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Reflecting back on the course, what are three major themes you would identify that connect that 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 I will be proposing, that connect various topics discussed in biochemistry this semester are enzymes, chemical bonds and energy. Starting with the six basic types of enzymes: oxidoreductases, transferases, hydrolases, lyases, isomerases, and synthetases (ligases). Those basic types of enzymes are the muscle behind metabolism of food sources to create adenosine triphosphate ATP. ATP is the key player to be utilized as energy by cellular processes. Enzymes can make chemical bonds to store energy or break chemical bonds to releases energy. These three themes are intertwined.
Development of restriction enzymes allows DNA sequences to be cut at known base sequences to allow researchers to analyze specific sequence of interest. DNA contains the genetic code (genes) that can pass on the information to RNA to create proteins. And enzymes are primarily composed of …. Proteins.
(Original photo by J Russell)
Here is where the hands on aspect of the class made the biggest impact for me this semester. The extraction of our own DNA in the laboratory experiment "369 - Human PCR Tool Box." The polymerase chain reaction was also my topic for my biochemistry wiki site. All the reading and research had an impact but the hands on processing of the sample of eye brow hairs and watching the tracking dye move across the electrophoresis gel made DNA something accessible. The viewing of the processed gel and finding bands to be analyzed to determine VNTR, ALU and regions of mitochondrial DNA was the best experience this semester. We utilized enzymes to break chemical bonds in the DNA and used the energy inherent in all cells to draw the fragments across the electrophoresis gel.
What knowledge have you connected with past knowledge?
(Original Photo by J Russell)
One piece of knowledge that is always good to go back to is the basic concept of structure determines function. I learned this vital piece of information in the beginning of my of study of biology and it still holds true for biochemistry today. Just as the mantra that carbon can only form four bonds from organic chemistry which comes back at the same time. Welcome to chapter sixteen which introduces a seemingly harmless topic of carbohydrates. Now who can hate carbohydrates? They provide the all important sugar (glucose) for our body to produce energy which is essential to live. Well here is the catch, not all carbohydrates (CHO) are created equal. The configuration, spacial arrangement, (structure) of the CHO has a direct impact on the function. Why is that important to know? Carbohydrates play a role in the processes that take palce at surface of cells and in immune recognition. So it would be important to know the structure of the CHO when designing drugs for interaction. The reemergence of stereochemistry involving concepts such as highest chiral C, carbon connected to four different groups, and alpha (opposite side) versus beta (same side) linkage were much easier to comprehend the second time around. Learning it for a second time and applying it to a new concept of metabolism seems allowed me to better understand and apply the concepts of organic chemistry.
The question was purposed on how would your explain the connection between glucose entering the body and energy created by the body to a friend, using your new biochemistry knowledge?
Original picture by J. Russell 2010
Glucose enters the body. I start explaining the process and my friends leave the room. Just kidding. It is a story involving the major component of most of our snack foods, my friend's and I enjoy. Glucose is a major source of energy for the body. It can be used for energy to running cell processes by the metabolizing of the glucose. The breakdown or catabolism of glucose converts this source of energy to adenosine triphosphate or ATP. Pause for dramatic effect. Oh, but it is not done so in one easy step. The high point is glucose is no slacker when it comes to producing the body's energy currency source. It yields 36 ATP molecules which is an average of 6 ATP per carbon atom. Not a bad rate of exchange. This conversion from food source to energy source is accomplished by the powerhouse of the cell called the mitochondria. The process that links catabolism to ATP consists of intermediate steps of the citric acid cycle (TCA), electron transport chain and oxidative phosphorylation. Now if my friends, if they have not left the room, want the basic details of what those consist of here it comes. TCA packs a punch to break down that glucose and put it to work with eight reactions utilizing eight different enzymes: citrate synthase, aconitase, isocitrate dehydrogenase, succinyl-CoA synthetaase, sucinate dehydrogenase, fumarase, and malate dehydrogenase. Painting with broad strokes, the catabolism of glucose produces acetyl-CoA that is then input into the TCA which through the cascade of eight reactions then produces oxaloacetate (oxidation of acetyl group), two NADH molecules, a GTP molecule, a FADH2 molecule and two CO2. Oxidative phosphorylation utilizes the electron transport chain to convert the TCA products. Pause again to let my friends refocus for the big finale. The electron transport chain consists of four protein complexes: complex I oxidation of NADH, complex II oxidation of FADH2, complex III oxidation of COQ and complex IV oxidation of cytochrome C. Interestingly, the product of the electron transfer chain is energy and water. But wait my friends say, "You said the energy currency of the body was ATP. Now you are rewritting the ending." Wait for it. This free energy is utilized by ATP synthase to produce ATP from ADP and inorganic phosphate within the mitochondrial matrix. Remember the powerhouse of the cell I interject. Finally, the ATP is released by the mitochondria to the cell to be used as energy for body processes. Pass the chips and dip my friends say. They need to fuel up on some ATP. Now we are talking lactate and starch, but that is a story for another day.
