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.
How to recognize common amino acid representations
How to estimate the space filled by an electron cloud
How to build peptides
What are constraints on peptide bond angles
One set of models
Four amino acids (Tryptophan, proline, arginine, glycine) in space-fill and stick
Five peptide bonds
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.
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"
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.
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:
Recognize a variety of molecular representations
Identify space filled by an amino acid
Identify features of the peptide backbone
Understand constraints on peptide bond angles.
Access Online Interactive Activity
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.