Chapter 3 – Proteins

This chapter proteins, the first of 4 important classes of macromolecules. We will revisit some of them later as we talk about biological systems or processes for which they are important. The chapter 3 reading guide is here.

To complete the work for this chapter you should:

Download and print the reading guides above if you don’t already have hard copies.

• Read chapter 3 in Freeman.
• Watch video on Proteins.

• You do not need to know the structures of all amino acids. Be able to recognize whether an amino acid is likely to be hydrophobic or hydrophilic and acid, neutral, or basic based on its structure. You will be presented with the structure for any you need to evaluate.

Below is an α-helix. You can see the backbone structure (NCC atoms) along the ribbon of the α-helix. You can also see that the side groups are protruding outward from the helix. The Hydrogen bonds are in green and connect the Oxygen of one amino acid to the nitrogen (technically, to the hydrogen attached to the nitrogen, but the hydrogen’s aren’t shown here) of other amino acids. Use your mouse to rotate and zoom these structures.

The following is Hemoglobin, which has a quaternary structure containing 4 polypeptides (colored differently here) that are made up of many α-helices. You can also see the 4 Heme groups, which include iron (burnt orange atoms) and nitrogen (blue atoms). Use your mouse to rotate and zoom these structures.

The following protein is called P53, and it interacts with DNA to help prevent many cancers. You can see that this protein has a mixture of β-pleated sheets and &alpha-helices. You can also see the double helix of DNA (purple and blue).

Finally, here’s what that same P53 protein (with DNA) might really look like (if you could see it), with only the atoms at the surface shown: