Three major themes that connect most topics discussed in biochem and its implications on previously learned knowledge

The three main themes are important bio molecules, processes that produce these bio molecules and how these bio molecules are used by prokaryotes and eukaryotes.

Bio molecules that were discussed this semester are water, amino acids, proteins & enzymes, lipids, carbohydrates and nucleic acids. Previously these topics were covered in depth and remained exclusive to that knowledge. For example, amino acids are made by connecting proteins through polypeptide bonds. Forming amino acid chains was a main idea taught in biochem that brought this information together and made it more complete.

Processes that produce these bio molecules are nucleic acid replication, transcription and translation, and thermodynamics. Previously these topics were covered in depth and remained exclusive to that knowledge. For example, during translation, the coded strand is what is being used for the individual amino acids. Each 3 bases makes a codon that then makes up a certain protein. Through biochem, the process was looked at thoroughly to the level of the subunit(s) on the strand bringing together anti-codon tRNA that also had the given amino acid attached. The tRNA comes in at the "ready" position A, then moves to position P where the amino acid chain is being formed, and then the E position which releases the tRNA disconnecting the amino acid from it leaving the amino acid on the chain forming. Eukaryotes do not posses the E position.

These bio molecules are utilized by glycolysis, storage mechanisms, citric acid cycle, electron transport, oxidation, phosphorylation, and lipid metabolism. Previously I have learned just the basics of these processes because what was important was knowing the molecules that partake in these processes. After having biochem, each of these processes and cycles were described in detail. Most importantly, the overall reactions including their products, and what enzymes catalyze them were key concepts.


The three themes I have identified focus on building the pyramid of science that has a foundation of genetics, biology, chemistry and molecular chemistry understanding.

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

Glycolysis begins by an input from either dietary glycogen and starch or glycogen stored in your cells. The glycolysis linear reactions occur in 10 steps. The first reaction uses water to break apart glucose molecules known as hydrolysis. A phosphate group is removed from an ATP molecule of energy producing ADP. This removed phosphate group is then added to the glucose molecule forming Glucose-6-phosphate (G6P). In reaction 2, an isomerase enzyme is used that creates an isomer of G6P. An isomer has the same number of atoms and types of atoms but is configured differently. The isomer created is D-Fructose-6-phosphate (F6P). In reaction 3, 1 ATP is used to phosphorylate F6P. Most phosphorylation reactions are done so via kinases which can add phosphate groups. D-Fructose-1,6-biphosphate is created. It is important to note that the product of the previous reaction becomes the reactant of the next. Glycolysis reaction 4 cleaves the F1,6P by using an aldolase creating Dihydroxyacetone phosphate and D-Glyceraldehyde-3-phosphate (D3P) which are isomers of eachother. In reaction 5 only D3P is formed and can then be used by reaction 6. This reaction is a redox reaction. These two reactions of adding oxygen and adding hydrogen happen together. Step 7 uses a kinase to remove the phosphate group of the 2 molecules creating 2 ATP molecules. Reaction 8 isomerases the product of the previous step. For the next reaction, the removal of water, dehydration, occurs. Finally, in reaction 10 hydrolysis and phosphorylation occur. The net gain of glycolysis is 2 ATP and 2 molecules of Pyruvate created. Gross gain is 4 ATP, but because the process of glycolysis uses 2 ATP, this results in the net gain of 2. Although the process seems complicated and overwhelming, what is important to take away is the idea that through glycolysis, energy is created that is then used by the body from molecular activities to muscle movements. By looking at how glycolysis works, I have great appreciation of how our bodies function.

What knowledge have you connected with past knowledge? (2)

Having struggled through organic chemistry, I realize now the connections and reasons why taking organic chemistry before biochemistry is useful. I am finding that I retained more information than initially thought. Monosaccharides and polysaccharides I have seen before in biology, along with glycosidic bonds and are depicted in many slides. I did not understand what mechanism the linkage used. The concern at the time was only to understand the basic shape and what role starches play with regard to aquiring energy from them. Now in biochemistry, I understand not only the reason for the shape and type of linkages but also why and how naming of the different starches are done. It completes the understanding of the whole starch concept by going deeper and filling in the gaps. Taking chemistry I learned about redox reactions, but did not know where these reactions were found and what practical applications they had. Biochemistry links the past knowledge with real applications that does make it easier to learn and understand.

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

http://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htm
This biochemistry website provides for interactive animation learning with a variety of related topics combined with knowledge gained to take quizzes or play games with biochemistry understanding. For people who learn best or easier by visual association, this website is found to be easy to use and connects ideas completely together. The main menus across the top once selected, give a brief summary of what will be covered in that section. From there the user can chose any specific topic they are looking for. For example, when glycolysis is chosen, another browser window opens and an interactive match up game of the glycolysis process begins. I have yet to cover this topic in my current biochemistry class, but I found this application super easy to use and had fun seeing what I already knew. No required sign in or membership is required which is a plus for me because this means one less password to remember!
The "Cutting Edge" menu has many interesting real world applications of biochemistry. Facts and statistics are listed even with input calculators such as a BMI index calculator. Possible biochemistry related careers are also listed. For further and more related topics such as structure databases, online journals and laboratory protocols to name a few, a link is provided. Overall, this website is easy to use, easy to navigate through and very informative. A++ rating from me.

What knowledge have you connected with past knowledge?

Before taking Biochemistry I knew of enzymes and some of their properties. Mostly I remember the Lock&Key analogy. However I didn't know that as of more recently, enzymes are thought to utilize an Induced Fit mechanism. This means that an enzyme can conform to several subtrates, not just 1 specific substrate as previously thought. Zymogens are enzymes that serve a function of rendering particular precursor enzymes irreversibly inactive. This is important because our body creates certain precursors that can be harmful and therefore must be inactivated and preferrably irreversively. While learning about the foot-and-mouth disease protein I am better able to understand the structure and what specific role the subunits play. Even subunits that have a domain of function that is still unknown, gets assigned a subunit label DUF; domain of unknown function. I am also very interested in phamacology and the way researchers can use what is known about enzymes to help them develop medicine that takes advantage of this knowledge. Since many proteins can be grouped by common subunits, this makes creating drugs easier by having one drug that works for multiple proteins.

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

The particular protein I have chosen, shown here at the left is the Foot-And-Mouth Disease Virus Oligosaccharide Receptor Complex. Located on this structure are many difulside bonds. When these bonds are in a state of reduction, the virus can maintain its infectivity which is a key factor of the virus life cycle. This protein also contains four sub-units; each of which contains beta pleated sheets depicted by yellow arrows while alpha helixes are presented by green crayons. Three of which sub-units are categorized as being part of the RHV-like superfamily. The RHV-like superfamily also contains the Seneca Valley Virus-100 along with many other virus proteins. This particular virus shares 179 amino acids with the Foot-And-Mouth Virus. The fourth sub-unit categorized as being part of the DUF-1865 superfamily. DUF stands for Domain of Unknown Function and is commonly found in viral proteins. The picture on the right depicts the DUF-1864 amino acid protein. Real world applications include research of the viral life cycle with respect to quaternary structure and methodoligies in the inhibition of replication of such viruses.

Photos can be directly viewed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=149869 and http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=1QQP

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

Biochemistry uses the disiplinary of Genetics, Biology and Molecular Biology to describe the molecular nature of life processes. With a backbone of Organic Chemistry, Biochemistry describes the processes by which molecules function on a larger scale to include cellular metabolism as well as other nature processes. Genetics pertains to molecular mechanisms and their expression of DNA within various individuals and the methods of DNA transmission. Biology and Molecular Biology describe the very basic of fundamentals of the cell processes and mechanisms in both plants and animals. Biochemistry ties a foundation of these disiplines and applies them at a macro level that helps explain observable scientific anomolies.