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?

     Reflecting back on the course, the three major themes that I identified with were the following:
1. Molecular Structure
2. Function
3. Pathways


      The importance of these themes are observed in how our body operates on a daily basis.  Molecular structure is important in determining its many chemical properties.  Throughout the course proteins/enzymes were essentials in key topics of biochemistry.  Understanding these structures provided us with an understanding of how these molecules are organized in our body.  Function is another theme that is closely related to structure.  The functions of these molecules are essential in providing the mechanism in which our biological body operates.  Key examples are enzymes which are catalysis in many biological reaction.  Without these enzymes, our biological reaction would take too long to react or would not react at all.  Lastly, pathways are important in directing actions of our biological molecules.  Glycolysis, critic acid cycle, and electron transport/oxidative phosphorylation are a prime examples of important pathways that are required for energy production.

     These themes were well connected well many courses I have taken.  Many of the courses would contributed these themes from their own perspective.  Biochemistry brought out more of in-depth analysis of topics like protein, metabolism, and many more.  I gained a clearer understanding of the many topics of biology by understanding these three themes during the course.

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 our body through our digestion process.  The daily food that we eat contain carbohydrates that are broken down by pancreatic enzymes into glucose.  Glucose is the simple sugar that our body and cell use for energy.  This energy in the form of ATP (adenosine tri phospate) is created through the pathway of glycolysis, the critic acid cycle, and electron transport. 

In glycolysis, there are 10 reactionary steps that occurs to transform glucose into two pyruvates and two ATPs.  In reaction 1, Glucose gets phosphorylated by hexokinase to form Glucose-6-phosphate.  In reaction 2, Glucose-6-phospate gets isomerize by phosphogluco-isomerase into fructose-6-phosphate. In reaction 3, phosphorylation of fructose-6-phosphate by phospho-fructokinase forms fructose-1,6-biphosphate.  In reaction 4, fructos-1,6-bisphosphate gets cleave by aldolase into two triose phosphates.  in reaction 5, the isomerization of triose phosphates forms glyceraldehyde 3-phosphate.  In reaction 6, glyceraldehyde 3-phosphate gets oxidized.  In reaction 7, substrate-level phosphorylation forms 3-phosphoglycerate and ATP.  In reaction 8, 3-phosphoglycerate gets isomerized to form 2-phosphoglycerate. in reaction 9, 2-phosphoglycerate gets dehydrated to form phosphoenolpyruvate.  Lastly in reaction 10, the coupling reaction of hydrolysis and phosphorylation on phosphoenolpyruvate forms pyruvate and ATP.  The end product of glycolysis is two pyruvate and two ATP.

The two pyruvates can be metabolized further into three separate pathways depending on the presence of oxygen and the organism.  For plants and animal and under aerobic conditions, the pyruvates enters the critic acid cycle and electron transport reaction to produce 32 to 34 ATPs for our cell's usage.

What knowledge have you connected with past knowledge?

So far in this course, I have made many connections to past knowledge.  Many of the topics learned in biology and genetics are reinforced and reintroduced from a biochemical point of view.  I enjoyed studying about the steps involved in DNA replication to the steps involved in protein synthesis. I also found the student's presentation to be very interesting and enjoyable. Many of the presentation made connected what was learned in class to the real world.

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

     An interesting website, that I found online that relates to biochemistry was ProteinLounge.  This website contained many amazing things related to protein. It has many protein pathways, fantastic animations, large database of proteins, and many other interactive software and tools.

    

     The interface of the website is clean and very easy to navigate.  The sample animation located under animation is a must see!!!  The only drawback to the website is that it cost quite a bit to subscribe as member.

Again the website is at:  http://www.proteinlounge.com/Default.aspx

What knowledge have you connected with past knowledge?

                So far, the class had made many connections to prior knowledge.  It was interesting to see and further expand on the topic of biochemical molecules like proteins.  In previous courses like biology and chemistry, discussions of molecules were limited to their respective aspect.  But in biochemistry, these discussions were integrated from all of their different aspects. 

                Protein is an interesting topic in biochemistry and it was amazing to see the actual structure of protein molecules that are important for life.  The protein database was exceptional in providing the public with intricate information of these protein molecules.  Hemoglobin and myoglobin are important molecules and was discuss extensively in biology and anatomy/physiology and their discussion in class provided me with further connection to its form, functions, and complications.

                There were many other connections made like acids/bases, buffering, Henderson-Hasselbach equations, enzymes etc.  These many topics were discussed in previous courses but biochemistry connected them to the process of life.

Protein from PDB explorer

Find a protein using PDB explorer–describe your protein, including what disease state or other real-world application it has. Protein: hiv-1 protease PDB ID: 7HVP HIV-1 protease is an important enzyme for the life cycle of HIV.  Its function is to cut long chain of proteins into its proper length for the maturation process of the virus. This is a critical process and when completed the matured virus can invade and infect other cells. The primary structure of the HIV-1 protease is a double chain peptide.  Each chain A and B is 99 amino acids in length and the secondary structure contains 1 helix and 10 beta sheets. The discovery HIV-1 protease and its function was important for the fight against these immunodeficiency viruses.  Drugs can be made to target HIV-1 protease to stop or inhibit the enzyme's function.  By preventing their actions, the maturation of the virus can be stopped and thereby preventing the infections other cells.

What is Biochemistry? How does it differ from other sciences like chemistry, biology, molecular biology, and genetics?

                Biochemistry is a branch of science that studies the chemistry of living organisms.  Its main focus is on the chemical reaction, structure, and pathways of bio-molecules in plants, animals, and microorganisms.  These bio-molecules include lipids, carbohydrates, nucleic acids, and amino acids.  The study of biochemistry integrates many aspects of other discipline (like biology, physics, chemistry and organic chemistry) to interpret essential chemical functions within living organism. 

                Biochemistry differs from many other sciences.   In comparison with chemistry and biology, biochemistry is more specific than either of the two and it focuses more on the biological reactions within living organisms.  Chemistry and biology provides a broad range of knowledge that serves as a basis for specialized disciplines like biochemistry. 

                Biochemistry also differs from more specialized studies like genetics and molecular biology.  In genetics, the primary focus is in on the science of genes, gene expression, heredity, and variation among organism.  Genetics essentially examines the results of the chemical reaction of life and not the reaction itself.  In molecular biology, the main focus is on the interaction between cells, organelles, and system in living organisms.  Their studies are centered around the transcription and translation of DNA and RNA where as biochemistry tend to focus more on molecular composition, structure, and functions of these molecules.

                Biochemistry can differ from these sciences but all similar in the fact that they all look to obtain knowledge from the study of life.  These studies are essential in helping with the fight against diseases to improve the quality of life itself.  Many of these different disciplines complement one other and are essential for the advancement of knowledge in science.