What knowledge have you connected with past knowledge?

In a pervious blog I mentioned that biology and chemistry are taught to students early in their scientific careers because it allows for a broad knowledge base. Having taken both biology and chemistry I often recognize concepts relevant to biochemistry.

Chapter 6 of our text “Protein and Enzymes” discusses the principles of thermodynamics which is a core topic in General Chemistry classes. I can remember learning these principles and found it challenging to grasp the concepts while in Gen. Chem. Today concepts such as activation energy, exergonic and endergonic reaction, and reaction rates are easily absorbed as I have a base knowledge. Biochemistry also allows us to connect these concepts to life processes. This allows me to conceptualize the information making it easier to get the big picture rather than a concept.

Chapter 8 of our text “Lipids and Membranes” directly correlates information I have discussed in detail while in anatomy and physiology. The phrase “structure depicts function” was repeated over and over again while in A&P, and is a concept I will continue to keep in mind while in biochemistry. The structure of the phospholipid bilayer membrane determines its function and ability to isolate the cell while allow certain molecules to pass through. The membrane of the cell performs many tasks, because of this many reaction take place to accomplish these task. While in A&P pathways were identified and discussed. In biochemistry we will build upon the base knowledge we have obtained to dig a little deeper.

As a science student I relate many of the classes to layers of an onion. Biology and chemistry we learn major concepts, and with each additional class we seem to pull another layer of the onion off, getting more and more detailed as we continue.

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

For this exercise we were instructed to search PDBlite.org, which is a website designed to search for, and download macromolecules. There were no restrictions limiting our search criteria for these macromolecules. I decided to narrow my search to molecules relating to human alcohol dehydrogenase. Forty one related results matched my search. From this list I chose to explore the structure of Human Zinc-binding alcohol dehydrogenase 1 (ZADH1) pdb id # 2VNA.

With the above information I searched the National Center for Biotechnology Information for my molecule. From here I was able to identify my molecule derived from humans, and had tertiary structure as it only had a single unit/subunit. Shown above is a 3D image of the molecule which clearly shows the secondary structures: alpha helix and beta pleated sheets. Little information was given about the real world application of this molecule but it is assumed that it has a role with the binding of zinc to alcohol dehydrogenase. It is also assumed by the name of this molecule that alcohol dehydrogenase is an enzyme.


Having access to this tool allows researches to search known molecules by name, related topics, and even primary structure sequencing. Researchers now have the ability to compare unknown proteins or amino acids against researchers around the world. Another huge tool for researchers is the ability to search for molecules with a similar sequence against an existing molecule with a known function and make assumption on what function the unknown protein might have.