Probing and improving student's understanding of protein α-helix structure using targeted...

Article

Jennifer Loertscher†*

Sachel M. Villafa~ne‡

Jennifer E. Lewis‡

Vicky Minderhout†

From the †Department of Chemistry, Seattle University, Seattle,Washington 98122, ‡Department of Chemistry, University of SouthFlorida, Tampa, Florida 33620

Abstract

The increasing availability of concept inventories and other

assessment tools in the molecular life sciences provides

instructors with myriad avenues to probe student under-

standing. For example, although molecular visualization is

central to the study of biochemistry, a growing body of evi-

dence 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 a-helix structure.

Because this incorrect idea was present even after a

semester of biochemistry instruction at a range of institu-

tions, an intervention was necessary. A community of

expert biochemistry instructors collaborated to design two

active learning classroom activities that systematically

examine a-helix structure and function. Several participat-

ing faculty used one or both of the activities in their class-

rooms 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 funda-

mental concepts. VC 2014 by The International Union of

Biochemistry and Molecular Biology, 42(3):213–223, 2014.

Keywords: assessment; curriculum design; action research;

communities of practice

IntroductionUndergraduate education in the molecular life sciences hasexperienced a sea change with regard to use of evidence-based practices to improve teaching and learning. A cor-nerstone of this transformation has been greater availabil-ity of assessment instruments and a cultural shift amonginstructors that promotes the collection of data related tostudent thinking. For example, concept inventories andother pre/post assessment instruments have been devel-

oped for biochemistry/molecular biology [1–4], biology [1,5–7], chemistry [8], geoscience [9], and physics [10]. Addingto this momentum, professional societies like the AmericanSociety for Biochemistry and Molecular Biology (ASBMB)have begun efforts to develop and consolidate assessmenttools for use by a wide community of instructors [11].

A key assumption in gathering information about stu-dent thinking, whether formally through pre/post adminis-tration of a concept inventory or informally through use ofclickers in a lecture class, is that it will be used to directchanges in instruction that ultimately lead to improved stu-dent competency within a given discipline. Authors of con-cept inventories commonly suggest general ways in whichtheir instruments could be used to inform teaching practiceincluding surfacing of commonly held misconceptions [6,7]. Authors of the enzyme–substrate interactions conceptinventory suggest that questions could be used as formativeassessment to inform instructors of students’ level ofunderstanding during class or after implementation of cur-ricular developments [1]. Others have more specific ideas

ws Additional Supporting Information may be found in the online

version of this article.

*Address for correspondence to: Department of Chemistry, SeattleUniversity, Seattle, WA 98122, USA. E-mail: [email protected] 27 January 2014; Revised 12 February 2014; Accepted 14February 2014DOI 10.1002/bmb.20787Published online 6 March 2014 in Wiley Online Library(wileyonlinelibrary.com)

Probing and Improving Student’s

Understanding of Protein a-Helix Structure

Using Targeted Assessment and Classroom

Interventions in Collaboration with a

Faculty Community of Practicews

Biochemistry and Molecular Biology Education 213

on how to modify instruction to address student shortcom-ings. For example, authors of the biology concept inventoryidentified specific gaps in the biology curriculum related tocomplex processes such as diffusion and drift and proposedthat conventional curriculum needs to be re-examined tomake room for these essential ideas [5].

Despite good ideas and intentions, there are reasons toquestion whether development and use of these assessmenttools have the desired effect of improving student knowl-edge and skills. Smith and Tanner [12] suggest that thevocabulary and format used in many concept inventoriesmay limit their usefulness in classroom assessment andsuggest other assessment methods that probe studentunderstanding more deeply. Although their point is valid,they stop short of acknowledging that any tool used forformative assessment is only useful in the extent to whichinstructors reflect on data and make appropriate changesin instruction. Recognizing that many college and universityfaculty are not trained to be reflective teachers, D’Avanzo[13] suggests that rich and sustained faculty developmentopportunities are needed to support faculty in interpreta-tion and use of student assessment data.

One model for promoting personal growth and steward-ing community knowledge over time is through sustainedmembership in a community of practice [14]. Sirum andMadigan [15] emphasize the urgent need for institutionaliza-tion of evidence-based teaching practices and describe suc-cessful, sustained faculty learning communities aimed atsupporting teaching innovation more effectively than one-time professional development workshops. In this program,faculty met regularly with a peer group to learn about effec-tive pedagogical techniques and to receive feedback on theirown implementation. Marbach-Ad et al. [16, 17] took theirlevel of community engagement further by linking nine dif-ferent microbiology courses through use of common learningobjectives, teaching strategies, and assessment tools. Partici-pants described deep professional satisfaction resulting fromcommunity-based reflection on and response to student datafrom a concept inventory that the group generated. Simi-larly, Murray et al. [18] describe a sustained community thatself-reported significant professional development and per-sonal growth through participation in collaborative produc-tion of teaching materials and assessment tools. The nextstep for this community is to use assessment data to cycleback into collaborative production of teaching materials tar-geting common and persistent student incorrect ideas.

Molecular visualization is an essential skill in biochemis-try and surveys of faculty show frequent, widespread use ofcomplex images in biochemistry classrooms [19–21]. Yet agrowing body of evidence indicates that students take lessaway from images of macromolecules than their expertinstructors assume they do. For example, using a pre-/postt-est, we previously showed that only a minority of studentswere able to correctly answer questions about the funda-mentals of protein a-helix structure even after a semester of

biochemistry instruction [22]. These difficulties may relate tothe fact that, although students are exposed to numerousrepresentations of proteins in biochemistry courses, they arerarely taught the conventions and ways of seeing used byexperts. For example, interviews probing how students inter-pret structural features of a potassium ion channel revealedonly a shaky grasp of visual conventions used by experts anda heavy reliance on prior knowledge to make sense of theimages [23]. Interviews further revealed that students coulduse larger-scale conventions, such as the vertical orientationof an a-helix, to make statements about placement of the atransport protein in a membrane. Furthermore, knowledgerelated to interactions between ions and the aqueous envi-ronment was highly fragmented [24]. Clearly, there is anopportunity for faculty to use assessment data to modifyinstruction to better support student development of skillsand knowledge related to protein structure and function.

The goal of this study is to investigate how a commu-nity of biochemistry instructors used assessments givenacross multiple-years at a number of different institutionsto inform and change teaching practice. Having previouslyidentified incorrect ideas commonly held by biochemistrystudents, we asked whether an established community ofbiochemistry faculty could effectively use these data tochange teaching and learning in their biochemistry class-rooms. Given the importance of protein structure and func-tion to biochemistry and the known challenges studentshave interpreting complex representations in biochemistry,this study focused on improving student understanding ofprotein a-helix structure and function. Comparison ofresults from pre/posttests administered in two differentyears at 13 different institutions nationwide suggest thatstudent understanding of key concepts was improvedthrough use of specially designed active learning materials.

MethodsProject ContextThis study was conducted as part of the evaluation of anNSF-funded project, POGIL Biochem: Advancing ActiveLearning Approaches in Biochemistry. The overall goal ofthe project was to field-test and disseminate a coherent setof Process Oriented Guided Inquiry Learning (POGIL) activ-ities for undergraduate biochemistry. As part of this effort, a21-question pre/posttest was developed to measure studentunderstanding of foundational concepts from general chem-istry and biology before and after biochemistry instruction[2, 22, 25]. The instrument was specially structured to havethree parallel questions related to each of seven concepts.Student response data from the three questions related tothe a-helix concept were analyzed for this study.

Faculty Workshop to Develop New TeachingMaterials Focused on the Protein a-helixA key component of the POGIL Biochem project was to involvea community of undergraduate biochemistry educators in all

Biochemistry andMolecular Biology Education

214 Probing and Improving Students’ Understanding of Protein a-Helix Structure

aspects of the project [18]. In June 2011, 20 facultymembers attended a 3.5-day workshop, part of whichwas devoted to improving student learning in biochemis-try using previously collected assessment data as a startingpoint. Specifically, workshop participants analyzed studentpre/posttest performance related to the a-helix concept andthen worked in teams to produce classroom activitiesintended to improve student understanding of this concept.Of the 20 participants, three taught at large research univer-sities, five taught at master’s level universities, and 12 taughtat small four-year colleges. All participants were engaged inwriting and/or revision of the activities, and seven of themused activities in their classrooms in the following semester.

Administration of the Pre/Posttest and Pilotingof New Teaching MaterialsA pre/posttest, described previously [2, 22], was adminis-tered in nine junior/senior level biochemistry classes nation-wide in fall semester 2010 (566 total students) and in 10 jun-ior/senior level biochemistry classes nationwide in fallsemester 2011 (512 total students). In total, 13 differentinstitutions participated in this study. Classes from 5 of the13 institutions participated in both 2010 and 2011. As shownin Table 1, a diversity of institutions was represented bothyears. In fall semester 2011, newly designed activities per-taining to protein a-helix structure were used in 7 of the 10classes. Throughout this article, classes taking the pre/postt-est in 2010 are labeled A–I, classes taking the pre/posttestand not using new classrooms materials in 2011 are labeled

J–L, and classes taking the pre/posttest and using new class-rooms materials in 2011 are labeled M–S.

Faculty Survey InstrumentA faculty survey was administered to learn about ways inwhich faculty used pre/posttest data to inform their instruc-tion and to gain faculty insight into student conceptionsrelated to the structure of the protein a-helix. Responseswere received from the seven faculty members who usednew protein a-helix activities in fall semester 2011.

ResultsIn this study, we describe a process whereby pre/posttestdata were used iteratively to inform faculty of studentunderstanding related to protein a-helix structure so thatthey could respond by producing classroom activities tar-geting incorrect ideas related to that concept. This process,summarized in Fig. 1, can be used as a model to improveteaching and learning in biochemistry in general.

As part of development of the pre/posttest, a group ofexperts had determined that students should bring basicunderstanding of protein a-helix structure from introduc-tory biology courses into biochemistry [2]. Specifically, theyagreed that students should understand that the interior ofa protein a-helix contains atoms from the backbone in close

Characteristics of participating classes

Research

universities

Masters

universities

Four-year

colleges

Total

classes

Total

students

a-helix

activity used

Class

label

2010 4 1 3 9a 566 0/9 A–I

2011 3 4 3 10 512 7/10 J–S

aTwo classes were from one institution resulting in the total number of classes being higher than the sum of the institution types.

Iterative use of assessment data to improve bio-

chemistry instruction.

Protein a-helix concept and incorrect ideas

Correct concept The interior of an a-helix contains

atoms from the protein backbone

in close contact.

Incorrect ideas The interior of an a-helix contains

the side chains (R-groups) of the

amino acid residues.

The interior of an a-helix contains

water molecules.

The interior of an a helix is empty.

TABLE 1

FIG 1

TABLE 2

Loertscher et al. 215

contact. This concept is important because it is an indicatorof student’s ability to think about biologically relevant mac-romolecules in three dimensions and to apply a founda-tional understanding of molecular structure (specificallyspace-filling models) to biochemistry. The experts alsoidentified three common incorrect ideas that students typi-cally have related to protein a-helix structure (see Table 2).Three parallel questions related to this concept were devel-oped for the pre/posttest. A sample question is shown inFig. 2. Previous administration of the pre/posttest revealedthat the most commonly held incorrect idea was that theinterior of the protein a-helix contains the side chains ofthe amino acid residues [22].

Student Understanding of Protein a-helix StructureBefore Teaching InterventionAnalysis of pre/posttest data collected from nine differentclasses in fall semester 2010 supported previous, limitedfindings from two institutions showing that only a minorityof students completing one semester of biochemistry had acorrect understanding of protein a-helix structure. To qual-ify as having a correct understanding of the concept, stu-dents must have answered all three questions related tothe concept correctly. Analysis of the data presented in Fig.3a shows wide variability in students’ pre- and posttestpercentages among institutions, but some trends can beobserved. First, in 2010, no more than 25% of students inany class (A–I) correctly understood this concept before bio-chemistry instruction (Fig. 3a, gray bars). Surprisingly, cor-rect understanding of this topic for classes A–I increasedonly marginally after completing biochemistry courses, allof which included protein structure and function in theirsyllabi. As seen in Fig. 4, three of the nine classes from2010 (E, G, and I) showed essentially no change in scorebetween pre- and posttests. Even in those classes that didshow some gain (A, B, C, D, F, H), the highest achievingclasses showed little more than 50% of students under-standing this concept correctly. Given how basic this con-cept is and how central protein structure is to biochemis-try, observing these results across such a wide range ofinstitutions was surprising and concerning.

Community-Based Effort to Improve Teaching andLearning Related to a-helix StructureData generated in fall semester 2010 were presented to 20biochemistry faculty members at a workshop in summer2011. Many of the faculty had been involved in productionof the pre/posttest and all had a strong interest in

Sample pre/posttest question related to protein a-helix structure.

Student performance on pre/posttest questions

related to the protein a-helix before and after tar-

geted teaching intervention. Data shown are per-

centage of students answering all three

questions related to the protein a-helix concept

correctly. Pretest data are given in black and

posttest data are given in white. Panel A shows

data from 2010, before teaching interventions,

and panel B shows data from 2011, when spe-

cially designed activities were introduced in

some classes, between administration of pre-

and posttests. Numbers given in parentheses are

number of students completing both the pre- and

posttests.

FIG 2

FIG 3



improving teaching and learning in undergraduate bio-chemistry. Three of the workshop participants wereinstructors of classes represented by the 2010 data, but theremaining workshop participants had no personal connec-tion to the data. All participating faculty were disheartenedby the data and were highly motivated to design instruc-tional materials with the goal of improving student under-standing of the basics of protein structure.

Discussion of the data and the literature related to vis-ualization in biochemistry available at the time [19, 26, 27],and reflection on their own teaching practices, led facultyto conclude that students are rarely, if ever, taught how tolook at biochemical representations. Faculty commentedthat molecules are much more complex in biochemistry ascompared to prerequisite chemistry courses. Furthermore,textbooks and other instructional materials move back and

forth among different ways of representing proteins includ-ing ball and stick, ribbon, and space-filling models, givinglittle or no guidance to students on how to interpretimages. Finally, although the relationship between struc-ture and function is central for expert biochemists, studentssometimes struggle to make these connections. In this case,posttest data showed that many students believed that asingle protein a-helix spanning a membrane could act as asmall molecule transporter.

Workshop participants decided to develop two differentactivities designed to improve understanding of protein a-helix structure. Learning outcomes for both activities areshown in Table 3. The purpose of the introductory activitywas to explicitly guide students through exploration of ele-ments of a-helix structure and commonly used representa-tions of protein a-helices. The activity authors were mindfulthat interpretation of complex external representations is aform of tacit knowledge for experts, who often forget thatstudents may not “see” what they do [23]. They thereforeprovided students the structure needed to learn how tomove back and forth between ball and stick, ribbon andspace filling representations (see Supporting Information 1for the complete activity). The purpose of the applied activ-ity was to explore elements of protein a-helix structurethrough the lens of transmembrane transporter proteinfunction. Specifically, students were guided to explore anumber of experimentally derived images of a potassiumion channel and answer questions related to size, structure,and function of the protein. Students were asked to com-pare and contrast ribbon and space filling models of theprotein. The two activities were similar in that they bothexplicitly guided students to explore images of proteinstructures to make statements about structural and/orfunctional characteristics. They differed primarily in thecomplexity of the images presented. In the introductoryactivity, students were only asked to explore a protein a-

Changes in student performance before and after

targeted teaching intervention. Data shown are

the differences in student performance on the

pretest and posttest in 2010 and 2011.

Stated learning outcomes for specially designed classroom activities

Introductory activity Applied activity

1. Recognize that the amino acid R-groups of a protein

a-helix point out from the helix.

1. Explore how primary and secondary structure relates

to the function of a protein of interest.

2. Recognize that the interior of the protein a-helix

consists of backbone atoms.

2. Given a transmembrane transporter protein: (a) identify

where polar and nonpolar amino acids would likely be

found and (b) identify where the solute would be transported.

3. Compare and contrast the three representations

(ball and stick, ribbon, space filling) of the structural

features of the protein a-helix.

3. Draw two a-helices within a protein interacting with

each other and explain the role that intermolecular forces

play in this interaction.

4. Identify distribution of R-groups around the turns

of an a-helix.

4. Given a non-transmembrane a-helical protein, describe

how it would interact with another molecule.

FIG 4

TABLE 3


helix, whereas in the applied activity, they examined com-plex images from a publication about the structure of atransmembrane transport protein. In both cases, activityauthors received formative feedback from other workshopparticipants on their drafts.

Implementation of New Activities and Effects onStudent Understanding of Protein a-helix StructureThe newly designed activities were implemented in sevenclassrooms in fall semester 2011. Six of the seven instruc-tors of these classes attended the summer workshopdescribed above. The seventh instructor shared teachingresponsibilities with an instructor who attended the work-

shop and was a primary author on the introductory activ-ity. As shown in Table 4, a variety of different implementa-tion approaches were used. Two instructors (N and O) usedthe introductory activity as written and two (P and Q) useda modified version. Modifications were made at institutionP because of time constraints, and modifications weremade at institution Q because the instructor combined thenew activity with a preexisting activity related to statedoutcomes. One institution (R) used the applied activity inclass and one (M) used it as homework. One institution (S)used both activities. In all classes, the new a-helix activitieswere used in addition to other activities and/or lecturesabout protein structure and function.

Faculty comments and student performance in classes using new teaching materials

Institution and

activity used

Posttest

correct

Instructor comments about

student performance

Why is the a-helix concept

difficult for students?

M Applied as

Homework

64% N/A I think they confuse it with the DNA

double helix, which has the bases

pointing toward the center of the helix.

N Intro 80% Students were asking why we kept asking them

what was in the middle of the alpha helix

and some. . .were making comments like

“I get it, I get it, the middle of the helix is

full of backbone atoms.”

Possibly the way we draw this.there

is rarely a “scale” to show that most

molecules would be much too big to

fit down the hole. . .

O Intro 62% They “got” it easily – the a-helix is an abstract

concept in introductory biology or cell biology

and once they understood what it is in

biochemical terms, there was no room

for erroneous concept.

It is not explained well in

biology courses.

P Modified Intro 53% From the discussions students had in class

and the questions they asked during the

small group discussions, I believe they were

evaluating the a-helix structure rather than

memorizing a list of facts.

Students need more exposure to

analyzing structures. They can

memorize a list of features for a

particular structure, but being able

to visualize the structure is worth

a thousand words.

Q Modified Intro 78% Student drawings and descriptions of

“what they saw” and about which molecular

renderings they used to most easily answer

each activity question were the most revealing

to me that, perhaps, this was getting them to

think along a more clear pathway.

Perhaps because the simple helix

drawing reminds them of the

DNA double helix. . .in that,

there’s definitely “room” for

things other than backbone

atoms on the INSIDE. . .

R Applied 74% Most. . .got a good grasp, but out of 41 students,

I had 4 who still said the R groups went to

the inside of the helix within 1 week of

intervention. Students do not interpret space

filling models well.

Mixing up folding with a-helix

structure

S Both 59% The students thought that the activities were

redundant and easy. I wonder if this means

that they finally got it.

The representations of the helix

have holes in them.

TABLE 4



The pre/posttest was administered to students at allseven of the institutions where new activities were usedand to students at three additional institutions. Although nostatistical analysis was performed because of variabilityresulting from differences among classes and years, thefact that data were collected before implementation of newactivities in 2010, and in nonimplementing classes in 2011,allows for some meaningful discussion of trends.

Figure 3b shows the percentage of students answeringall three questions related to the a-helix concept correctly in2011 (classes J–S). Interestingly, the percentage of studentsanswering all three questions correctly on the pretest is, ingeneral, higher in 2011 (Fig. 3b) than in 2010 (Fig. 3a),which highlights the limitations of making year-to-yearcomparisons. However, despite these differences, sometrends are notable. Posttest scores for students not exposedto a specially designed a-helix activity are never higher than56% correct (Figs. 3a and 3b, classes A–L). In contrast,posttest scores for those using the new activities in somecapacity are never lower than 53% correct with scores ashigh as 80% correct (Fig. 3b, classes M–S). Figure 4, show-ing the differences in percent correct on the pre- and postt-ests for each class, also reveals some notable trends. In 4 ofthe 12 classes not using the new activities, no change ordecreased percentages correct are observed (institutions E,G, I, and K). Little change or a decline in score is neverobserved among the seven classes using the new activities(M–S). Furthermore, the increase in the percentage of stu-dents answering all three questions correctly on the posttestas compared to the pretest was greater than 20 for 86% ofclasses using the activities, where only 33% of classes notusing the activities showed gains greater than 20.

Although greater gains are observed in most classesusing the activities than in classes not using the activities,these specially designed activities are not a panacea. Evenin the best case scenario (institution N), 20% of studentsstill do not understand basic a-helix structure after asemester of instruction, which incorporated the targetedintervention. In most classes, 40–50% of students still hadtrouble with the concept even after using specially,designed activities. Furthermore, Fig. 3a shows that someinstructors (classes A, D, and F) were doing something thatsupported student understanding of this concepts and thatwhatever was performed, was as effective as the speciallydesigned activities. Interestingly, no clear trends wereobserved linking institution type to student understandingof this concept. Clearly, and not unexpectedly, deep learn-ing of protein structure needs to be supported in a numberof ways.

Faculty Use of Pre/Posttest Data to ImproveInstructionIn addition to analyzing student performance on the pre-and posttests, instructors at the seven institutions using thenew activities completed a survey about their use of pretest

data and their ideas about student understanding of a-helixstructure. Analysis of surveys revealed that faculty usedpre/posttest data to inform instruction, but not for analready ongoing semester (data not shown). Specifically,faculty members were motivated to make changes ininstruction in the fall after discussing student performancedata with a group of peers in the summer. However, facultydid not report making changes in real time when given theresults of their students’ pretests a couple weeks into thequarter. Therefore, planning ahead and supporting discus-sion among colleagues before the start of the academicyear is an issue of practical importance when consideringhow to use assessment data to motivate faculty to try newinstructional approaches.

Faculty were also asked what observations they madethat suggested use of the new activity or activities helpedstudents overcome incorrect ideas related to the protein a-helix concept. A summary of responses is shown in Table4. All faculty reported feeling optimistic about studentunderstanding of this concept after completing an in-classactivity devoted to deepening understanding. However, stu-dent and instructor impressions during class and students’performance were not always in alignment. For example,instructors at institutions N, O, and S report that studentsthought the activities were easy and redundant and thatstudents really “got it”. However, at two of these institu-tions (O and S), 40% of students still showed incorrectunderstanding on the posttest. Another interesting trendwas that many of the faculty, especially those at institutionsP, Q, and R, appreciated having the glimpse into their stu-dents’ thought processes that this targeted active learningactivity provided. The tone of their comments suggests thatwatching students work in real time provides for a depth ofreflection on instruction that may not be as readilyprompted when instructors read students responses onhomework or exams.

Finally, faculty were asked why they think studentshave difficulty understanding a-helix structure, specificallythat the R-groups of amino acids do not point in toward thecenter of the helix and that a single membrane-spanninghelix cannot act as a small molecule transporter. Resultssummarized in Table 4 show some common ideas. At leasttwo instructors acknowledge that the way a-helices arecommonly depicted is confusing. Scale is rarely correctlyrepresented at the atomic level and many representationsshow large holes down the central axis of the helix. Otherssuggested that students confuse the protein a-helix with theDNA double helix, in which the bases do point towards thecentral axis of the double helix. Others suggest that stu-dents need more practice looking at and analyzing complexbiochemical molecules. All of these ideas relate broadly tothe fact that students are less familiar with visual conven-tions than expert biochemists. As seen by Harle and Towns[23], students could be relying on prior knowledge to fill inthe gaps in their visualization skills.


DiscussionImplications for Teaching and Learning MolecularVisualization in BiochemistryThis study shows that students do not have clear under-standing of the fundamentals of protein structure evenafter one semester of biochemistry instruction. Althoughtargeted interventions show promise in increasing under-standing of one aspect of protein structure, more workremains. Sch€onborn and Anderson [19, 27] have convinc-ingly made the case that explicit teaching of visual literacyshould be part of the biochemistry curriculum and haveprovided instructors guidelines for supporting visual liter-acy in their classrooms. In addition to these practicalguidelines, two research-based, biochemistry-specific mod-els provide detailed descriptions of students’ ability to inter-pret external representations [26] and of classifications ofexternal representations [21]. These models can be used byinstructors to improve their practice related to teaching vis-ual literacy, but more importantly provide a starting pointfor research about student interpretation of external repre-sentations in biochemistry that could lead to specific rec-ommendations to improve instruction. A faculty commu-nity, like the one described herein, could be used tosupport implementation of such recommendations.

The activities that were designed as part of this studyincorporated many of the 10 recommendations put forth bySch€onborn and Anderson [19] on teaching visual literacy.Both activities were designed to align with theories on howindividuals learn. For example, the constructivist theory oflearning and active engagement with material forms thebasis of all POGIL activities, including those described here.The recommendation to foster a multiple representationsapproach to visualization was the driving principle thatguided production of the introductory activity. Specifically,students are prompted throughout the activity to moveamong three different modes of representing a-helix struc-ture. Related to this, the introductory activity makes stu-dents aware of the visual language and knowledge used inrepresentations of protein structure. For example, the dif-ferent kinds of representation (ball and stick, ribbon, andspace-filling) are named and students are asked to explorefeatures that are and are not explicitly shown in each. Bothactivities, but especially the applied activity, make studentsaware of the limitations of different representations by ask-ing them about limitations after guiding them through anexploration of the images. Despite these strengths, a majorshortcoming of the activities is that students are not askedto produce their own representations, a practice that issupported by research about student understanding ofexternal representations [28].

Of course, we as instructors cannot expect to fullydevelop student visual literacy through the use of one ortwo activities. Instead, biochemistry instructors shouldrethink the way they teach (or do not teach) visualization

skills throughout their courses. Becoming familiar with theTOBER framework [21] would be a good first step in help-ing instructors become more self-reflective in how they useimages in their own classrooms. In addition to those men-tioned above, Sch€onborn and Anderson recommend a num-ber of practices that should be incorporated not just in sin-gle activities, but every time new representations areintroduced. These include, but are not limited to, askingstudents to link specific concepts to images, discussingadvantages and limitations of every image used in instruc-tion, asking students to perform varied tasks related toimage processing and helping students develop metacogni-tive skills related to their understanding of biochemicalimages. Many of the members of the community describedhere already use some or all of these practices in theirteaching. This community is therefore poised to use sharedexpertise to further improve teaching practice related tovisual literacy.

Although the research related to visualization andinterpretation of external representations in biochemistryis limited, several studies suggest starting points forinstructors wishing to improve how students interpretimages. In their investigation of student understanding ofexternal representations of the potassium ion channel pro-tein, Harle and Towns [23] found that students rely heavilyon prior knowledge to interpret complex images of proteinstructure. Unfortunately, their prior knowledge is often lim-ited and not sufficient to fully and correctly interpret theimages. For example, students’ understanding of potassiumion channel protein structure and function was hindered bytheir fragmented understanding of the interactions betweenions and the aqueous environment [24]. Similarly, Krameret al. [29] found that students’ difficulties understandingimages were often “upstream” of biochemistry, meaningthat difficulties related to interpretation of images arose inbiochemistry because of incomplete or incorrect under-standing of foundational concepts from prior coursework.These observations demonstrate that understanding stu-dents’ prior knowledge and how they apply it to the inter-pretation of images is essential. Linenberger and Bretz [1]suggest use of a modified student interview methodology inclass to uncover student understanding of external repre-sentations, including prior knowledge, with the aim of ini-tiating a deeper discussion about the images and what theycan tell us about macromolecular structure and function.These studies also show that students need guidance andperhaps detailed instruction from their teachers on how tointerpret complex external representations [23, 29]. Finally,a study in which students were asked to draw their ownrepresentations of protein structures prompted Harle andTowns [28] to emphasize that asking students to draw rep-resentations of biochemical molecules is an important com-ponent of developing proficiency in interpreting biochemi-cal representations.



Using and Sustaining Evidence-Based TeachingPractices—Implications for Faculty ProfessionalDevelopmentNumerous faculty development workshops and commun-ities of practice aimed at improving teaching in the life sci-ences have been previously described [11, 15, 17, 30].Many of these efforts have resulted in instructors changingtheir teaching practice to include a more prominent rolefor active learning, use of formative assessment, and atten-tion to diversity in their classrooms [31]. However, somequestions remain as to whether the degree to whichinstructors report making changes in their teaching prac-tices align fully with the reality of what happens in theirclassrooms [32]. Furthermore, Offerdahl and Tomanek [33]have shown that even when faculty collect formativeassessment data in their classrooms, for example throughuse of clicker and/or reading questions, they may notreflectively use this feedback from students to change theway they teach. In many ways these findings are not sur-prising, because as Black et al. [34] point out, turningresearch into effective classroom practice is an iterativeand challenging process.

This study describes an effort by a group of facultymembers to reflectively use student assessment data todesign targeted teaching materials in response to observingchange-resistant incorrect ideas held by biochemistry stu-dents nationwide. This group of faculty members has char-acteristics that distinguish it from previously described fac-ulty working groups and enabled it to effectively completethe assessment loop shown in Fig. 1. First and most impor-tantly, the community described here is a sustained com-munity that has worked together to improve biochemistryteaching and learning for nearly 8 years. The group mem-bers have a history of talking about and making change intheir teaching practice. They also share a set of tools,namely the pre/posttest and POGIL activities that many hadbeen involved in producing. Second, although a core groupof community members has worked together consistently,new people have been continually invited to join the groupover the years, thus increasing the size of the communityand ensuring influx of fresh ideas. Third, after spendingtime together in workshops, many participants remain inclose contact with each other and continue to develop andrefine materials produced collaboratively during work-shops. Taken together, these characteristics enabled partic-ipants at the 2011 workshop to move quickly and confi-dently to use student assessment data to make changes ininstruction.

The process described above, in which a group of facultymembers worked together to identify a problem with stu-dent learning, formulate and implement an intervention andobserve the impact of the intervention, is an example ofaction research. Action research, also called practitionerresearch, is a method of “on-the-job research” [35] usedmost frequently in education and the social sciences. Using

this approach, a group of practitioners work collaborativelythrough iterative cycles of planning, executing, and reflect-ing to investigate a relevant issue with the goal of generatingpossible solutions [36]. Action research empowers practi-tioners to achieve a desired outcome, in this case improvedstudent understanding of protein a-helix structure, throughpersonal and professional growth [35]. Because of the poten-tial for real-world solutions and professional developmentfor practitioners involved, engaging in action research goesdeeper than participation in isolated faculty developmentworkshops and provides a powerful means for continualimprovement in teaching and learning.

Lewin [37], one of the first social scientists to use theterm action research, proposed that to generate useful newknowledge that results in desired outcomes, actionresearchers must engage in multiple iterative cycles ofinvestigation involving planning, executing, observing, andevaluating. McNiff [35] later refined this view by proposingspirals of research that arise spontaneously and sometimesarrive at different places than those anticipated by theresearchers. This study described here and summarized inFig. 1, clearly represents one such cycle. To ensure thatthe work accomplished thus far results in a real and sus-tained change in student understanding of basic biochemi-cal concepts, additional cycles of inquiry would be helpful.Specifically, it would be useful for this community to reflecton data from the 2011 implementation and plan a subse-quent intervention and assessment. This next step has beenaccomplished in the authors’ classroom and likely in otherisolated classrooms, but the entire community has notengaged in reflective discussion of these data. Given thegeographical distribution of community members, regularin-person meetings are challenging to coordinate, but tech-nology could be used to facilitate ongoing communication.

Although we have only completed once cycle of investi-gation directly related to the protein a-helix project, a num-ber of generative spirals, described by McNiff, have fed intoand arisen from the work described here. The communitydescribed in this article has been active in some form since2007 and has participated in a number of projects toimprove undergraduate biochemistry instruction [18]. Forexample, the pre/posttest used to measure student under-standing of protein a-helix structure was developed collabo-ratively and refined over years using iterative cycles [2,22]. Furthermore, this faculty community has met asrecently as 2013 to work on a broader project related toteaching and learning in biochemistry. Specifically, we arein the process of identifying threshold concepts for bio-chemistry [36, 38] with the goal of designing instructionaland assessment materials related to these pivotal ideaswithin the discipline. Interestingly, the authors were moti-vated to focus on threshold concepts, in part, because ofthe student difficulties reported here. Therefore, subse-quent cycles of inquiry are occurring with the broad aim ofimproving teaching and learning in biochemistry.


Results presented here and extensive work on facultygrowth as teachers strongly suggest that a sustained com-munity of diverse practitioners who rely on a shared visionand set of resources is an excellent model for supportingreal student-centered change in teaching practices overtime. As Tanner [39] emphasizes in her analysis of the limi-tations of thinking about quick-fixes in student learning,systems that support teachers in their efforts to be reflec-tive and make changes based on evidence from their ownstudents have been repeatedly shown to be most effectivein promoting high-quality teaching. A deeply reflectiveteaching practice will necessarily require time to develop.Indeed, research in higher education shows that facultyexperience conceptual change related to their teachingpractice, which takes multiple years of teaching to fullyexperience [40, 41]. Furthermore, Feldman suggests thatcommunities of practitioners may be required to supportconceptual change related to teaching practice. In ourcase, faculty survey results show that faculty members arewilling to examine and respond to assessment data fromtheir own students and students from other institutions, butonly when given enough time and community support todevelop the necessary teaching tools. All of these observa-tions strongly support investment in efforts that promotesustained communities of practice related to teaching andlearning in the molecular life sciences.

ConclusionsUsing data from a pre/posttest, we have shown that stu-dents from diverse institutions nationwide hold persistentincorrect ideas about the basics of protein a-helix structure.Documented poor performance that persisted even afterbiochemistry instruction motivated faculty to make changesin instruction aimed at strengthening student understand-ing of fundamental principles related to protein structure.Interestingly, faculty members who engaged in a commu-nity of practice with other like-minded colleagues weremotivated to make changes in their own classrooms basedon assessment data from students other than their own.This study provides a model for other communities ofinstructors on how to work collaboratively to modifyinstruction based on assessment data.

AcknowledgmentsThe work described in this document was supported by theNational Science Foundation DUE-0717392. Any opinions,findings, and conclusions or recommendations expressed inthis material are those of the authors and do not necessarilyreflect the views of the National Science Foundation. Specialthanks to faculty who were closely involved in writing andediting the activities: Danielle Cass, Stephen Dunham, BruceHeyen, Anne Kruchten, Julie Verdoni, and Tracey Murray.Thanks also to participating faculty and project advisory

committee members: Cheryl Bailey, Robert Bateman, CherylCoolidge, Colleen Conway, Kathleen Cornely, ElizabethDorland, Shari Dunham, Pam Hay, Tim Hayes, Pam Higgins,Sunil Malapati, Larry Martin, David Parkin, Terry Platt,Charlotte Pratt, Christine Rener, Sharon Rozovsky, JohnShabb, Jeff Sigman, Janet Schottel, Carin Thomas, HaroldWhite, Linette Watkins, and Adele Wolfson.

References

[1] Bretz, S. L. and Linenberger, K. J. (2012) Development of the enzyme-

substrate interactions concept inventory. Biochem. Mol. Biol. Educ. 40,

229–233.

[2] Villafa~ne, S., Bailey, C., Loertscher, J., Minderhout, V., and Lewis, J.

(2011) Development and analysis of an instrument to assess student

understanding of foundational concepts prior to biochemistry course-

work. Biochem. Mol. Biol. Educ. 39, 102–109.

[3] Howitt, S., Anderson, T., Costa, M., Hamilton, S., and Wright, T. (2008)

A concept inventory for molecular life sciences: How will it help your

teaching practice? Aust. Biochemist 39, 14–17.

[4] Wright, T. and Hamilton, S., In ATN Assessment 08: Engaging Students

with Assessment (2008) Assessing student understanding in the molec-

ular life sciences using a concept inventory, Adelaide, Australia.

[5] Klymkowsky, M. and Garvin-Doxas, K. (2008) Recognizing student mis-

conceptions through Ed’s tools and the biology concept inventory.

PLOS Biol. 6, 14–17.

[6] Shi, J., Wood, W. B., Martin, J. M., Guild, N. A., Vicens, Q., and Knight,

J. K. (2010) A diagnostic assessment for introductory molecular and cell

biology. CBE Life Sci. Educ. 9, 453–461.

[7] Smith, M. K., Wood, W. B., and Knight, J. K. (2008) The genetics con-

cept assessment: A new concept inventory for gauging student under-

standing of genetics. CBE Life Sci. Educ. 7, 422–430.

[8] Mulford, D. R. and Robinson, W. R. (2002) An inventory for alternate

conceptions among first-semester general chemistry students. J. Chem.

Educ. 79, 739–743.

[9] Libarkin, J. C. and Anderson, S. W. (2005) Assessment of learning in

entry-level geoscience courses: Results from the geoscience concept

inventory. J. Geosci. Educ. 53, 394–401.

[10] Hestenes, D., Wells, M., and Swackhamer, G. (1992) Force concept

inventory. Phys. Teach. 30, 141–158.

[11] Mattos, C., Johnson, M., White, H., Sears, D., Bailey, C., and Bell, E.

(2013) Introduction: Promoting concept driven teaching strategies in

biochemistry and molecular biology. Biochem. Mol. Biol. Educ. 41, 287–

288.

[12] Smith, J. I. and Tanner, K. (2010) The problem of revealing how stu-

dents think: Concept inventories and beyond. CBE Life Sci. Educ. 9, 1–5.

[13] D’Avanzo, C. (2008) Biology concept inventories: Overview, status, and

next steps. BioScience 58, 1079–1085.

[14] Wenger, E. (1998) Communities of Practice - Learning, Meaning, and

Identity, Cambridge University Press, Cambridge, UK.

[15] Sirum, K. L. and Madigan, D. (2010) Assessing how science faculty

learning communities promote scientific teaching. Biochem. Mol. Biol.

Educ. 38, 197–206.

[16] Marbach-Ad, G., Briken, V., Frauwirth, K., Gao, L. Y., Hutcheson, S. W.,

Joseph, S. W., Mosser, D., Parent, B., Shields, P., Song, W., Stein, D. C.,

Swanson, K., Thampson, K. V., Yuan, R., and Smith, A. C. (2007) A fac-

ulty team works to create content linkages among various courses to

increase meaningful learning of targeted concepts of microbiology. CBE

Life Sci. Educ. 6, 155–162.

[17] Marbach-Ad, G., McAdams, K. C., Benson, S., Briken, V., Cathcart, L.,

Chase, M., El-Sayed, N. M., Frauwirth, K., Fredericksen, B., Joseph, S.

W., Lee, V., McIver, K. S., Mosser, D., Quimby, B. B., Shields, P., Song,

W., Stein, D. C., Stewart, R., Thompson, K. V., and Smith. A. C. (2010) A



model for using a concept inventory as a tool for students’ assessment

and faculty professional development. CBE Life Sci. Educ. 9, 408–416.

[18] Murray, T. M., Higgins, P., Minderhout, V., and Loertscher, J (2011) Sus-

taining the development and implementation of student-centered teach-

ing nationally - The importance of communities of practice. Biochem.

Mol. Biol. Educ. 39, 405–411.

[19] Sch€onborn, K. J. and Anderson, T. R. (2006) The importance of visual liter-

acy in the education of biochemists. Biochem. Mol. Biol. Educ. 34, 94–102.

[20] Craig, P. A., Michel, L. V., and Bateman, R. C. (2013) A survey of educa-

tional uses of molecular visualization freeware. Biochem. Mol. Biol.

Educ. 41, 193–205.

[21] Towns, M. H., Raker, J. R., Becker, N., Harle, M., and Sutcliffe, J. (2012)

The biochemistry tetrahedron and the development of the taxonomy of

biochemistry external representations (TOBER). Chem. Educ. Res. Pract.

13, 296–306.

[22] Villafa~ne, S., Loertscher, J., Minderhout, V., and Lewis, J. (2011) Uncov-

ering students’ incorrect ideas about foundational concepts for bio-

chemistry. Chem. Educ. Res. Prac. 12, 210–218.

[23] Harle, M. and Towns, M. H. (2012) Students’ understanding of external

representations of the potassium ion channel protein. Part I: Affordan-

ces and limitations of ribbon diagrams, vines, and hydrophobic/polar

representations. Biochem. Mol. Biol. Educ. 40, 349–356.

[24] Harle, M. and Towns, M. H. (2012) Students’ understanding of external

representations of the potassium ion channel protein. Part II: Structure-

function relationships and fragmented knowledge. Biochem. Mol. Biol.

Educ. 40, 357–363.

[25] Bailey, C. P., Minderhout, V., and Loertscher, J. (2012) Learning trans-

ferable skills in large lecture halls: implementing a POGIL approach in

biochemistry. Biochem. Mol. Biol. Educ. 40, 1–7.

[26] Sch€onborn, K. J. and Anderson, T. R. (2009) A model of factors deter-

mining students’ ability to interpret external representations in bio-

chemistry. Int. J. Sci. Educ. 31, 193–232.

[27] Sch€onborn, K. J. and Anderson, T. R. (2010) Bridging the educational

research-teaching practice gap: Foundations for assessing and developing

biochemistry students’ visual literacy. Biochem. Mol. Biol. Educ. 38, 347–354.

[28] Harle, M. and Towns, M. H. (2013) Students’ understanding of primary

and secondary protein structure: Drawing secondary protein structure

reveals student understanding better than simple recognition of struc-

tures. Biochem. Mol. Biol. Educ. 41, 369–376.

[29] Kramer, I. M., Dahmani, H., Delouche, P., Bidabe, M., and

Schneeberger, P. (2012) Education catching up with science: Preparing

students for three-dimensional literacy in cell biology. CBE Life Sci.

Educ. 11, 437–447.

[30] Handelsman, J., Miller, S., and Pfund, C. (2007) Scientific Teaching, W.

H. Freeman and Company, New York, pp 184.

[31] Miller, S., Pfund, C., Pribbenow, C. M., and Handelsman, J. (2008) Sci-

entific teaching in practice. Science 322, 1329–1330.

[32] Ebert-May, D., Derting, T. L., Hodder, J., Momsen, J. L., Long, T. M.,

and Jardeleza, S. E. (2011) What we say is not what we do: Effective

evaluation of faculty professional development programs. BioScience

61, 550–558.

[33] Offerdahl, E. G. and Tomanek, D. (2011) Changes in instructors’ assess-

ment thinking related to experimentation with new strategies. Assess.

Eval. Higher Educ. 36, 781–795.

[34] Black, P., Harrison, C., Lee, C., Marshall, B., and William, D. (2007)

Assessment for Learning, Open Univeristy Press, New York.

[35] McNiff, J. (2013) Action Research, 3rd ed., Routledge, New York.

[36] Cousin, G. (2009) Researching Learning in Higher Education, Routledge,

New York.

[37] Lewin, K. (1946) Action research and minority problems. J. Soc. Issues

2, 34–46.

[38] Meyer, J. H. F., Land, R., in Meyer, J. H. F., Land, R., Eds. (2003) Thresh-

old Concepts and Troublesome Knowledge: Overcoming Barriers to

Student Understanding, Routledge, London, pp. 3–18.

[39] Tanner, K. D. (2011) Reconsidering "what works." CBE Life Sci. Educ.

10, 329–333.

[40] Akerlind, G. S. (2003) Growing and developing as a university teacher -

Variation in meaning. Stud. Higher Educ. 28, 375–390.

[41] Feldman, A. (2000) Decision making in the practical domain: A model of

practical conceptual change. Sci. Educ. 84, 606–623.


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