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Biology - Biochemistry

The main things that goes on inside the cell, are chemical reactions. Catalyst helps reactions happen faster. Enzymes are organic catalyst that catalyzed biological reactions. They help get reactants together and therefore, make the reactions happen more quickly. 

The word substrate is used to refer to reactants in an enzyme catalyzed reaction. The place at which the substrate attached to the enzyme molecule is called the active site. Enzymes specificity refers to the fact that one enzyme is usually designed to fit the reactants for only one particular reaction. When the substrate is attached to the enzyme they caused a slight change in the shape of the enzyme which is called an induced fit. When the reaction is over, the enzyme resumes its usual shape. Remember that an enzyme is not a reactant and that all enzymes are made of protein. 

A living cell is similar to a bag full of chemicals. Many of the chemicals have the potential to react with many other of the chemicals. Enzymes determine which chemicals will react with which chemicals. Therefore, it is the availability of enzymes that determines what reactions will take place in a cell and what reactions will not. An enzyme would not work just anywhere and it would not work under any and every condition either. One of the very important things to remember about enzymes is that everyone has an optimum pH, which is the pH at which it works best. When pH differs even a little bit from an enzymes optimum pH, the enzyme works very poorly. Enzymes also work better at high temperatures. As temperature increases enzymes work better. For every enzyme there some temperature that is too high. When temperature is raised high enough, any enzyme denatures. When an enzyme denatures, it does not work anymore. 

Once the amount of substrate added matches the amount of enzyme at work, the reaction rate levels off and adding substrate will not increased the reaction rate. Many enzymes would not work alone, but need to perform in the presence of inorganic substance called cofactor or an organic molecule called coenzyme. The activity of enzymes is also affected by feedback inhibition. Feedback inhibition means that a function of an enzyme is inhibited by the product of the reaction it catalyzes. This way you do not end up with too much of any one product in the cell because an excess of the product will turn off the enzyme. 

Every cell uses energy and they get their energy from ATP. ATP is the energy currency. ATP is made of an adenosine molecule which is the nitrogenous base adenine with the rival sugar tacked on and three phosphate molecules attached to it. In almost all living cells, ATP is the lowest recognizable chemical form in which energy is found before it is taken to perform work. 

You will have to know a little bit how cellular energy is stored and the initial and final compounds of each step. Cells store energy in the form of glucose. Glucose is a six carbon molecule and it has energy in it. The energy is in the chemical bonds between carbon atoms and in the chemical bonds between carbon and hydrogen atoms. ATP is made by putting together an ADP molecule and a phosphate molecule using the energy from glucose. When cells need to get some glucose out of storage to form some ATP, they start with the process called glycolysis. In the process of glycolysis the cell starts with the molecule of glucose. Glucose uses two ATPs to start the process. 

The cell ends up with two molecules of pyruvic acid and four ATPs. Therefore, when a glucose molecule goes through the process of glycolysis, it ends up with the net production of two ATP molecules. Remember that the glycolysis is anaerobic process. It occurs without oxygen. After glycolysis is complete the cell has form some ATP and is left with tow molecules of pyruvic acid. Each molecule of pyruvic acid is then converted to a molecule of acetyl CoA, which is a two-carbon molecule by oxidative decarboxylation. 

The cell now has two molecules of acetyl CoA. With its two molecules of acetyl CoA, the cell next undergoes the Kreb cycle which is also called the citric acid cycle. When the cell undergoes the Kreb cycle, acetyl CoA combines with the four-carbon molecule to form a six-carbon molecule. Within the Kreb cycle each molecule of acetyl CoA produces one molecule of GTP. The GTP molecule is then readily converted to an ATP molecule. The cell starts out with two molecules of acetyl CoA, which means that it undergoes the Kreb cycle twice. 

So, for each molecule of glucose that cell starts out with, the Kreb cycle yields two molecules of ATP, four molecules of CO2, six molecules NADH, and two molecules of FADH2. The Kreb cycle is the final common pathway in the oxidation of fatty acids into amino acids. The Kreb cycle requires oxygen that means the process is available to aerobic organisms but it is not available to anaerobic organisms. Anaerobic bacteria can conduct glycolysis because that does not require oxygen but they cannot conduct the Kreb cycle because that requires oxygen. 

The Kreb cycle occurs inside a cells mitochondrion. A mitochondrion has an outer membrane and inner membrane a space between the two membranes and a matrix. After the Kreb cycle there are two more processes that occur, the electron transport via the electron transport chain and oxidative phosphorylation. After the Krebs cycle is complete the cell is left with lots of NADH and FADH2. Each FADH2 gives up H2, then the H2 molecule divides to form 2 hydrogen atoms and each hydrogen atom gives up an electron. NADH gives up an H atom and then H atom gives up one electron. Each electron is transferred to the electron transport chain. The electron transport chain involves a lot of carrier molecules that contain iron. Once, the electrons are transferred over to the electron transport system. The system hands each electron down from one carrier to the next. With each hand down of an electron, energy is released. 

The cell takes the energy and uses it to pump hydrogen ions from the inside of the mitochondrial matrix to the space between the two mitochondrial membranes. That means the cell ends up with more hydrogen ions outside the matrix than inside. That produces an electro chemical gradient. Once an electron has been handed down through all of the carriers in a series of redox reactions, it gets together with another electron that has come down the carrier system and the two electrons are passed finally to an atom of oxygen. That forms a negatively charged oxygen. Each negatively charged oxygen ion then gets together with two charged hydrogen ions and forms a molecule of water. Since the electron transport system ultimately passes each electron to an oxygen molecule, it requires oxygen and its anaerobic process. 

Because of the electrochemical gradient that is produced during electron transport, hydrogen ions start right away via passive diffusion to diffuse inward back into the mitochondrial matrix. Now, as the hydrogen ions diffuse back across the inner mitochondrial membrane ADP and phosphate that are sitting right on the membrane, get together and form ATP. So when the hydrogen ion crosses the inner membrane, it causes the production of ATP from ADP and phosphate. The hydrogen ion crosses the inner mitochondrial membrane by passing through channels made of a substance called ATP synthase which is also sitting on the inner membrane. 

Even though there are separate processes, electron transport an oxidative phosphorylation happen at the same time. As the electron transport chain starts to pump hydrogen ions out across the inner mitochondrial membrane, the hydrogen ion start right away to cross back into the matrix. So the hydrogen ion gradient is not allowed to progress very far. In anaerobic organism the cell conducts fermentation. This means that the two molecules are pyruvic acid left from glycolysis are transformed to either ethanol or lactic acid. Fermentation produces only two ATPs. When a rapidly exercising human muscle can’t get all of the oxygen it needs to conduct aerobic respiration, it conducts fermentation and produces lactic acid.