What knowledge have you connected with past knowledge?

This course has been a recurring source of flashbacks to organic chemistry. Between chemical kinetics, chemical structures and the importance of functional groups, there has been a lot of review on the subject of organic chemistry. In ties with the name of the field, chemistry isn’t the only knowledge to bear connections with biochemistry, there have also been numerous times where the knowledge overlap between biology and biochemistry have become apparent. Most recently with the discussion of how enzymes work, although when I first learned it, I had know the “lock and key” variant of the process, and knew nothing of the induced fit model. Other previously known information includes: amino acids, primary, secondary, tertiary and quaternary structures of proteins and formation of polypeptide chains. No information so far has been “new” so to speak, but it has gone more in depth into ideas discussed in previous classes.

Find a protein using PDB explorer–describe your protein, including what disease state or other real-world application it has.

My protein, lymphoid tyrosine phosphatase (LYP) is composed of alpha helixes and beta pleated sheets. Having only one unit, and no subunits, this protein has no quaternary structure. An important protein in the function of the human autoimmune system, LYP is a target for modern drugs and possesses a large risk factor. Recent studies of the structure of this protein have revealed a rather unusual disulfide bond between the catalytic CYS and a local non-catalytic CYS. This disulfide bond is important to the regulatory function of LYP. The study also found a phosphate ion bonded in the active center of LYP which, upon dephosphorylation but before the actual release of the phosphate, the protein will take on an intermediate conformation. These finds help us understand more about the regulation of this protein, which in turn helps us find out more about the human immune system.