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?

In my opinion, the three major themes of this Biochemistry course would be the structures of life, the functions of those structures, and the generation of energy. Each of these themes connect to multiple topics. The structures of life include topics discussesd such the structures of various biomolecules such as amino acids, proteins, membranes, nucleic acid structure, and carbohydrates. Fuctions of those structures include the function of biomolecules proteins as enzymes (and their mechanisms), nucleic acid replication, transcription, translation and storage mechanisms for carbohydrates. The generation of energy is discussed in the review of all of the metabolic processes such as glycolysis, the TCA cycle, the electron transport chain, photosynthesis, nitrogen metabolism and photocynthesis. You can look at each of these themes with regards to its biological or chemical properties as well as looking at the structure and function specific components of the cells (i.e. the study of nucleic acids in genetics)

Before this course, I took many classes that focused on the structures and functions of biomolecules as well as the generation of energy. Examples of this include biology, cell biology, genetics. However, I have also learned a lot of information that pertained to the chemistry portion of this class. This class has helped me to understand the chemistry behind biological processes discussed in other courses and has really united the two fields of biology and chemistry. In regards to each of these three themes, I have been better able to understand the chemistry behind the biomolecules, their functions, and the generation of energy. For example, we have discussed stereochemistry with molecules such as carbohydrates. Also, we have gone more into depth in the study of enzyme kinetics, with regards to the function of biomolecules. Finally, we have discussed free energy change in depth with regards to glycolysis and the citric acid cycle. I would say that the addition of the knowledge of chemical properties to biological processes that have been discussed in other classes in detail has been the most beneficial knowledge that I have gained in Biochemistry this semester.

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?

Carbohydrates are a large source of energy for our bodies. Glucose is an important simple carbohydrate that, when ingested, can yield a lot of energy for cells in the body. When we ingest glucose, it gets taken into the cell where it is acted upon by many enzymes in a process known as glycolysis to yield energy. Some examples of alterations to glucose during glycolysis include adding a phosphate molecule (phosphorylation), rearranging the molecule (isomerization), splitting the molecule in half (cleavage), losing a phosphate molecule (dephosphorylation), removing electrons (oxidation), and losing a water molecule (dehydration). Glycolysis yields two pyruvate molecules as well as 2 net Adenosine Triphosphate, or ATP molecules. ATP is the cell's energy currency and can be used to perform many important cellular processes. Pyruvate has three different fates, all of which yield much more ATP that can be utilized by the cell. As you can see, glucose is an important food source which produces energy yielding molecules to be used by the cell.

What knowledge have you connected with past knowledge?

The topic of DNA replication and repair has appeared throughout my academic career. This topic was touched on in my introductory Biology courses and was taught very much in depth in courses such as Genetics. Such important cellular processes such as replication (and, next week, transcription) really resurface again and again in courses such as Biology.
Another interesting connection that I've made with biochemistry has to do with the presentation on why you should eat more salmon. For 3rd grade testing (which was more years ago than I'd like to admit!) I remember teachers telling us to go home and eat fish, since it's considered to be "brain food". I remember hearing the same phrase again from a 6th grade teacher when we were doing school-wide testing. Now, many years later, it is interesting to know more about the biochemistry behind why fish, such as salmon, is considered brain food!
Finally, as I work on a cardiac floor in the hospital, I hear a lot about diet and especially, cholesterol. I have learned a little about cholesterol and it's role in the cell in courses like Cell Biology. However, it is interesting to learn about the chemical structure of cholesterol and why we need it to make other things (such as steroid hormones); on the flip side, it is important to know that we don't need too much!

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

The website I found was http://bio-alive.com/animations/biochemistry.htm. The main page, http://www.bio-alive.com/ is filled with many videos about various scientific subjects such as anatomy, cell biology, cancer, histology, and many more. The biochemistry section has videos and animations that explain biochemical processes. I have found that occasionally, when information in textbooks and in lecture is confusing, it can help to watch animations or videos to clear up the material. The animations and videos found on this website, pertaining to biochemistry and other subjects, can be helpful to anyone that is struggling in any science class.

What knowledge have you connected with past knowledge?

As biochemistry is a complex subject area that connects with many other scientific areas of study, it is understandable and expected that knowledge learned in this class can relate to many learned in the past. One area that I have been able to connect with past knowledge is the discussion of RNA as the first biomolecule, as it can both catalyze as well as encode knowlege. This ties in nicely to the Cell Biology class that I took. We discussed Tom Cech, Nobel Laureate, and his experimental discovery of RNA as a catalyst in great detail. Also, in Animal Physiology, we discussed Michaelis Menten kinetics and its application to the rate of reactions and the uptake of glucose into an animal cell. Finally, the induced fit model of enzyme-substrate binding tied into material learned in Principles of Biology, Anatomy and Physiology, and Animal Physiology. In this case, however, the model was modified. The new model of enzyme-substrate binding replaced the "lock and key" model that was taught in those classes in the past.

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

The protein I selected is called 3B8E; however, it is more commonly known as the Sodium/Potassium Pump or Sodium/Potassium ATPase. This protein has a quarternary structure that consists of an alpha, beta, and gamma subunit. Each subunit is 998, 46, and 29 amino acids long, respectively. The 3B8E contains a large amount of alpha helixes and a few beta pleated sheets, and arranges itself in a globular arrangement.
The 3B8E Sodium/Potassium Pump is found in the cell membrane of every cell in the body of animals. It is responsible for maintaining the gradients of both sodium and potassium. In order to maintain proper functioning, animal cells must have a high gradient of sodium outside the cell and a high gradient of potassium inside the cell. The Sodium/Potassium ATPase uses active transport to pump three sodium ions out of the cell and two potassium ions into the cell. This protein uses a molecule of ATP to acheive this, since it pumps the ions against their gradient. Without this protein, cells would not be able to function at all. This makes the 3B8E, or Sodium/Potassium Pump a very important biomolecule.

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

Biochemistry is the study of the function and role of various biomolecules. Biochemistry examines and evaluates the chemistry of molecules such as lipids, carbohydrates, nucleic acids. Biochemistry is also concerned with the vital, chemical processes of life that these biomolecules are involved in, such as metabolism and enzyme-catalyzed reactions.
Biochemistry, although distinct in its focus, is related to many other scientific fields. Genetics is a field of study which involves the examination of biomolecules, specifically nucleic acids. However, the field of genetics is interested in the genetic variation between individuals and it's effect on the organism or cell, rather than the chemical properties and processes of biomolecules. The broad field of biology is the study of life and living creatures; while biochemistry studies the chemical properties of biomolecules, the field of biology is much broader in that it is concerned with the development, growth, and distribution as well as structure and function of living things. Chemistry and biochemistry are inherently linked. However, chemistry is a much broader field that examines matter and chemical reactions. Biochemistry is merely chemistry applied to the structures of life. Finally, molecular biology and biochemistry deal with the same sorts of molecules and molecular pathways. However, the focus of molecular biology is to understand the interaction between different parts of the cell, particularly between DNA, RNA, and proteins. Biochemistry instead deals with the same molecules, but examines the chemistry of the molecules and reaction rather than looking for an overall understanding of function and physiology. It is clear that biochemistry is linked to all of these fields; however, it is evident that biochemistry is alone in it's concentration on the specific chemical properties and processes of biomolecules.