From the lecture on 9/22, what exactly is a chaotropic agent? You provided urea as an example but how does it work. You mentioned it is very soluble in water and thus is good at disrupting hydrogen bonds. Hydrogen bonds are important in the secondary structure of alpha and beta helices. Amino Acids have peptide bonds between them. Thus does urea ONLY disrupt the secondary structure and not the primary?

Yes, urea disrupts secondary and tertiary and quaternary, but not primary structure nor disulfide bonds. How it works is not so clear, but probably by interfering with the proper formation of hydrogen bonds that are important for secondary structures and for interaction between side chains in tertiary structure.