3 major themes

Three major themes that I have identified in this course are: the storage mechanisms in metabolism/glycolysis, proteins and their functions, and thermodynamics.

I learned about glycolysis in biology, but it the knowledge about it never was very indepth. In biochemistry I have not only learned about glycolysis, but I have gained an enormous amount of insight into what it does, how it does it, the major control points in it, the major enzymes involved in it, and the major outputs by it. I also learned about the "reverse" process of it, gluconeogenesis. I had previously learned about proteins, in both biology, chemistry, and nutrition. I had learned how proteins were made up of amino acids, were a key nutrient, and that they body used them alot in certain processes. Now throughout this biochemistry course I see how proteins do what they do, and just how many processes in the body they control. I know understand how proteins work as enzymes and the mechanisms they use in the body, for example- having allosteric control. Thermodynamics is also a term I learned about in chemistry. I had known that were spontaneous reactions, and non spontaneous reactions but I didn't realize how much it had to with energy, and how that ties into our bodies metabolism. I know know that spontaneous reactions take place without outside intervention or energy, these are exergonic, and an example of that would be the aerobic metabolism of glucose. I also learned that non-spontaneous reactions are endergonic, and example is the phosphorylation of ADP, it's how metabolic processes provide energy. I was also able to tie in my knowledge of oxidation and reduction that I learned in chemistry to metabolism even further when I learned about thermodynamics in biochemistry. I learned that in metabolism both catabolism and anabolism take place. In catabolism, there is a breakdown, energy is released, and this is an oxidative process. I also learned that anabolism is the building up of things, it requires energy, so it is non-spontaneous, and is a  reductive process, it involves biosynthesis.

Glucose and how energy is used in the body.

If I had a friend who wanted to know how glucose enters the body, and how they create energy from that glucose I'd make it very easy for them. I would explain that when they eat glucose (sugars), if their body is in need of ATP, for example if they are exercising, it will enter the glycolytic pathway. But if they don't need to make any more ATP,  the body will store glycogen, the by product of gluconeogenesis , for later use. I would explain that glycogen is the branched form of glucose that gets stored in the muscles and liver. Once those glycogen stores are full the body takes the rest of the glucose and it gets stored as fast.

 Later, when they need to create energy from that stored glucose they are four initial energy sources available to the muscle of the  person exercising- the body first uses up its creatine phosphate stores in the first sixty seconds. Then, after that the body uses up the glucose from the glycogen of the muscles stores, which is initially  consumed by anaerobic metabolism. Next the body uses the glucose from the liver, from both its glycogen stores and the gluconeogenesis from lactic acid produced in the muscle, again initially consumed by anaerobic metabolism. Time wise, their is about ten to thirty minutes worth of glycogen stored in the muscle cells. So glycogen loading can be a key component if the person is training for a marathon or something that involves high intensity training.

It is important to understand how glucose is stored and how energy is created in the body, especially when you are an athlete. I have learned so much about the body by taking this biochemistry course, not just in the term of biological molecules and how they are processed and used, but from how I can use this knowledge on a daily basis to make my life, and healthy, that much better.

Connecting Past Knowledge 2

I have found connecting past knowledge learned in my science courses to the biochemistry knowledge I am obtaining now interesting, but what I find especially interesting is connecting my new biochemistry knowledge to not just other science courses, but connecting it to information I learn about in the workplace.
For example, I shadow a neurologist at the Faulkner Hospital in Boston one day a week and many people come to see him for migraines. He routinely prescribes them an "old fashion" antidepressant. He calls them 'old fashion' because they have been on the market for years and years and use the same basic principle, which thanks to biochemistry I now understand. Migraines can be due to many reasons, but one main reason is lack of serotonin. These old-fashioned antidepressants, in low doses (doses much lower than the dose to treat depression,) can increase serotonin in the brain and prevent migraines. I know understand the biochemistry theory of amino acids and SSRI's, selective serotonin reuptake inhibitors, that we learned in class and how they prevent the uptake of serotonin leading to a higher mental state in depressed patients when taken at the correct dosage, or in low doses prevent migraines by increasing serotonin in the brain.
Another connection I was able to make between Biochemistry and my work/internship involves prostaglandins and stroke. Many patients that we see have had strokes, and the neurologist always makes sure they take a daily dose of aspirin and I never truly understood why. Now, thanks to my new Biochemistry knowledge of lipids and fatty acids, I understand that aspirin is a prostroglandin inhibitor, so it inhibits the formation of blood clots that can reach the brain and potentially cause a stroke.
I also was able to connect my new understanding of proteins and amino acids to my previous nutrition knowledge, and everyday grocery shopping. Quinoa, a grain that can be purchased at most Whole Foods super markets is referred to as a 'complete protein', and now through biochemistry I see that it is complete because it has all 20 common amino acids, which doesn't happen in nature very often in one single source of food. I now realize what an important role amino acids have in my life and functions of my body, and now because of that, I buy Quinoa almost every week.

Biochemistry website

The Biochemistry website I chose was http://themedicalbiochemistrypage.org/. I chose this specific biochemistry website because it has to deal with medical biochemistry, which is extremely interesting to me since I wish to use my knowledge of biochemistry to pursue a job in the medical field. It also has many useful applications to our class, for example in lecture we have talked about sickle cell anemia, MAOI's (Monoamine oxidase inhibitors), Histinde in allergies, and PKU disorder which for the most part can all be found in detail on this site. It also goes into many 'pop culture' topics that have to do with biochemistry that can include: healthy diets, the obseity epidemic, and muscle biochemistry; which are all topics that many Americans have a growing interest in.
Another helpful aspect of this website are the diagrams. I feel that many websites that cover biochemistry topics can be confusing, this website helps to break down the bulk of the challenging topics, and gives useful images to help demonstrate the topics and how they incorporate the different biochemistry aspects. You can also subscribe to the page so that you can be updated on the new information posted onto it.

Connecting knowledge with past knowledge.

Since I have been a biology major at UNH, I how come to see how important proteins in Biology. Biochemistry in particular has made me realize just how crucial proteins are, and the functions that they have in organisms. In the past I knew that amino acids were the building blocks of most things in life, but I didn't know the extent of the levels of protein structure. Now I know about there primary structure, and which is the certain amino acid structure; and that there are secondary structures. There are also tertiary structures, which are the overall structure of the protein which can be seen through X Ray crystallography, and nuclear magnetic resonance spectroscopy. More specifically I know the structure of each basic amino acid: they have an amino group, carboxy group, side chain group, and alpha carbon. I can also tell if there are R group is polar or nonpolar, acidic or basic. I also know about the bonds that form it, for example the peptide bonds, and how they limit the possible orientations of the peptide backbone in protein. I also know about the L-form amino acids. In the past during Chemistry class, I learned what compromised a hydrogen bond, but I didn't realize how important they can be to certain biochemical structures, for example in the a-helix, the hydrogen bonds are parallel to the helix axis, and stabilize the protein ribbon structure.
In the past I learned the pH scale, the values it had from 1-10 and that more acidic things had lower pH, and more basic things had higher pH. Now I know about how amino acids ca be titrated. I can also determine the pKa values from the amino acid structure and curves. I also realize how we can choose buffers from amino acids, by looking to see if they have a suitable pKa, and the rule of thumb that the pKa should be plus or minus 1 pH unit fro the pH of the reaction. I have also been able to connect that buffer system to things I learned in Anatomy and Physiology about blood, like how the blood buffer system works. Thus far, I have enjoyed learning how Biochemistry impacts the systems and processes that I've been learning about all of these years in biology, chemistry, anatomy, immunology and serology, body fluids, and so on. The study of biochemistry allows me to further extrapolate how the subjects relate and overlap.  I look forward to gaining even more knowledge about how biochemistry influences, and relates to all the past knowledge I have acquired through my studies.

Find a protein using PDB explorer

The protein I chose was Collagen. The code was PDB-101. Collagen is a critical protein to human life, one fourth of all the proteins in the human body are collagen. It is a structural protein that gives resilience to muscles and tendons, and creates sheets to support our skin and internal organs. Collagen is composed of three chains, which are tightly wound together making up the collagen triple helix; it a relatively simple protein. Every third amino acid in the chain is a glycine, which is vital because it is a very small amino acid that fits perfectly into the helix, helping make it so resilient. Vitamin C, and hydroxyproline are crucial for collagen to be a stable molecule.  If one does not get the necessary amount of vitamin C in our diets and develop a deficiency, it will slow the production of hydroxyproline and stop the production of collagen. This causes the disease state known as scurvy. When an individual has scurvy, they can lose their teeth and bruise quite easily due to this lack of collagen which would normal fix the everyday wear on the body. On a lesser scale, loss of collagen production as the normal aging process occurs allow the skin, especially on the face to wrinkle and lose its elastic recoil. There are many cremes, serums, and facial treatments coming onto the market to help boost natural collagen production to help maintain firm, youthful skin.

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

The fields of biochemistry, genetics, biology, chemistry, and molecular biology tend to overlap, their chief differences involve which aspects of science each field focuses on.  Biochemistry is the study of chemical substances and processes that occur in living organisms. It focuses on the function, role, and structure of different biomolecules. Genetics studies the effect that genetic differences have on different organisms. It focuses on genetic variability, genetic interactions, inheritance, and how these factors are expressed and effect organisms. Molecular biology focuses on the molecular foundation of the processes of replication, transcription, and translation of an organisms genetic material. Chemistry studies the composition, structure, properties, and the reactions of matter- focusing heavily on atomic and molecular systems. Biology studies life and living organisms, including their structure, function, growth, origin, and evolution. 
There is no hard line between biochemistry, genetics, and molecular biology, but to put the differences in broad simplistic terms: biochemistry in large part focuses on the relationship between proteins and their functions, molecular biology focuses on the relationship between proteins and genes, whereas genetics focuses on the relationship between genes and their functions.