Biological energy production

What are the biochemical processes involved in the breakdown (catabolism) of fatty acids?
The breakdown of fatty acids or the catabolism of fatty acids is often referred to as beta oxidation. It is basically a biological process in which the fatty acids that remain in the form of Acyl-CoA molecules are broken down either into perosisomes or into mitochondria. Again, the fatty acids, during the process of fatty acid catabolism, the fatty acids are broken down into both mitochondria and peroxisomes. The result of the process of beta oxidation or fatty acid breakdown is the generating of Acetyl-CoA that happens to be the entry molecule for the Krebs cycle.
There are mainly four recurring steps of the entire process of beta oxidation of fatty acid catabolism. However, the activation of fatty acids is quite necessary before that. The fatty acids are able to penetrate the plasma membrane because of the high fat solubility and poor water solubility of the plasma membranes. A fatty acid can react with ATP after it gets in the cytosol, and give a fatty acyl adenylate in addition to inorganic pyrophosphate. It is this reactive acyl adenylate that reacts with free coenzyme A in order to produce fatty acyl-CoA ester and AMP.
The first step of fatty acid catabolism or beta oxidation is the oxidation of the fatty acid by the Acyl-CoA- Dehydrogenease. A double bond is formed between the C-2 and C-3. The purpose that the enzyme serves is to catalyze the process of formation.
In the second step of fatty acid catabolism the bond between the C-2 and C-3 goes through the process of hydration. This is a stereospecific reaction that forms only the L isomer. The third step of fatty acid breakdown is the oxidation of L-beta-hydroxyacyl Co A by NAD+. In this process the hydroxyl group is converted into a keto group.
The last step of catabolism of fatty acid is called Thiolysis. It is the cleavage of beta-ketocyl CoA by the thiol group of a different molecule of CoA. It is between the C-2 and C-3 that the thiol is inserted. (Miles, 2003)
Identify the sites where ATP is both produced and used within cells during aerobic respiration.
Aerobic respiration is one kind of cellular respiration that takes place in the cells of the living objects to convert the biochemical energy from the nutrients into ATP or adenosine triphosphate. The principal condition for the aerobic respiration to take place and generate ATP is that this biological process necessitates the presence and participation of oxygen.
There is more than one part of the cells that are involved in the entire process of ATP being generated and used. One of the major and important phases of the production of ATP is that Pyruvate has to be broken down from glycolysis and has to enter the mitochondrion so that it can get fully oxidized by the Kerbs cycle. Therefore, mitochondrion can be regarded as one of the cell parts that are involved in the production of ATP in aerobic respiration.
Though it is believed that mitochondria, that is considered to be the powerhouse of the cell, is the cell part where all ATP is produced. The fact remains that all ATP is not produced in mitochondria, though most of them are. Since the process of oxidative phosphorylation takes place in mitochondria, it is thought that all ATP is produced in mitochondria. Some of the ATP is also produced in the cytoplasm.
The production of ATP also takes into account the creation of chemiosmotic potential through the process of the protons being pumped across a membrane. The membrane, therefore, comes to be one of the parts of the cell that are involved in the production of ATP in aerobic respiration. (Porter and Brand, 1995; Kaiser, 2001)
Identify the sites within cells where ATP is both produced and used up during anaerobic respiration.
So far as anaerobic respiration is concerned, pyruvate is not metabolized without oxygen by cellular respiration. In fact, it goes through a process of fermentation. Apart from the fact that the production of ATP in aerobic respiration necessitates oxygen while the anaerobic respiration does not require the presence of it, there is another difference between the two kinds of cellular respiration. In case of anaerobic respiration, the pyruvate is not carried to the mitochondrion. Cytoplasm is the part of the cell where the pyruvate remains and gets converted into waste products.
It, therefore, has to be noted that while the production of ATP in aerobic respiration takes place in a number of parts of the cell including mitochondria and cytoplasm, in case of anaerobic respiration the ATP is generated in cytoplasm only and not in mitochondria. (Campbell, 2004)
Evaluate how cells regulate the process ofglycolysis in terms of energy requirements.
All the reactions that are catalyzed with the help of hexokinase, PK and PFK-1, proceed with a decrease of free energy in a comparatively big amount. These reactions that are described as non equilibrium reactions are thought to be the ideal elements to serve the purpose of regulating the flux through glyco lysis.
It needs to be mentioned in this regard that the regulation of hexokinase is not the most important point that controls glyco lysis. It is so owing to the fact that the breakdown of glycogen or the catabolism of glycogen results in the derivation of a large amount of G6P. As a consequence, the hexokinase reaction becomes not mandatory to take place. Rather, it becomes quite unnecessary. On the other hand, the regulation of PK happens to be of immense importance and significance for the purpose of reversing glyco lysis at the time when ATP is quite high for activating gluconeogenesis. This reaction that is catalyzed by enzyme is not an important factor as a control point in the process of Glyco lysis. PFK-1 is the element that serves the purpose of a catalyst in the reaction that takes into account the rate limiting step in glycolysis. (King, 2009)
PFK-1 happens to be a kind of tatrameric enzyme thathas its existence in the two conformational states that are termed as R and T. It is to be mentioned that both of them are in equilibrium. ATP is not only a substrate but also an allosteric inhibitor of PFK-1. Each of the subunits possesses two ATP binding sites. One of these two ATP binding sites is an inhibitor site while the other is a substrate site. When the tetramer remains in either conformation, the substrate site binds the ATP. On the other hand, ATO is bound by the inhibitor site essentially when the enzyme happens to be in the T state. There is another substrate for PFK-1, in the name of F6P that binds to the enzyme in the R state. The inhibitor site comes to be occupied when the ATP is in a state of high concentration.
Again, AMP overcomes the inhibition of PFK-1 and it binds to the R state of the enzyme, resulting in the conformation of the enzyme that is capable of binding, F6P being stabilized. The factor that plays the most important role as an allosteric regulator not only for glycolysis but also for gluconeogenesis is fructose 2, 6-bisphosphate that is an intermediate neither in gluconeogenesis nor in the process of glycolysis. (King, 2009)

References
1. Campbell, I. 2004, Cell biology and gene expression, Anaesthesia &intensive care
medicine, Volume 5, Issue 5, 1 May 2004, Pages 169-173
2. Miles B. 2003, Fatty Acid Catabolism, by Bryant Miles, March 21, available at:
3. http://www.tamu.edu/classes/bmiles/lectures/fatcatii.pdf (accessed on February
16, 2009)
4. Kaiser, G. 2001, THEORETICAL ATP YIELD FOR AEROBIC RESPIRATION,
Available at: http://student.ccbcmd.edu/biotutorials/cellresp/yield.html (accessed
on February 16, 2009)
5. King, M.W. 2009, "Regulation of Glycolysis", available at:
http://themedicalbiochemistrypage.org/glycolysis.html (accessed on February 16,
2009)
6. Porter R.K, Brand M.D. 1995. "Mitochondrial proton conductance and H+/O ratio are
independent of electron transport rate in isolated hepatocytes". Biochem. J. 310 (Pt 2):
379-82

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