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?

The three major themes in this class have been Nucleic acids, enzymes and energy production. We went into deep detail about how each apply to biochemistry but also how they apply to different diseases and how they can can be altered to cure those diseases. All three are crucial to all life and keeping the transfer of energy and genetics flowing. These topics can be discussed in not only biochemistry but in almost every biology course taught because they are the reason why there is life and differentiation between individuals.

Nucleic acids were a common theme throughout this course and were really focused on when we looked at translation. Nucleic acids contain our genetic makeup and the genes that are made up of them are what make us unique. If there is a mutation in that gene the expression could be much different than what it was originally, it could be beneficial and it can also be benign. This class reinforced how they were assembled from the bases up to the DNA strands.
 

Enzymes are very crucial in not only catalyzing reactions within the cell but they are also important in keeping the cell running as it is suppose to one mutation and the cell can turn cancerous . We talked a lot about enzymes in class, recently we have talked about the metabolism of glucose and the processes  including glycolysis, Krebs cycle and the oxidation phosphorylation.This class helped reinforce how important enzymes are in all processes in the body.

Energy in the form of ATP is our main energy source that runs most of our bodily processes and keeps our hearts beating and our neurons firing. ATP  is produced during many cycles in the body but primarily in the Krebs cycle. We have talked about the Krebs cycle a lot in the past few weeks of class and my presentation involved the cycle in it as a way to differentiate between cancerous cells and regular cells.

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?

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?

First stage is cellular respiration which happens within the cytoplasm. In  this stage enzymes interact with glucose and oxidizes it by taking away some of its electrons. . Two electrons and one proton are added onto a  coenzyme NAD+ to produce the NADH molecule. Glycolysis produces NADH, 2 pyruvate molecules and 2 ATP for every glucose molecule broken down. . The second stage is The citric acid cycle which only uses the Pyruvate molecules that came from the Glycolysis. The citric acid cyles takes place in mitochondria and only takes place if oxygen is present at the time (Aerobic metabolism). When pyruvate molecules enter the cell's mitochondria. Carbon dioxide is released which changes the molecules composition. Enzymes interact with these changed molecules and as did the glucose the pyruvate is oxidized losing some of its electrons. NADH and FADH2 molecules are formed. The citric acid cycle produces carbon dioxide, NADH, FADH2 and energy in the form of ATP. The NADH and FADH2 molecules move onto the 3rd stage oxidative phosphorylation stage. This stage as was the citric acid cycle is present in the the cell's mitochondria. The electrons that are oxidized from the NADH and the FADH2 are used in the electron transport chain which helps synthesize 34 ATP per glucose molecule absorbed which is the energy the body mostly uses to perform its processes.  Sources: mpbell, Mary K, and Shawn O Ferrell. Biochemistry. N.p.: Brooks/Cole, 2011. N. pag. Print.

What knowledge has connected with past knowledge?

       This last half of the semester the knowledge I have connected back to past knowledge has been the concept of chemical pathways in the body and the cycles that produce energy within the cell. With the chemical pathways the review was good because information was gone over that i haven't revisited since first semester freshman year. Understanding the difference between active and passive transport coupled with facilitated transport is key when working with medicines on how to administer the drug  and diseases on how to either treat the disease or dull the effects. Also the knowledge of how the cells produce energy in the form of ATP is crucial in identifying which cells are performing correctly. The presentation I did in class on how to treat cancer with Pyruvate Kinase Isozymes showed that a simple enzyme can make a cell go from energy producing in the form of aerobic metabolism of glucose (citric acid cycle) for the body to anaerobic metabolism using the energy to produce more cancer cells which is harmful to the body. By reviewing these two points it helped better understand the more advanced topics used in class.

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

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

http://themedicalbiochemistrypage.org/ 

I picked this website because it not only explains in great detail the importance of the topics as it applies to medical applications. For anyone who is looking to get into the medical field this site is great for individual use, studying and for research. This is a good place to go to not only learn the basic building blocks but to examine different biochemical processes that help the body perform correctly and efficiently.This site is definitely not for people who don't have any background in the sciences because there is a lot of abbreviations and  science specific words that would confuse and lose the reader. Overall the website is very informative and i will probably be using it in the future when i don't understand things in this Biochemistry class.

What knowledge has connected with past knowledge?

          

 

 

               Most of what has been taught in class so far has connected and reinforced past knowledge very well. It expanded on the more chemistry side of biology which to me made more sense than general chem because i could apply it to past knowledge. It is always good to cover things like structures and chemical bonds over and over so when using it in a future job or in future research it will be like second nature and it will be much easier to pick out if for example a lipid bi layer is loose because of  double bounded tails on a fatty acid when it should be rigid and tightly arranged. 

              Even if it seems like the information is redundant its the best way to learn it and master it. This class helps to pull together my past classes including Biology 1+2, Genetics, Organic Chemistry, and surprisingly psychology. Many diseases are formed by chromosome malfunctions and deletions.This class is a strong foundation for all science classes and as it seems at least one of the social sciences. It gives a good understanding to what structures and compositions the body has that makes it work properly.

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

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

 Anti-freeze Proteins

Picture from (http://www.rcsb.org/pdb/101/motm.do?momID=120)

          Anti-freeze proteins are proteins that naturally occur in certain organisms that live in harsh cold climates. When subjected to below freezing conditions an organisms water within its cells will form small ice crystals that will grow larger and larger until it ruptures the cell. Eventually this would lead to death of the organisms. Some adapted organisms like the ocean pout, the winter flounder, the yellow meal-worm beetle, the spruce bud-worm moth and the snow flea have what are called antifreeze proteins. These proteins attach themselves to the small growing ice crystals and slow down if not completely stop the growth of them. It does this by lowering the freezing point  of the water in the cells about 6 degrees which effectively halts the crystals from rupturing the cell thus preserving the organisms health. 

          These proteins have been harvested and used in other applications. For instance anti-freeze proteins have been used in ice cream to keep it from that unpleasant icing which ruins the ice cream. Just as it does in the cells it attaches to any freezing moisture and stops growth by lowering the freezing point. Another thing that is interesting about these proteins is that they lower the freezing point but they do not lower the melting point which normally goes hand in hand with freezing point.

 Sources:

Goodsell, D. (n.d.). Antifreeze Proteins. Retrieved from RCSB PDB-101 database.

 http://www.rcsb.org/pdb/101/motm.do?momID=120