What knowledge have you connected with past knowledge?

Biochemistry involves many other fields of science. Many of these fields have been studied by us previous to taking this course. We started talking about Animal versus Plant cells and their structure. We also talked about endosymbiosis, DNA and RNA along with Photosynthesis. These are all subjects that we learned in an intro to Biology course. This information was a nice review since I haven’t taken Biology in a few years.

We talked about functional groups, catalysis and energy processes. Bonds (especially hydrogen bonds), bond energies, hydrophobic versus hydrophilic molecules, proteins, fatty acid chains and pH (acids and bases, pKa and Ka, Henderson-Hasselbach equation) were also reviewed. We discussed different amino acids that are used in proteins and how they are bonded as well as titration curves. These are all topics that were covered in organic chemistry or general chemistry. This also was a nice review, since organic chemistry was not a strong class for me. We reviewed them in a way that was understandable and gave me a nice refresher of the material.
We then went deeper into amino acids and proteins beginning to expand more on the topic. We learned that Proline is actually an imino acid versus an amino acid and also learned about some uncommon amino acids that are modified amino acids. We went deeper into the ionization of amino acids and reviewed peptide bonding. The majority of the information we went over up to this point, I had touched upon at least briefly in another course, whether it was general Biology, General Chemistry, Organic Chemistry or Anatomy and Physiology. We took the information that was previously learned and either simply reviewed it or looked at it a little more and expanded our knowledge on the subject.

It wasn’t until we got to protein structure that I really began to learn something completely new. I had talked a little bit about protein structure in other courses, but did not actually learn the differences between primary, secondary, tertiary and quaternary structure until this course. Super secondary structures, motifs, and domains are completely new to me. A-helix and B-pleated sheets are a review from both Biology and Anatomy, but I had only learned about the involvement in DNA for the most part in previous courses. Proteins as Enzymes were a little bit of a review, but also included new information. I had learned about enzymes in General Chemistry, Anatomy and Organic Chemistry and knew that most enzymes are proteins but only some proteins are enzymes. I learned reaction orders in Organic Chemistry but did not really understand the concept until it was reviewed in this course.

I never realized how much one branch of science could really involve so many others. We are able to see all of the science courses that I took at my previous school, in Biochemistry. Not only is it a nice review, but it helps to know that all of the stuff we learned is actually useful in real life. All of the branches are intertwined and interrelated to one another.

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

The protein I chose to look at in class was 1N5O. It is related to Breast cancer and is critical for BRCA1 tumore suppressor function. It is also involved with how BRTC mutations affect BRCA1 function. This is a rather small and sinple protein in comparison to others that were seen in class. Its secondary structure consisted of 6 alpha-helix (displayed as green crayons) and 8 beta-pleated sheets (displayed as tan flat sheets). There was no quaternary structure because there were no subunits within the protein. Viewing the protein in the "backbone" mode shows the backbone of the protein with no R groups. The "all atoms" mode shows the entire protein including the R groups.

Using the online technology that we learned about in class, we would be able to determine if any amino acid sequence is already part of a currently known protein or what other known proteins come close to the sequence. Looking at similar proteins, we may also be able to relate the function of a new amino acid sequence to one very similar to it.