The Forms, Functions, and Complex Stories of Biomolecules
Living organisms depend on biomolecules, and their nature is as varied as the functions they perform.
Most biomolecules are macromolecules, which often include repeating units. They include proteins, carbohydrates, lipids, and nucleic acids. Living organisms are literally born from biomolecules, such as DNA, and we also rely on them to build tissue, obtain nutrients from food, drive our metabolism, and make our organ systems function properly. Furthermore, form commonly matches function. Biomolecular engineers use that fact in order to manipulate such molecules to change or enhance their functions. Such manipulations may be applied in the fields of medicine, environmental remediation, agriculture, and biofuels, for example.
So, what do your students already know about molecules? Post the following terms for students to see and begin discussion: amino acids, proteins, lipids, carbohydrates, and enzymes. Have students get into small groups of two or three and plan to use a particular color of writing pen and a large sheet of butcher paper. Without reliance on any reference materials, instruct students to develop a graphic organizer that describes and illustrates what they know or believe about the relationships between those terms. Suggest they include one or more examples, as well. Direct students to leave plenty of space between and around terms, so they can fill in more information later.
Tell students that they will visit various Web sites. As they do so and find new information to add to their organizer, they should use another pen color for writing in the additional notes. As needed, students should cleanly strikeout any inaccurate information they had included initially, so that their misconceptions can still be easily read while clearly indicating which statements in the organizer are correct.
Set students free on a few different sites to continue to fill in their graphic organizer. John Kyrk’sÂ Cell Biology AnimationÂ site provides an excellent place to start. In theÂ Amino AcidsÂ module, for example, glycine, the simplest amino acid molecule, is shown with both its structural formula and 3D visual illustration. When students hover over each element in the illustration, the corresponding element highlights in the formula. This “stereo pair” helps students make the connection between the formula and the molecule’s form.
Clicking the arrow button moves the animation to the next stage. In this Amino Acids animation, the next screen shows students what happens to the basic structure when a particular side chain is added. Students can select through each of the 20 most common amino acids that occur in proteins to view each stereo pair. Suggest that students copy the stereo pairs onto a sheet of paper for comparison and as examples to include in their graphic organizers.
Continuing through the module reveals additional information about amino acids, including how their combinations can include different types of bonding and grow more complex structures. Students may also jump to additional, related animation modules, such as the one that featuresÂ DNA AnatomyÂ andÂ Glycolysis.
Another good site for students to examine these particular biomolecules is theÂ Amino Acid Explorer. This site from the National Center for Biotechnology Information is more advanced than the one produced by John Kyrk, but is easy to navigate provides more in-depth information that is generally digestible for high school students. TheÂ Biochemical PropertiesÂ section displays a table that shows the general abundance of each of the common 20 amino acids. Using the search criteria on the left-hand side of the page, students can also select between two of the amino acids to compare them using either text or graphics display. The text version is a table with various data for each acid for comparing characteristics such as side chain flexibility, interaction modes, hydrophobicity, and other pertinent properties. The graphic version shows each acid’s structural formula and 3D visualizations with and without electron cloud effects.
In the Structure and Chemistry section of the Explorer, students can select a single amino acid to view its text and graphics display on one page. Once they have selected to view one, then the left-hand side menus for comparison are available as on pages in the Biochemical Properties section.
Other sections that students can explore include being able to seeÂ Common SubstitutionsÂ for an amino acid. Using theÂ Mutations Analyzer, students can choose from multiple combinations of criteria in order to compare the results of different types of mutations. The final two sections of the Explorer are even more complex in content, so they may be skipped or suggested to more advanced students.Â Amino Acids at WorkÂ provides a way for students to explore functional sites within proteins can change, and theÂ Amino Acids as LigandsÂ section shows 3D protein structure containing a given amino acid as a ligand.
An interactive animation site will help students answer the question, ”What is an enzyme?Â In this illustration, students should begin with the basics, which clearly and simply explains how enzymes are proteins that act as catalysts in a reaction. This animation excels in showing how an enzyme’s form directly relates to its function, acting like a piece in a puzzle. The animation also illustrates the difference between competitive and non-competitiveÂ Inhibitors, as well asÂ Allosteric EnzymesÂ andÂ Feedback Inhibition. Remind students to add more information about what they learn to their graphic organizers.
The LearnersTV Web site provides dozens of freeÂ Biology AnimationsÂ in its library of resources. Allow students to browse the various animations in the sub-category of Biochemistry, which provide great interactive visualizations and explanations on not only biomolecular structures but also their functions and related processes.Â Â Available modules include ones that explainÂ Cholesterol,Â Fatty Acid Metabolism, andÂ Protein Synthesis, to name just a few. One or more of these animations may help provide students with ideas for their final project.
For the final project, ask the student groups to use their graphic organizers, along with any additional notes they may have recorded, to develop a more formal presentation in a story-like format. Ask students to find and choose an example of structures and processes in a living organism or using a real-world bioengineering application that encompasses the associations of all the key terms. Instruct students that they must include at least one reference to each of the original terms posted. The story must define each term and in some way explain and illustrate the relationship between those terms in their story’s context. If one of the terms does not exactly fit the story directly, then it is okay for them to explain the term and its association with the other terms generally, but then describe why that one term does not fit into their particular story. Encourage students to use multimedia or theater-like presentation to enhance their storytelling.
NS.9-12.2 Physical Science
Structure and properties of matter
NS.9-12.3 Life Science
Matter, energy, and organization in living systems
Â§112.34. BiologyÂ (9)Â Â Science concepts. The student knows the significance of various molecules involved in metabolic processes and energy conversions that occur in living organisms. The student is expected to:Â (A)Â Â compare the structures and functions of different types of biomolecules, including carbohydrates, lipids, proteins, and nucleic acids;Â (C)Â Â identify and investigate the role of enzymes; andÂ (D)Â Â analyze and evaluate the evidence regarding formation of simple organic molecules and their organization into long complex molecules having information such as the DNA molecule for self-replicating life.
Reference:Cell Biology Animation
http://www.johnkyrk.com/Â Â Amino Acid Explore
http://www.ncbi.nlm.nih.gov/Class/Structure/aa/aa_explorer.cgiÂ Â What is an Enzyme
http://programs.northlandcollege.edu/biology/Biology1111/animations/enzyme.htmlÂ Â LearnersTV Biology Animation