I am confused about the various protein purification and analysis methods. Are we separating individual amino acids, rather than proteins?  The lecture covered two sets of methodologies within our discussion of proteins.  First, we discussed the monomers of proteins, the amino acids. Our discussion of PE (Protein Electrophoresis) and PC (Protein Chromatography)  showed how these free amino acids can be separated, one from the other. In thinking about these two methods, we became more aware of the properties of net charge and hydrophobicity/hydrophilicity that are dictated by the different amino acid side groups. Fingerprinting showed how molecules larger than individual amino acids could also be characterized by these two properties: peptides of modest size, say 5 to 20 amino acids in length, exhibited properties that were just the composite of their amino acid constituents. Later I talked about protein purification, so  hat we could appreciate the  complexity of a full protein (100 to 100 amino acids in length, and with a function in the cell). These methods brought new characteristics to consider: molecular weight and shape, as well as the old net charge. Our primary purpose in discussing these methods is to have you think about these small and large molecules in chemical and  physical terms, often at the level of the functional groups that are present. The division of the methods between the small molecules and the macromolecules is a natural one, as the methods used are different and the goals are usually different: for small molecules, the goal is usually analysis; for the proteins the goal is often purification as well as analysis