Sometimes, it's the little things
Regular protein structures reoccur throughout nature because they are within the physical constraints imposed on amino acid rotation and have repeated, strengthing bonds.
This 30-minute activity asks students to build various dipeptides and test their rotation with stick or space fill models.
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How to recognize common amino acid representations
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How to estimate the space filled by an electron cloud
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How to build peptides
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What are constraints on peptide bond angles
Where's the data?
Want to know if the activity is effective? We did too. Check out our peer-reviewed publication here.
The Models
One set of models
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Four amino acids (Tryptophan, proline, arginine, glycine) in space-fill and stick
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Five peptide bonds
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N-terminus
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C-terminus
After printing, cut the wire connecting each piece to make a useable model set. We recommend printing in two contrasting colors to create two sets with the amino acids in one color and the peptide bonds in the opposing color.
Printing files
There are two versions available for download, a .blend file that can be opened and modified in Blender, and a .stl file that can be opened by most 3D printers. Note that your printer needs to be able to print support material.
(Opens a UNL Digital Commons page with download files at the bottom)
"Click and ship"
models
If you don't have access to a 3D printer, you can print these using Shapeway's professional 3D printing services. They will ship, finished, to your address.
The Activity
This 30-minute activity is designed to be completed in class, in groups.
We recommend a printed version only for small classes and a combination of printed and interactive online activity for large classes.
Activity learning goals:
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Recognize a variety of molecular representations
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Identify space filled by an amino acid
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Identify features of the peptide backbone
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Understand constraints on peptide bond angles.
Access Online Interactive Activity
The Slides
These slides describe:
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Prerequisite class knowledge
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An introduction to why protein structure is important
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Model description
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Clicker question
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Protein methods image
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A summary of what Dr. Roston's class should know about Amino Acids
Looking for Assessment Questions?
Or activity answer keys? Our data suggests that students will perform better on typical biochemistry test questions regarding protein structure after doing this activity. However, Dr. Roston is happy to provide assessment questions and answer keys.