutions X X XRecombinant DNA X X XSequence determination-DNASequence determination-peptides X XSite directed-mutagenesisSmall molecule characterization XSpectroscopy-spec 21 X X X XSpectroscopy-UV/Vis X X X XSterile techniques-growing bacteriaSterile techniques-solutions & plates XGroup work

Knowledge acquisitionLiterature searches XNCBI databases X X

Experimental design and protocolPerform work using literaturePerform work using kitsDesign appropriate controlsDesign and prepare experimentsWriting a grant proposal

Data keepingNotebooks (legal) X X X XElectronicSpreadsheetShare data

Communicating resultsLab report XJournal-style articlePosterDept, local or national conference

Types of experimentsSkill building X X X XDiscovery X XResearch

a X indicates the topic is covered to some degree.

14 BAMBED, Vol. 32, No. 1, pp. 11–16, 2004

The BMB skills matrix is designed so that individualprograms can evaluate laboratory skills and techniques atseveral levels. It can be used in the following manner. Eachfaculty member or department determines which skills,techniques, and theories are taught in relevant courses orlaboratories. It can then be determined if a specific matrixelement is learned and used as a quantitative or qualitativeskill. Faculty must then determine at what level the stu-dents must master the technique. If a laboratory techniqueis presented as theory, one can then ask whether studentsactually learn the technique and use it once, or whetherthey use it several times, improving the skill and becomingproficient. For example, most students in biochemistry willlearn the theory of mass spectral analysis, but they do notusually perform actual experiments. On the other hand,they will likely perform polyacrylamide gel electrophoresisat least once but will not be very proficient at trouble-shooting the technique. By comparison, by the time BMBmajors graduate they should have a good deal of experi-ence and be very proficient at making buffers and reagentsolutions, with little direction. According to the matrix,each skill would be designated at one or more differentlevels of understanding and proficiency. Using the exam-ples above, the use of mass spectral analysis, as de-scribed above, might be classified as theoretical and qual-itative usage; student exposure to gel electrophoresismight be classified as qualitative and/or quantitative us-age, but not at a proficient level; and reagent preparationmight be classified as proficient and at a quantitative level.

In some cases, the material will be taught in more thanone course, and the level of each experience can be eval-uated either in a specific course or throughout the curric-ulum. For instance, the theory of buffers usually will beintroduced in general chemistry courses, but the actualhands-on use of buffers will not be learned until later incourses such as quantitative analysis or introductory bio-chemistry. This represents a progression from skills thatmay be described in class but not performed, to experi-enced but not practiced in lower level laboratories, to skillsthat are mastered by students in upper-division laboratorycourses. In this type of evaluation using the matrix, facultywill follow the thread of skill progression throughout thecurriculum.

While completing the BMB skills matrix, faculty will havean opportunity to discuss their experiments and the designof their program with colleagues who are also responsiblefor developing or assessing the curriculum. In fact, thisexercise allows for significant interaction, allowing for theexchange of logic, goals, and the solicitation of ideas. Atthe University of Michigan-Dearborn, conversations be-tween the chemistry and biology faculty revealed that thebiologists were re-teaching water and buffer chemistry.Similarly, some chemists were surprised to find that sev-eral advanced biochemistry texts taught the chemistry ofwater in the first or second chapter. This led to changes inboth course and laboratory curricula. This type of interac-tion can reduce duplication of topics or lead to reinforce-ment of key concepts. It is also useful to discover that thejargon used by scientists may differ depending on theapplication. For example, the Greek symbol � indicateswavelength to chemists and physicists but may indicate a

measurement of microliter volume to a molecular biologist.Helping students navigate the cross-disciplinary bound-aries is crucial to an integrated curricular design.

DEVELOPMENT AND SELECTION OF LABORATORY EXERCISES

There are many sources for laboratory exercises—Bio-chemistry and Molecular Biology Education journal beingone primary source. It is not an uncommon practice forlaboratory instructors, or even departments, to write lab-oratory manuals for their courses or use exercises avail-able on the web, including sites such as the digital libraryprojects [9, 10]. BMB programs might simply choose oneof several available laboratory texts. A commercially pre-pared laboratory manual offers the advantages of an out-lined series of experiments, lists of reagents needed foreach experiment, detailed introductory information, theo-retical background, and references.

Many of the participants at the 2001 PKAL conferencewere considering, or in the process of developing, a newbiochemistry program. In preparation for the PKAL work-shop, we decided to review the content of four popular,commercially available biochemistry laboratory texts [11–14] to determine what topics, techniques, and laboratoryskills the authors included in their texts. Our intent was notto review the laboratory texts, surveyed in this article, forcorrectness, accuracy, or reliability. Instead, we surveyedthe topics presented in each text against the BMB skillsmatrix to compare which topics are presented in thesecommercial texts. If a matrix category is described in somedetail, the category is indicated by an X, even if it was notdirectly involved in an experiment in the text (Table II).Hopefully, this analysis and comparison will help in theselection of biochemistry laboratory manuals that mightmeet the programmatic needs and goals of those consid-ering new biochemistry programs, as well as those seekingto evaluate or alter their laboratory curriculum. AlthoughTable I can be applied to BMB programs, Table II is gen-erally more applicable to biochemistry laboratories.

SUMMARY

The BMB skills matrix (Table I) can be used for thedevelopment of a new BMB program and for the indirectassessment of an existing one. The matrix can be resortedand adjusted as needed for specific departments, as de-sired. A copy of the matrix list or matrix comparative study(Tables I and II) can be accessed online and downloadedas an Excel or a PDF file [8]. The BMB skills matrix has alsobeen adapted to address the needs of those looking for acommercially available laboratory text for an introductorybiochemistry laboratory course. We believe that one orboth of these tools will be useful to faculty or departmentsdeveloping BMB curricula, and to departments wishing toevaluate and assess the effectiveness of their currentprograms.

Acknowledgments—We thank Rodney Boyer (Hope College,Holland, MI), Ellis Bell (University of Richmond, Richmond, VA),Fred Rudolph (recently deceased; Rice University, Houston, TX)and Kazem Mostafapour (University of Michigan, Dearborn, MI)for additions and suggestions for the matrix. We thank JeanneNarum and the Project Kaleidoscope staff for all their work inorganizing the Summer Institute, where much of the discussion

15

concerning the organization and content of skills matrix occurred.Specifically, we thank all 2001 PKAL BMB workshop attendeesfor their valuable input and assistance. We also thank Dr. KeithRhodes (Missouri Western State College, St. Joseph, MO) forcomments and suggestions regarding the manuscript.

REFERENCES

[1] American Society for Biochemistry and Molecular Biology (2003)Website, www.ASBMB.org/.

[2] American Chemical Society (2003) Website, www.acs.org/.[3] International Union of Biochemistry and Molecular Biology (2003)

Website, www.iubmb.unibe.ch/.[4] E. Bell (2001) The future of education in the molecular life sciences,

Nat. Rev. Mol. Cell Biol. 2, 221–225.[5] R. Boyer (1999) Does biochemistry have a core? ASBMB News VIII,

6, 10–12.[6] J. G. Voet, E. Bell, R. Boyer, J. Boyle, M. O’Leary, J. K. Zimmerman

(2003) Recommended curriculum for a program in biochemistry andmolecular biology, Biochem. Mol. Biol. Educ. 31, 161–162.

[7] R. Boyer (2003) Concepts and skills in the biochemistry/molecularbiology lab, Biochem. Mol. Biol. Educ. 31, 102–105.

[8] B. Caldwell, C. Rohlman, M. Benore-Parsons (2003) A curriculumskills matrix for development and assessment of undergraduate bio-chemistry and molecular biology laboratory programs, Website,curie.umd.umich.edu/parsons/.

[9] University of Leeds (2003) Virtual labs, Website, www.tlsu.leeds.ac.uk/courses/bioc2060/proteinlab102/ProteinLab.html.

[10] American Society for Microbiology (2003) Digital resources, Website,www.microbelibrary.org/.

[11] R. Boyer (2000) Modern Experimental Biochemistry, 3rd ed., Benja-min Cummings, San Francisco, CA.

[12] R. L. Switzer, L. F. Garrity (1999) Experimental Biochemistry, 3rd ed.,W. H. Freeman and Co., New York.

[13] A. J. Ninfa, D. P. Ballou (1998) Fundamental Laboratory Approachesfor Biochemistry and Biotechnology, Fitzgerald Science Press,Bethesda, MD.

[14] S. O. Farrell and R. T. Ranallo (2000) Experiments in Biochemistry: AHands-on Approach, Harcourt Brace and Co., Philadelphia, PA.

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