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PROTEIN FOLDING MODEL“SNACK” APPROACH

Gary Benz and Claudia Winkler

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WHAT IS A “SNACK”?

• The term “Snack” is used at the Exploratorium in San Francisco (www.exploratorium.org)

• "Snacks" are miniature science exhibits that teachers can make using common, inexpensive, easily available materials.

• “By using Snacks in their classrooms, teachers can climb out of the textbooks and join their students in discovering science for themselves”.

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Introduction

• Proteins are composed of sequences of amino acids.

• One amino acid in a protein can be attracted to another part and form a hydrogen bond. This bonding causes the protein to fold.

• This model will allow the user to physically see how this folding of a protein occurs.

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Topics of Discussion

• How the model is assembled will be addressed in the first set of slides.

• Each part of the assembly will be followed by a picture of the assembly process.

• How the model is used to demonstrate protein folding will be addressed in the second set of slides.

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Materials Needed• Low temperature glue gun or wood glue.• Three feet of quarter inch dowels.• Exacto-knife.• Connector atom from standard chemistry model kit

with 120 degree holes • Small block of wood for platform. • Four small magnets.• Felts pens or paint optional.• Petroleum jelly. * Styrofoam balls can be used as a less durable substitute.

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General Assembly

• The assembly of the demonstration takes place in three stages.

• The amino acid strands are constructed by gluing the cut wood dowels together.

• The magnets represent charged portions of the amino acids. They are glued and secured on the completed strands.

• The completed strands are then placed in the pivoting holes in the wood platform.

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Model Skeleton

• Each strand consists of two inch pieces of wood dowel.

• The first strand consists of 4 – 2 inch dowels, while the second strand is made of five dowel sections.

• The second will have three dowel sections, the atom connector, and two dowels following.

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Strand Assembly

• Each dowel should be glued to provide an angle in between 109 and 120 degrees.

• The cuts should be made with an exacto knife and need to be flat in order to avoid problems during gluing.

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Strand Assembly (cont.)

• Each dowel represents an individual amino acid.

• Individual dowels can be colored with felt pen or paint to indicate different amino acids, if desired.

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Strand Assembly (cont.)

• The strands are most easily assembled by gluing one dowel at a time to each strand.

• Wood glue needs 24 hours to dry, whereas a glue gun greatly speeds up this process.

• The strands should be constructed so they move upward, avoiding any helical patterns.

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Placement of Magnets

• Drill holes into the wooden platform about a half inch deep and approximately two inches apart form each other.

• Place a little petroleum jelly in the holes, so the strands can be easily rotated.

• Place each strand in the drilled holes.• Turn the strands until they come in contact

at one point. Mark the contact point on each strand.

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• Glue the smallest strand (2 dowels) into the connector atom ball.

• Place a little petroleum jelly on top of the smaller strand that is in the platform.

• Place the connector atom on top of the second strand.

• Carefully rotate the model atom until the two dowel strand comes in contact with the first strand. Mark the contact points.

Placement of Amgnets (cont.)

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Placing the Magnets

• Glue the magnets to the four contact points (two on each strand). Make sure the magnets are glued so they are attracted to each other.

• Often the magnets will separate even if glued to the wood. Completely encase the magnets with glue, making certain the glue touches the dowel.

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Adjusting Magnet Strength

• If the magnets are too strong, they may separate from the dowel when pulling the model apart.

• In order to prevent this, tape or plastic wrap should be wrapped around the magnet and the section of dowel the magnet is attached to. The tape or wrap should be melted with a hair dryer.

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Presentation

• Before the presentation, rotate the base of the strands and the connector atom, so none of the magnets make “hydrogen bonds”.

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Presentation

• Rotate the two strands at their bases, until the fixed strand makes a hydrogen bond.

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Presentation

• Rotate the top of strand two ( the model atom ) until the second hydrogen bond is formed.

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Conclusion

• Students can observe that hydrogen bonding chemically holds a protein in its folded structure or tertiary structure or native structure.

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What is occurring?

This model shows the student how folding forms.

The magnets represent parts of an amino acid that has electrical charge. The charges are attached to an amino acid with opposite electrical charge.

This bonding is responsible for the folding of the protein.

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