This document is intended for use by instructors and their students. The activity contains steps to introduce students to the MACH model involving analyzing and discussing explanations about biological mechanisms. Initially, students read modified articles about biological mechanisms during class, although instructors may prefer to assign readings outside of class before the activity. During the activity, students are required to analyze the readings for evidence of research methods, analogies, context, and mechanisms. In so doing, students learn how to integrate the information pertaining to each of the MACH model components into a coherent explanation about their biological mechanism. After performing the above activities individually, students discuss findings in pairs, and then share their ideas with the class. After discussion, the instructor presents the MACH model. In our experience once the above activity has been successfully completed, students show strong evidence of competence in the writing of explanations about mechanisms. Details of the tetrahedral MACH model, and its related class activities, are freely available in the Purdue International Biology Education Research Group (PIBERG) ePubs collection. Together with the description of the activity, we have included advice on suggested topics, citations of suggested readings, and examples of typical student analyses of such readings. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Anderson, Trevor R

Pelaez, Nancy J

Trujillo, Caleb M

English

Purdue E-Pubs

Purdue UniversityPurdue e-PubsPIBERG Instructional Innovation Materials Purdue International Biology Education ResearchGroup (PIBERG)12-3-2014An Activity Aimed at Improving StudentExplanations of Biological MechanismsCaleb M. TrujilloPurdue University, ctrujil@purdue.eduTrevor R. AndersonPurdue University, ander333@purdue.eduNancy J. PelaezPurdue University, npelaez@purdue.eduFollow this and additional works at: http://docs.lib.purdue.edu/pibergiimPart of the Cell Biology Commons, Other Cell and Developmental Biology Commons, and theScience and Mathematics Education CommonsThis document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact epubs@purdue.edu foradditional information.Recommended CitationTrujillo, Caleb M.; Anderson, Trevor R.; and Pelaez, Nancy J., "An Activity Aimed at Improving Student Explanations of BiologicalMechanisms" (2014). PIBERG Instructional Innovation Materials. Paper 2.http://docs.lib.purdue.edu/pibergiim/2For contributions, the authors would like to acknowledge the Kamali N. Sripathi, and Sara L. Johnson.  An Activity M. Trujillo, Trevor R. Anderson, and Nancy J. Pelaez is licensed under a 4.0 International License, which means it may be modified so long as the authors are acknowledged and as long as others share alike.  An Activity Aimed at Improving Student Explanations of Biological MechanismsCreated by Caleb [NotModified by [Read  Individually, read the biological explanation[Approx. 5-10 minutes. Instructors may prefer to assign the reading readings about any topic with an explanation about a biological mechanism or encourage students to find one of their own choice.  Previously we have usedtrafficking, aquaporin and ion channelshandouts: Skwarecki, B. (2014). Cystic Fibrosis Might Be 2 Diseases.http://www.scientificamerican.com/article/cysticTrivedi, B. P. (2013). Doorway to a Cure for Cystic Fibrosis. http://discovermagazine.com/2013/september/14von Heijne, G. (2003). Advanced information on the Nobel Prize in Chemistry. http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2003/advancedZierath, J. R. & Lendahl, U. (2013). Machinery ReCells. Nobelprize.org http://www.nobelprize.org/nobel_prizes/medicine/laureates/2013/advanmedicineprize2013.pdf ] Think What components does the author with the respective shapes as follows• Science research methods • Models, figures, graphs, or analogies• Biological and/or social contexts• How the phenomenon works through physical causes (• Places where the above componentsBe prepared to share with a partnercomponents into a coherent explanation[Approx. 5 minutes. Examples from the text are shown on next pagePair With a partner, come to consensus about what the explanation.  Share what you notedfrom the above list and address how well the author blended the [Approx. 5 minutes.] Share Report the ideas you discussed with your partner[Approx. 5 minutes.] Learn Learn from your classmates and the summary by the instructor.[After the activity, we distribute the tetrahedral tetrahedral MACH model can be found at the Purdue International Biology Education Research Group (PIBERG) ePubs collection (https://www.bio.purdue.edu/pibergVisualization in Biochemistry Education (VIBE) group, John Alaniz, Aimed at Improving Student Explanations of Biological MechanismsCreative Commons Attribution-NonCommercial M. Trujillo, Trevor R. Anderson, and Nancy J. Pelaez Purdue University e to instructors: Edit bracketed sections] Your name, your institute, and the date]  provided. for outside of class.  Instructors may provide  topics of cystic fibrosis transmembrane conductance regulator, vesicle  functions.  We modified readings such as the following to create one Scientific America. -fibrosis-might-be-2-diseases/  Discover. -doorway-to-a-cure  Nobelprize.org-chemistryprize2003.pdfgulating Vesicle Traffic, A Major Transport System in our integrate into their explanation?  Analyze and mark : ();  including anthropomorphic stories ( (); ); and  blend and interweave ().  your thoughts about how the author integrates these .  for instructors.] components the author did and did not include in  about the passage.  Be sure to discuss any missing items components in the explanation to the class.   MACH model and teach students to use the MACH model./).] by Caleb -ShareAlike  -page . . ] ced-the text ); .   The An activity to improve biological explanations Trujillo, Anderson, & Pelaez   2 Examples of the MACH components found in the assigned text. Component Examples from Skwareck (2014) on the topic of cystic fibrosis transmembrane conductance regulator (CFTR). Analysis of example M “Whitcomb’s team screened a group of nearly 1,000 patients with pancreatitis and found nine abnormal but supposedly harmless versions of the CFTR gene.” “The techniques the researchers used to figure out the details of how each mutation changes the protein are ‘extremely challenging’ and ‘kind of an art form,’ ”  “Different diseases that all look the same on CAT scans.”  “Computer simulations confirmed...” References how scientists sampled patients for data. Reports about the research methods.  References to tools and data collected. Uses modeling software of investigate. A Figure: [http://discovermagazine.com/~/media/Images/Issues/2013/September/gene-mutations-in-CF.jpg?mw=900] “Seemingly benign mutations break the switch that turns CFTR from a chloride portal to a channel for bicarbonate.”  “CFTR leads a double life.” Displays a cartoon model of a protein.  Uses of a switch as an analogy. Anthropomorphizes the entity. C “The hereditary disease affects 30,000 Americans, and patients die unless they receive treatment to clear their lungs.”   “They can suffer from painful pancreatitis, as well as sinusitis and, in men, infertility.” Includes a social context; the disease affects the lives of many people. Includes a biological context; many organ systems are affected. H “Cystic fibrosis results from mutations in a gene that produces a tube-shaped protein known as CFTR, essential to the balance of electrolytes in the body. Specifically, this protein allows chloride ions to pass in and out of cells.”  “Whitcomb’s eventual goal is to disentangle the distinct causes of what, until recently, appeared to be a single disease.” Includes specific entities (proteins and ions) interact with spatial and temporal organization. Focuses on the causes of the disease(s).  An activity to improve biological explanations Trujillo, Anderson, & Pelaez   3 Examples of the MACH components found in the assigned text (Cont’d). Component Examples from Trivedi (2013) on the topic of cystic fibrosis transmembrane conductance regulator (CFTR). Analysis of example M “Tsui had read about a technique for locating a desired gene through DNA markers present in sick people but absent in healthy ones.” * “They added a chemical called genistein, a known door-opening drug that, unfortunately, was so weak it worked only in the test tube. Finally, a robotic eye scanned each mixture.  If cells were unaffected, the dye caused them to glow orange.” References the research methods. Includes a technique used in drug discovery to visualize channel activity. A Figure: [http://discovermagazine.com/~/media/Images/Issues/2013/September/gene-mutations-in-CF.jpg?mw=900] “The protein was shaped like a tube and wedged in the outer surface of the cells, resembling the kind of biological valve that would move chloride in and out.” “Instead, the defective protein remains stuck inside the cell, like a Cheerio trapped in a balloon.”  Includes diagrams of disease and non-disease states. Uses shapes, wedges, and valves as analogies. Uses macroscopic objects as analogies. C “Laura and Cate are among thousands of Americans who have cystic fibrosis”  “Affecting one in every 3,900 births in the U.S., CF is one of the most common genetic disorders known.” Includes social context; CF affects personal lives. Includes social context, the disease. H “A CFTR protein with this mutation cannot fold properly and cannot navigate its way to the surface of the cell where it would normally reside, providing a channel for chloride to flow in and out.”  “Riordan was an expert on proteins called ABC transporters, molecular elevators that shuttle things like fats, drugs and other molecules back and forth across cell membranes.”  “A mutated gene that produced a broken protein involved in chloride flow could cause a salt imbalance and all the devastation observed.” Explains disease state by the properties of the protein and its spatial organization. Addresses spatial organization and activity of the transporter. References how physical entities prevent the activity of chloride channels.  * The modified version of the article used during a Fall 2014 course had all excerpts of research methods (M) removed such that students could contrast articles with and without research methods.An activity to improve biological explanations Trujillo, Anderson, & Pelaez   4 Examples of the MACH components found in the assigned text (Cont’d). Component Examples from Zierath and Lendahl (2013) on the topic of vesicle trafficking. Analysis of example M “To test the SNARE hypothesis, Rothman used an in vitro reconstitution assay and revealed that SNAREs could indeed fuse membranes.”  “He used temperature-sensitive mutants and screened for genes affecting the intracellular accumulation of secretory enzymes.” References specific methods used by scientists. Includes screening, a specific technique used in research. A Figures [http://www.nobelprize.org/nobel_prizes/medicine/laureates/2013/advanced-medicineprize2013.pdf] “The vesicle fuse at the right location and that cargo molecules are delivered to the correct destination.” Indicates cartoon models of vesicles.  Tells a story as if vesicles have an end goal. C “…For example, metabolic disorders such as type 2 diabetes are characterized by defects in both insulin secretion from pancreatic beta-cells and insulin-mediated glucose transporter translocation in skeletal muscle and adipose tissue…” “This is the case for example for neurotransmitter release in the brain and for insulin secretion from the endocrine pancreas.” Makes connections to a disease, a social context.  Includes a biological context; compares different functions of the mechanism. H “…target and vesicle SNAREs (t-SNAREs and v-SNAREs) were critical for vesicle fusion through a set of sequential steps of synaptic docking, activation, and fusion.”  “…rapid exocytosis of synaptic vesicles, which is under tight temporal control and regulated by the changes in the cytoplasmic free calcium concentration…” References entities like SNAREs, their activities and how they are organized. Considers exocytosis as an activity and temporal organization.  An activity to improve biological explanations Trujillo, Anderson, & Pelaez   5 Examples of the MACH components found in the assigned text (Cont’d). Component Examples from von Heijne (2003) on the topic of aquaporins and ion channels. Analysis of example M “Shortly thereafter, Agre proved this conclusively by demonstrating that expression of CHIP28 in Xenopus oocytes made the cells swell rapidly when placed in a hypo-osmotic medium” “In 2000 and 2001, the first high-resolution 3D structures of AQP1 and a related glycerol-selective bacterial channel protein (GlpF) were reported” References experiment and observation. Includes structural research. A Figures [http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2003/advanced-chemistryprize2003.pdf] “Based on these structures, detailed models have been put forward to explain the high permeation rate…” Shows models of experiments and channels. Indicates models used for explanation. C “Aquaporin-like proteins have since been found throughout the living world; in humans alone, there are at least 11 different aquaporin-like proteins, many of which have been linked to various diseases.” “Plants have an even higher number of aquaporins, with no less than 35 different versions found in the model plant Arabidopsis thaliana.”  “The cloning and overexpression of a bacterial K+ channel with high homology to eukaryotic K+ channels (Schrempf et al., 1995) suggested to some workers that prokaryotic channels might finally provide the missing key to structural studies of ion channels.” Connects to disease, a social context.  Includes biological context; comparing to other domains. Indicates channels of different organisms of varying biological contexts. H “The local electrostatic field generated by the protein switches polarity in the middle of the channel, forcing the passing water molecules to rotate in such a way that their dipole moments are oriented in opposite directions in the upper and the lower halves of the channel.” “A comparison of the KcsA and MthK structures suggested a general mechanism for channel gating, in which a conformational change in the sensor domain pulls the transmembrane helices apart near the intracellular end of the channel.”  “Some K+ channels conduct ions in only one direction, serving as ‘molecular diodes’.  Such inward rectifying channels are blocked by Mg2+ and polyamines that penetrate into the channel from its cytosolic end when the membrane is depolarized.” References entities, their interactions and organization.  Includes entities changed states through conformational changes. Addresses the entities, the activity (or lack of activity when ‘blocked’), and the state of the membrane. An activity to improve biological explanations Trujillo, Anderson, & Pelaez   6 Work cited: Skwarecki, B. (2014). Cystic Fibrosis Might Be 2 Diseases. Scientific America. http://www.scientificamerican.com/article/cystic-fibrosis-might-be-2-diseases/ Trivedi, B. P. (2013). Doorway to a Cure for Cystic Fibrosis. Discover. http://discovermagazine.com/2013/september/14-doorway-to-a-cure  von Heijne, G. (2003). Advanced information on the Nobel Prize in Chemistry. Nobelprize.org. http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2003/advanced-chemistryprize2003.pdf. Zierath, J. R. & Lendahl, U. (2013). Machinery Regulating Vesicle Traffic, A Major Transport System in our Cells.  Nobelprize.org. http://www.nobelprize.org/nobel_prizes/medicine/laureates/2013/advanced-medicineprize2013.pdf 

An Activity Aimed at Improving Student Explanations of Biological Mechanisms

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An Activity Aimed at Improving Student Explanations of Biological Mechanisms

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