8. Reflecting back on the course, what are three major themes you would identify that connect the various topics discussed in this course...?

Three major themes I have noticed during this biochemistry class have been enzymes, ATP, and amino acids. Each of these three topics were talked about almost every class.Not only are these three topics important in our biochemistry class, but they are so important in life. 


Enzymes are defined as a single or group of proteins that ac as catalysts in specific biochemical reactions. We are always talking about enzymes in class, how they help aid along with a series of reactions to get the end product. They have been very important in the past few classes when we have been talking about glycolysis, Krebs cycle, etc. I learned that how important enzymes are and how needed they are by the body in various cycles and processes.

ATP is also very important, it is our main energy source in order to live. We need it to survive and function on a daily basis. ATP  is produces through various cycles in the body that have been discussed the second part of the semester a lot. I have gained a much better understanding of how ATP is produced during the electron transport chain.

Amino acids were discussed the second week of class and looked at again during translation.  Amino acids help build our genetic make up, if there is a mutation in an amino acid, our genetic make up could be very different, or we could have a mutation and then have a disease that could change everything. I feel like I am walking away with a much better grasp of that. 

Each of these three topics I have seen in just about all my other science classes. It is interesting to learn it a different way, and each time gets easier and easier.  

7. 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?

      Glucose enters the body and undergoes many changes in order for the body to create energy. First glucose enters the body and a phosphate attaches to the glucose molecule to create glucose 6-phosphate, this phase actual results in a loss of energy since the phosphate comes from ATP and converts to ADP. Then the glucose 6-phosphate rearranges into fructose 6-phosphate where after another phosphate attaches creating fructose 1, 6-diphosphate and more energy is being used. This molecule then splits into two different molecules: dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. The dihydroxyacetone phosphate rearranges into glyceraldehyde phosphate since they are isomers (same amount of molecules in a different arrangement) the process then continues with 2 glyceraldehyde 3-phosphate molecules which turn into 2 molecules of 1, 3-bisphosphoglycerate which then loses a phosphate molecule to create 2 molecules of 3-Phosphoglycerate, which now creates 2 molecules of ATP (energy) for a net of 0 ATP created. These molecules then rearrange into 2 molecules of 2-Phosphoglycerate then it loses water and becomes phosphoenolpyruvic acid. Then the 2 molecules of phosphoenolpyruvic acid loses a phosphate which results in 2 ATPs created which is more energy created. Phosphoenolpyruvic acid then either transforms into Acetyl CoA, ethanol and carbon dioxide, or lactic acid. If it turns into Acetyl CoA it will then enter the Krebs cycle where a lot of energy is created because the molecules lose phosphate groups which results in ATP which is your primary energy source.

5. What knowledge have you connected with past knowledge?

     I would have to say that DNA replication has been talked about in every single science class I have taken probably since 8th grade. Throughout the years though, I have learned something new each class. Sophomore year, it was taught in depth, I didn't really understand it until I had one-on-one time with my teacher. She did a great job on explaining it and I have a great understanding it. Talking about it in biochemistry was just another refresher, plus some details that was forgotten over the past two years.
     Also RNA synthesis has been something I have learned in many classes. This process always confused me, going through the detail once again has helped with a better understanding.
     Going over and over again on certain topics proves how much of an impact the introductory classes are, and how they truly build for your future.

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

Biomed Central

     I liked this website because it has a lot of offer. It is completely geared towards biochemistry and has open access to articles, reviews and a variety of information. The website has no fees to access the articles. You are able to email the editorial team by easily finding their email addresses on the website. If you want to email an author of an article or view certain articles you must create an account to view. Creating an account is very easy and again, free of charge.
    The articles are user friendly and easy to read. There is also a place where it shows the most popular articles. Also the latest articles are also an option to read, this way you stay up to beat with the biochemical world.

3. What knowledge have you connected with past knowledge?

   There has been a lot in class that we've talked about so far that has sparked some memory of past classes. It's nice knowing you've learned something in the past, especially when you're in class and know exactly what is being taught.
   A lot from the first lecture was all review, especially the part about hydrogen bonds. I already knew a good chunk of what we talked about: that they are weaker  than covalent bonds, there is a positive end and a negative end , etc.
   The pKa values I remember learning in organic chemistry and had a hard time with them. Rehashing them in class like we did helped a better understanding of them.
   When we started chapter three  and started talking about chiral molecules I was a little excited. We were taught all about them in organic chemistry and I spent a long time learning them and understanding the differences.
   There have definitely  been a lot of things I've seen before in other classes, I just feel like we are going into a deeper learning of them and actually understanding why they are important.

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

The Protein I looked at was fibrillin-1 which mainly causes Marfan Syndrome, a connective tissue disorder.

Fibrillin is a glycoprotein, which is very important for the development of elastic fibers (microfibrils) that provide strength and elasticity to connective tissue in the human body. Connective tissue holds the body together and helps control the growth and repair of tissues and other organs. Fibrillin normally is abundant in the connective tissue found in the aorta, in the ligaments that hold the  lenses in the eye's in place, in the bones and in the lungs.

This protein can also cause isolated ectopia lentis, autosomal dominant Weill-Marchesani syndrome, MASS syndrome, and Shprintzen-Goldberg craniosynostosis syndrome.

Fibrillin-1 is a building block for elastic tissue in the body. This gene defect can also cause bones to grow too much, causing people to have long limbs. The two domains are in a rigid, its arrangement is rod-like, there are also calcium binding and hydrophobic interactions.It is a fairly simple structure. 

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

     Biochemistry is the study of chemical composition of chemical compositions of living matter and chemical processes that happen in living organisms. Genetics is the study of heredity, biology is the study of living organisms, chemistry is a part of science that works with the chemical composition and properties of a substance, and molecular biology is a part of science dealing with the studying of structure, functions and reactions of molecules involved in the life process.
     Biochemistry is applied in many fields within science, medicine, medical, industries, and society. Biochemistry works with the function and structure of cellular components. Biochemistry strives to focus of understanding how biological molecules help aid the process in living cells. This information helps with understanding an organism as a whole. Looking at the molecular processes of how an organism works can help us understand diseases and look for a cure or reversal of incorrect processes. while we have learned a lot, we still have so much more we can learn.