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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
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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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Placement of Amgnets (cont.)
• 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.
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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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