f02j Protein Tertiary Structure: Physical Model (WordPress embed)
Physical Model of Trypsin
A polypeptide in its cellular environment will spontaneously fold itself into a unique, specific three-dimensional structure that is related to the purpose that it serves in the cell. In addition to the formation of secondary structures such as alpha helices and beta sheets, the secondary structures themselves move into particular positions within the folded polypeptide. The overall shape of the molecule is called tertiary structure. The positioning of the parts of the polypeptide is influenced by interactions of hydrophilic R groups with water, attraction between hydrophobic R groups of one part of the polypeptide and those of another, and stabilization of the overall structure by disulfide bonds.
In the case of enzymes (catalytic proteins), the tertiary structure of the molecule produces an active site, a pocket which holds the enzyme’s substrate in a position favorable for facilitating the completion of the catalyzed reaction.
Many features of tertiary protein structure can be seen in the physical model of trypsin at the front of the classroom.
Video: History of the trypsin model (optional)
Experimental procedure: Viewing the physical model of trypsin
Note: If you are viewing this on a smart phone or other portable device, you can take these notes and videos with you as you view the model.
13. Locate the amino and carboxyl terminal ends of the molecule. Trace the backbone for some distance to confirm that the entire molecule is one continuous chain. (Refer to the following video for help.)
14. Examine the location of R groups on the surface and the interior of the molecule.
Learning objective 2.8: explain how non-random distribution of hydrophilic and hydrophobic side chains in an alpha helix would influence the position of that structure within the tertiary structure of a protein.
15. Locate an alpha helix and part of a beta sheet.
16. Examine the active site. (Note: the video erroneously says that the substrate has a negatively charged end – it’s actually positive.)
Learning objective 2.9: give examples of interactions that can occur between a substrate and specific residues in an enzyme at its active site that allow the enzyme to catalyze a specific reaction. Illustrate using trypsin as an example.
17. Consider the possible effects of mutations.
Learning objective 2.10: explain why mutations resulting in a substitution of a certain amino acid in a protein might have little effect on the function of the protein, while another change might render the protein non-functional.