Reflecting back on the course, what are three major themes you would identify that connect the various topics discussed in this course – how are they connected to more than one topic, and how do they connect with what you knew before this course? What knowledge have you gained with regards to these three themes you have identified?

Reflecting back on the course I would say proteins, enzymes, and mechanisms are the three themes that connect various topics. Mainly anything in this course has to do with a specific protein, and enzyme usually associated with that protein and a mechanism in how they work. This could apply to translation where we create a protein. Different enzymes are used and this happens by many different mechanisms. These connect to what I knew before in other courses. Almost all of my previous courses for science somehow involve proteins, enzymes, and mechanisms. I have learned alot of new information regarding these three themes. I have learned for most proteins there are an enzyme that is namely similar. I learned how each of these proteins and enzymes work together and the different mechanisms by which they work. I have seen all three of these themes relate to several different subjects.

How would you explain the connection between glucose entering the body and energy created by the body to a friend, using your new biochemistry knowledge?

If I was to explain the connection between glucose entering the body and energy created by the body to a friend I would talk about glycolysis and glyconeogenesis. I would talk about glycolysis if the body is in need of energy. If the body needs energy the glucose would enter the body and it would enter the glycolytic pathway. This will help produce ATP which is energy. I would talk about glyconeogenesis if the body doesn't need energy. In glyconeogensis, the glycogen enters glyconeogenesis to get stored. This stores the energy to be used at a later time when the body would need it. These two pathways are the opposite of eachother and are difficult to understand but I would explain it in these ways and use diagrams that we used in class to help diagram the explanation of the connection between glucose entering the body and energy created by the body.

What knowledge have you connected with past knowledge?

I have connected alot of new knowledge with past knowledge. I remember learning in previous courses about transcription, translation, and DNA. These topic were covered very briefly and did not go into as much detail as we have gone into in biochemistry. For example, I have learned about DNA in several courses. We maninly talked about how it was an alpha helix with base pairs and a sugar phosphate back bone. We learned about which base pairs connect together but in biochemistry, we talked about much more. We talked about how the sugar phosphate back bone came to be and we talked about the hydrogen bonds and which base pairs have a stronger bond because they have a triple hydrogen bond opposed to a double hydrogen bond. We talked about transcription in a way that it is more than just transcribing the information from DNA to make RNA and then how it is translated into the protein. In biochemistry, we learned what enzymes, complexes, innitiaters, promoters, enhancers, etc. that were involved. It always helps to have previous knowledge to help one remember that knowledge and build upon it.

Find an interesting biochemistry website and put its link in this entry and describe what is found there.

http://www.wiley.com/college/boyer/0470003790/animations/animations.htm This biochemistry website that I found is not only interesting but will also be of value to myself and other students who read my blog. This website is loaded with different interactive animations that show one what happens along with providing an explanation. Some of the animations that are found on this website include an amino acid game, catalysis, cell structure, citric acid cycle, DNA replication, enzyme inhibition, glycolysis, protein folding and synthesis etc. the website also has chapter indexes, concept reviews, structure tutorials, and quizzes. I think this website was an awesome website to stumble upon. I will be using this website and I hope other students will as well.

What knowledge have you connected with past knowledge?

I have connected much of my knowledge from previous classes with the new information we are learning. I have learned quite a bit of knowledge about enzymes in previous classes. I knew that they increase reaction rate but I was unaware of how they do this and how much they are actually speeding up the reaction. I also learned alot about different types of bonding such as hydrogen, covalent, etc. I did not know the application of these types of bonding except for different molecules using these to bind to one another. I did not know that proteins use these types of bonding. For example, the alpha helix has hydrogen bonds and these bonds hold the structure of the protein in the alpha helix. If these hydrogen bonds were not there the structure would change and would result in a change of the function of that protein.

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

         The protein data bank appears to be a website where all the proteins and their functions are located.  This is very useful for record keeping.  The protein that I chose to look at, Kinesin-5 (K5), is found in bipolar disorder.  The protein is 451 amino acids long.  The protein has several β pleated sheets  linkers, and multiple α helix's.  There are approximately 5 subunits.  This protein is a target for small molecule inhibitors which is being used in cancer clinical trials. 
         In conclusion, I think this website was interesting.  It was fun to look at different proteins to see that they look similar yet have a minor difference that changes the function completely.  This data base is extremely useful in identifying the proteins that cause specific disorders.

What is biochemistry, and how does it differ from the fields of genetics, biology, chemistry, and molecular biology?

Biochemistry is very different yet similar to genetics, biology, chemistry, and molecular biology. Biochemistry involves the use of chemistry to explain biological processes as well as studying the structure and the chemical aspect of molecules in living organisms. Chemistry mainly studies the reactivity of these molecules as well as the structure and characteristics of these molecules.  The major difference is that chemistry is not about the living organism; its focus is mainly molecularly. It does not go far on the structural organization of the human body. Genetics is extremely different from biochemistry. It actually studies how characteristics are inherited and not so much about the reactions and characteristics of these molecules.  Biochemistry is also quite different than biology.  Biology is basically the study of life.  It focuses on their behavior, environment, origin, function, and evolution opposed to reactions of these organisms.  Molecular biology is surprisingly quite similar to biochemistry.  Molecular biology also uses chemistry to explain the interactions of the molecules.  It differs mainly in the way that it is interested in the DNA/RNA processes.
         In conclusion, biochemistry has many differences as well as similarities to each of these fields.  They are very similar in the way that some study the human life and some study the chemical reactivity of these molecules.  They are very different in the way that each of these fields do not incorporate both chemistry as well as biology.  They are mainly similar to one of these fields; either biology or chemistry.