Download Pipe Cleaner Protein Folding Activity My

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NAME ___________________________________
DATE _____________ PER ___
PIPE CLEANER PROTEIN FOLDING
ACTIVITY
Proteins are polymers constructed from different
arrangements of 20 amino acids linked together by peptide bonds. These polypeptides, once folded and coiled
into a specific three dimensional structure can become proteins with various shapes and hence various
functions. In this activity, students will identify the four levels of protein structure. Students will understand
how changes in the amino acids can affect the shape and overall function of a protein by developing a simple
model using beads and pipe cleaner.
Procedures:
1. Obtain 1 pipe cleaner and a set of beads
2. Place the 29 beads on the pipe cleaner in the order listed in columns 2, 4, and 6.
3. Prevent the two end beads from falling off the pipe cleaner by wrapping a small portion of the pipe
cleaner around the last bead at each end.
4. Lay the string of beads horizontally in front of you.
5. To simulate the various interactions that occur during protein folding, bend the pipe cleaner so that the
two red beads are touching the closest two green beads. Repeat so that the two blue beads are touching
the two yellow beads. White beads do not form interactions with other beads.
6. Crisscross the red and green beads and twist the pipe cleaner material several times to simulate a
chemical interaction. Repeat for the blue and yellow beads.
Results:
Amino Acids
Color of Amino
Acid Card
1.MET
2.ASP
3.ASP
4.VAL
5.MET
6.TRP
7.PHE
8.MET
9.ARG
10.LYS
Amino Acids
Color of Amino
Acid Card
w
y
11.HIS
g
y
12.HIS
g
w
13.PRO
w
w
14.MET
w
w
15.PHE
w
w
16.LEU
w
w
17.TRP
w
b
18.GLU
r
b
19.GLU
r
g
20.ASP
17 White/pink/black/lavender 4 Green 4 Red 2 Yellow 2 Blue
Amino Acids
Color of Amino
Acid Card
21.ASP
22.PHE
23.MET
24.LEU
25.PHE
26.TRP
27.LYS
28.ARG
29.LEU
g
w
w
w
w
w
r
r
w
Research Questions:
Pipe Cleaner Protein Folding Activity My-Nga Ingram AP Biology Modified Vdraper 2015
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1. Which level of protein structure is represented by the string of beads on the pipe cleaner?
2. At what point in the folding exercise did the second level of protein structure exist in your model?
3. What level of protein structure is represented when the three loops are created to form the three
dimensional form?
4. What characteristic of the amino acid determines whether a tertiary structure will form? What type do
the white beads contain?
5.
One form seen in this model is of a dog. What other forms could be created by the string of beads?
6. How could you simulate a quaternary structure?
7.
How would a mutation in the first amino acid from a white bead to a different color affect the tertiary
structure?
8.
How would a deletion of the second amino acid affect the tertiary structure?
9.
Proteins are categorized based upon their function. Enzymes are a unique category of proteins that have
biological catalytic properties due to their shape. These catalytic processes occur in specialized regions
of the enzyme called active sites. The model made in this activity is an enzyme whose active sites are
the loops created by the folding process. To what degree would the enzyme still function with the
deletion described in question 8?
SUPPLEMENTAL:
You may want to explore the following site: http://www.dnai.org/a/index.html and click on READING THE CODE, then
PUTTING IT TOGETHER. Watch the video on TRANSLATION and then try the INTERACTIVE on being a ribosome.
Pipe Cleaner Protein Folding Activity My-Nga Ingram AP Biology Modified Vdraper 2015