Fold It: Solving Puzzles for Science- Dorothy Ahlf

Fold It: Solving Puzzles for Science- Dorothy Ahlf

Purpose

This lesson is intended to follow up from previous lessons about the nature of polymers and how shape can drastically change function. Students will have the opportunity to use their previous knowledge to fold proteins into usable shapes while thinking about the reasons behind it.

Overview

In this activity, students will work in small groups with the research program FoldIt, talking through the initial reasons behind problems with folding using their previous knowledge. At the end, students will have the chance to see if they can solve some harder puzzles and find the best form for the protein.

Student Outcomes

Students will be able to recognize proteins as polymers, and connect their previous learning about molecular interactions to folding. Students will also start to become familiar with research-grade programs and how scientists visualize 3D-structures.

Illinois State Standards:

11.A.3e Use representational methods to analyze scientific data.

12.C.3b Model and describe the chemical and physical characteristics of matter

13.B.3a Identify and explain ways that scientific knowledge and economics drive technological development.

13.B.3b Identify important contributions to science and technology that have been made by individuals and groups from various cultures.

13.B.3c Describe how occupations use scientific and technological knowledge and skills.

Time

This lesson is intended for one 45 minute class period.

Level

This lesson is intended for 8th grade students who have just finished chemistry and are moving into genetics.

Materials and Tools

FoldIt is a program that is freely available online (in beta) version, but requires a username and internet access to download. This should be setup ahead of time, but to avoid the need for each student to have a username I would advise the school setup 3 or 4 accounts ahead of time. These can also be used if the students wish to continue later on their own time. In the first application, we had 2 students per laptop.

A SmartBoard will also be helpful to show the students enlarged pictures, as well as a whiteboard or other large writing surface to write down their ideas.

Suggested Resources:

FoldIt’s makers have published several papers now solving structures previously unknown. These are good background reading to show what the program is capable of doing.

http://fold.it/portal/node/990356

http://www.nature.com/nsmb/journal/v18/n10/full/nsmb.2119.html

Teachers are also advised to be familiar with polymers and molecular interactions.

Preparation

Setup: A whiteboard and markers should be available. FoldIt should be setup on laptops enough for small groups of students and the Smartboard computer for the teacher to try. If the teacher does not have access to a Smartboard, a computer with a large monitor may serve. Alternately, this lesson may be good for a pull-out small group of students rather than a large classroom.

Prerequisites

This lesson is intended for students who are just finishing up two trimesters about chemistry and physical interactions, then moving into genetics. Students should be familiar with molecular interactions and how molecules are drawn, as well as basic intermolecular forces and bonding.

Background

Periodic trends, types of atoms, some knowledge of types of molecules helpful, covered types of bond and molecular interactions, what a cell looks like and what might be inside (from long ago) for the part to bridge into genetics.

Review: Types of Bonds and Interactions

Covalent: Strong bond sharing electrons where the electronegativity difference between the two is small

Ionic: Attractive bond between two ions of opposite charge.

Dipole-dipole: An interaction between molecules where opposite polarities keep the atoms close together

Dispersion (London) forces: General interactions between atoms and molecules due to instantaneous dipoles forming because electron cloud is not uniform around the atom.

Hydrogen Bonding: a very strong dipole-dipole bond resulting from electronegativity differences between Hydrogen and Oxygen, Fluorine, Chlorine, etc.

Teaching Notes

FoldIt is a software program originally developed for researchers working on modeling protein structures. 3D structure problems are a big cause of many diseases as proteins can’t function properly.

Foldit is a real scientific research tool. It has solved problems that some scientists have been working on for years. How? Several ways Foldit helps: It makes solving proteins a game, it opens this problem up to more people, and allows thousands of people across the country to work together finding a solution and having fun doing it. They use some different terminology though that we need to think about before we can begin.

1st of all, why do we care? If a protein is folded correctly in our body, the polymer is shaped the right way. That means it can do whatever work it’s supposed to do. But suppose the protein isn’t folded right—it’s hanging like a limp piece of spaghetti when it’s supposed to be all curled up like penne. Can it do the same job? Suppose someone handed you a book to read but all of the pages were mixed up, sewn backwards and upside down, with no page numbers. Could you read the book the way it was supposed to be read? Probably not right? So this is what causes a lot of diseases in the body or problems with lots of things.

Clash: These are shown on the screen as small stars. If two sides of the molecule are clashing, what do you think that means? (It means the interaction isn’t favorable, they don’t like each other, so they won’t want to stay that way). So when a protein is folded correctly, there are few if any clashes so that all of the sides are sitting the way they are supposed to be. Remember Nature is lazy, things generally will like to go the path of least resistance. It’s only by putting energy into something that we can usually fight the chaos.

Void: What would happen if things are too far apart? Think about the book if you need to. If one page was here and another downtown, the book would be hard to read. Voids are the same thing. So when you fold a protein, voids are generally a bad thing. There are a few special cases though—can someone think of anything?

Backbone: This is the part of the protein with the covalent bonds (what are those again?). This part is all made up of the same connections, and then the part poking off (called the sidechain) effects how things are packed together.

Now that you know some of the basics, have fun! See what you can do to solve some of these puzzles. They’re 3D problems that are being worked on right now to try to give us all a better future, plus you can try to get the high score.

Assessment

The students will be able to make it through at least 10 of the introductory puzzles on the FoldIt tutorial. Students will be able to answer the questions posed about proteins as polymers and what the different situations presented in the FoldIt program mean. Students will be able to see why scientists and engineers sometimes build simulations of molecules to study how they interact.

Part of the success of this lesson may also be measured by continued interest in the program. At the school where this was tested, the science classroom has a student-use computer which will have this program loaded for future interest.

Additional Information

Students could also just use the program as an example of what programming can do to help science if the simulation was approached in an engineering/computer science setting. For this application we are not focusing on how the simulation was made, but rather what it is useful for in science.

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