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Learning Connections Science Seeing the Unseen In high school biology, students are challenged by many molecular concepts and structures. Th ey meander through a number MMoolleeccuullaarr of molecular structures, some in Visualization macromolecular form: carbohydrates, amino acids, fatty acids, nucleotides. in Biology Student diffi culties arise in part from inability to visualize what they can’t easily see. Students struggle moving from chemical name to symbolic chemical formula and from symbolic representation to the physical one. Th e problem with physical representation resides at opposite ends: the macroscopic level of directly observ- able physical and chemical properties and the microscopic level of molecular form and dimensions. We addressed these challenges as participants in a federal research project known as Michigan Teachers’ Technology Education Network (MITTEN), a component of the Preparing Tomorrow’s Teachers to use Technology (PT3) initia- tive. A MITTEN project calls for the engagement, interaction, and collaboration of student teachers, cooperating teachers, and education faculty to develop and fi eld-test authentic projects in which technology enhances teaching and learning in specifi c subjects. Our project incorporated several free technology appli- cations into our a biology class taught by Jeff as part of his student teaching By Jeff Finnan, Kim Taylor- experience at Redford Union High School in Redford, Michigan. He Papp, and Mesut Duran worked in concert with his cooperat- Subject: Biology, chemistry The research reported in this article is based ing teacher Kim along with input by on a project funded by the U.S. Department of his educational technology professor Grades: 10–12 (Ages 15–18) Education through Preparing Tomorrow’s Teachers Mesut during the design and imple- to Use Technology (PT3) Grant #P342A0110073. mentation. We discovered that this The views and conclusions expressed are those Standards: NETS•S 2–5; NETS•T II, of the authors, and no endorsement by the U.S. alternative learning environment en- III (http://www.iste.org/standards/) Department of Education should be inferred. hanced the understanding of abstract 24 Learning & Leading with Technology Volume 32 Number 4 Copyright © 2004, ISTE (International Society for Technology in Education), 1.800.336.5191 (U.S. & Canada) or 1.541.302.3777 (Int’l), [email protected], www.iste.org. All rights reserved. Science concepts covered in our biology curriculum. Building One Atom at a Time Students, on individual computers, started the project using eChem, a stand alone Java-based program that allows construction of simple compounds. Although it is a limited program, eChem allows the formation of some fairly sophisticated molecules. Students were already knowledgeable about atomic planetary models and bond formation through electron sharing. Th ey introduced themselves to eChem with an extensive tutorial. A quick review of this tutorial as- sisted the transition to other ways of Students can view the same molecule in the three possible display modes and rotate them characterizing bonds and molecular simultaneously while maintaining the same aspect view. They can be compared with other shapes. Beginning with methane, molecules in any mode if desired. students explored some simple molecules that we had constructed for them. Th e students stepped through alternative display modes. Th ey could opt for multiple views to compare the same or other molecules simultaneously. (Editor’s note: Find the URL for eChem and other Resources men- tioned in this article on p. 29.) Before building molecules from scratch, students transformed some of the premade molecules into others. Th e tutorial then guided the students through the construction of ethanol from its formula in straight-line notation, where straight lines represent bonds between element symbols. As the students constructed other simple molecules from straight-line formulas, they progressed rapidly through the tutorial. After teacher review of the student-built molecules, a few students had to correct errors. But most students were able to construct cyclo- hexane from its straight-line notation When students open up ethanol, they are presented with the ball-and-stick display, which can be without direction on how to assemble freely rotated with the mouse. In all displays, the molecular formula appears in the upper right. cyclical molecules. December/January 2004–05 Learning & Leading with Technology 25 Copyright © 2004, ISTE (International Society for Technology in Education), 1.800.336.5191 (U.S. & Canada) or 1.541.302.3777 (Int’l), [email protected], www.iste.org. All rights reserved. Science To convert ethanol to ethylamine, students can delete the oxygen atom of ethanol (left) and insert a nitrogen atom with three single bonds followed by adding another hydrogen to complete the [Empty] bond (right). eChem does not require the user to be knowledgeable of molecular orbitals. When selecting a particular element, icons offer the bonding options (single, double, triple, or combinations) unique to that element. CCCCoooonnnnnnnneeeeccccttttiiiinnnngggg SSSSttttrrrruuuuccccttttuuuurrrreeeessss ttttoooo PPPPrrrrooooppppeeeerrrrttttiiiieeeessss AAlltthhoouugghh ssttuuddeennttss ccaannnnoott ccoonnssttrruucctt Stick) off ers a great way to present Students explored these molecules their own molecules in Chime, they the volume occupied by atoms with further on Chemfi nder. Th is Web can rapidly click through more dis- informative visual cues about the site is a depository of thousands of play combinations than in eChem. structural backbone. Students chose molecules with physical properties Chime off ers an additional stick their own path. Th ey viewed other and structures. In Chemfi nder, mo- presentation and a zoom feature. Stu- pages incorporating various mole- lecular structures are often shown as dents can render a view at any time to cules of biological interest: fatty bond-line formulas, in which implicit its bond-line structure, and two- and acids, carbohydrates, even a lipid carbon and hydrogen atoms often are three-dimensional representations bilayer. Chime views of starch and not shown. Students retrieved some can be directly bridged. You can cre- cellulose off ered students insight physical data for these molecules and ate molecular surfaces that can be into the chemical and physical compared the formula notation. Th ey color-coded to show the structures’ diff erences between these two obtained additional information from comparative water and fat solubility. compounds. (Editor’s note: Find Th e Merck Index using a paid link in You can script Web pages to feature the Web pages Jeff created in his Chemfi nder. specifi c molecular aspects or to show online portfolio in the Resources animation. Chime can include and section on p. 29.) Extending the Range of Vision is particularly suited for visualizing In class, we demonstrated the de- Although eChem allows students to macromolecules, such as protein and pendency of water solubility of alco- create molecules whose spatial rela- DNA. You can also turn on hydrogen hols on the hydrocarbon chain length. tionships can be explored, detail and bonds or simplify helical regions as In a Chime Web page, students exam- molecular complexity is limited. Th e strands or ribbons. ined these alcohols as transparent sur- Chime Web browser plug-in off ers After introducing themselves to faces, color-coded to show relative fat more robust microscopic information Chime with a Web page Jeff created solubility. Students correctly identi- of unlimited molecular complexity. to show how the Chime representa- fi ed that as hydrocarbon chain length However, the instructor has to build tions were diff erent than those in increased, the molecules had a greater Web pages incorporating desired eChem, students followed a tutorial proportion of lipophilic colors (fat molecules. You can fi nd some links illustrating how to generate molecular soluble) relative to hydrophilic ones to tutorials that will help you code surfaces. Making surfaces transparent (water soluble). Th at is, they became these pages in Jeff ’s online portfolio. in some display modes (e.g., Ball & less water soluble. 26 Learning & Leading with Technology Volume 32 Number 4 Copyright © 2004, ISTE (International Society for Technology in Education), 1.800.336.5191 (U.S. & Canada) or 1.541.302.3777 (Int’l), [email protected], www.iste.org. All rights reserved. Science ISTE is… Making it Happen! Thank you to Making It Happen Sponsor Peter Li Education Group fortheir support in helping ISTE to recognize outstanding Ed Tech Leaders! To sponsor, participate, orlearn more about thisoutstanding program, visit www.iste.org/ makingithappen or e-mail us Scripting the Chime plug-in allows the student to correlate the relative proportions of color at [email protected] and atoms types to water solubility. During their introduction to the used in their paper gene. genetic basis of life, students built a Chime’s diff erent display modes paper replica of the insulin gene. Th ey allowed them to appreciate the used Chime to explore a short seg- backbone and the stacking of the ment of helical DNA. Th e Web page base pairs. Th e students could allowed students to color-code the explore the hydrogen bonding nucleotides to match the colors they between the base pairs. December/January 2004–05 Learning & Leading with Technology 27 Copyright © 2004, ISTE (International Society for Technology in Education), 1.800.336.5191 (U.S. & Canada) or 1.541.302.3777 (Int’l), [email protected], www.iste.org. All rights reserved. Science ronment fostered a level of understanding of the abstract concepts beyond the traditional classroom experience. Students, however, did have some diffi culty understanding the two- dimensional bond- lliinnee nnoottaattiioonnss wwiitthh ssoommee elements not shown. We had to draw many in straight-line notation to help them understand. In the future, we will address this issue from the beginning to make it easier for students to read those simplifi ed formulas. Resources Chemfi nder: http://chemfi nder.cambridge soft.com/ Chime: http://www.mdlchime.com/products/ framework/chime/ eChem: http://www.hi-ce.org/soft_echem.html Jeff Finnan’s portfolio: http://www.umd. Students color-coded nucleotides to match the colors in the paper gene exercise. They could umich.edu/mitten/jfi nnan/. Here you will show hydrogen bonds in white. fi nd exhibits and annotated resource links. Th ese links show how to script Web pages to incorporate Chime molecules and where Taking Ownership structure, and a link to a simple Web to get or generate suitable molecules. Th e opportunity for refl ection came page we supplied with a Chime pre- Jeff Finnan’s Molecular Visualization site: as soon as the students, now familiar sentation of their specifi c molecule. http://expedioscientiam.net/molvis/ with eChem and Chemfi nder, learned MITTEN Project: http://umd.umich.edu/ to navigate with Chime. Th ey under- Seeing the Unseen mitten took their My Molecule project. Stu- Th e day the students fi red up eChem dents chose a molecule of biological for the fi rst time, we worried that Jeff Finnan, PhD, spent 20 signifi cance to build with eChem, our curriculum would exceed the years in corporate research and found physical and biological data, students’ capabilities. Would their development as a chemist. Th en and incorporated this information comprehension improve through he embarked on a second career into PowerPoint, which most students these largely inquiry-based technolo- in teaching. He is currently pursuing opportunities in sec- were familiar with from their required gies? But our apprehension was mis- ondary science education. computer literacy course. A list of placed. Students quickly mastered suggested molecules included alco- building and controlling their own Kim Taylor-Papp teaches biology, molecular biology, hols, amino acids, fatty acids, small molecules. Th ey moved so quickly forensics, and earth science at carbohydrates, and two dipeptides. through the eChem tutorial we had Redford Union High School. Besides minimal requirements, stu- to throw in the challenge of making a She has been there for 16 years dents could garner more points based cyclical molecule to slow them down. and is currently the science oonn tthhee ccoommpplleexxiittyy ooff tthhee Students fi gured out, on their own, chairperson. mmoolleeccuulleess cchhoosseenn,, aaddddii-- how to use [Empty] in the eChem Mesut Duran is an assistant ttiioonnaall formula to guide them while building professor of technology at the University of Michigan- ssccrreeeenn-- molecules. Th e students precisely cor- Dearborn and is director sshhoottss,, related solubility with structure. of the MITTEN Project. CChheemm-- As we refl ected on the entire proj- fifi nnddeerr ect, we found the new learning envi- December/January 2004–05 Learning & Leading with Technology 29 Copyright © 2004, ISTE (International Society for Technology in Education), 1.800.336.5191 (U.S. & Canada) or 1.541.302.3777 (Int’l), [email protected], www.iste.org. All rights reserved.