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UB BIO 205 - Exam 4 Study Guide

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BIO 205Exam #4 Study Guide: Chapters 23-38Part IV: Sugar MetabolismChapter 23: Introduction to Metabolism- Catabolism is the breakdown of molecules into smaller pieces, which allows for the storage of energy in “high-energy compounds” (ATP). Anabolism involves using ATP to synthesize large macromolecules. - Important intermediates of glucose metabolism:Low energy High energyCoA Ac-CoANAD+ NAD:HFAD FAD:H2ADP ATP- Overall map of glucose metabolism:1. Glycolysis – glucose is cut in half and converted into two molecules of pyruvate.2. Dehydrogenation and decarboxylation – pyruvate dehydrogenase (PDH) is the enzyme that dehydrogenates pyruvate. Pyruvate also loses one carbon (CO2) and attaches to CoA as an acetyl group. Pyruvate + CoA  acetyl-CoA + CO23. Krebs cycle – the basic function of this cycle is to convert the acetyl group into two carbon dioxide molecules and store energy in the form of NADH and FADH2. 4. Electron transport – NADH and FADH2 pass their electrons to a series of proteins embedded in the inner mitochondrial membrane. The flow of electrons creates an H+ gradient and they eventually join with oxygen to form water. 5. ATP synthesis – the H+ gradient flows through ATP synthase, creating ATP. 6. Beta-oxidation – fatty acids can be used to create acetyl molecules that are joined with CoA. 7. Fermentation – when oxygen is not present, an organism will perform anaerobic metabolism. In animals, pyruvate is turned into lactate, whereas yeast cells create ethanol and carbon dioxide. Anaerobic metabolism only produces 2 ATP, which is very small compared to the 38 ATP produced by aerobic metabolism.8. Gluconeogenesis – two molecules of pyruvate can be converted back to glucose. 9. Urea cycle – amino acids and nucleic acids can be incorporated into the Krebs cycle to produce ATP. The nitrogen from these molecules is excreted as urea.10. Fatty acid synthesis – just as acetyl molecules can be taken from fatty acids and givento CoA, acetyl molecules can also be taken from CoA and used to make fatty acid chains.11. Glycogen storage – food storage polymers of glucose (starch and glycogen) can be processed by pathways that link them to glycolysis. - Beta-oxidation is named so because the acetyl group is cleaved at the beta carbon of the fatty acid chain. The first step in beta-oxidation is a condensation reaction that links CoA tothe carboxyl group of a fatty acid. Next, the beta carbon (2nd carbon from carboxyl carbon) is oxidized to a ketone. Then, the two end carbons (carboxyl and alpha) are cut off to form acetyl-CoA while another CoA molecule attaches to the beta carbon, which becomes the new carboxyl carbon. The process then repeats until the fatty acid has been broken down. - When pyruvate is decarboxylized and dehydrogenated, it forms acetyl, carbon dioxide, and NADH. Acetyl and carbon dioxide come from the separation of the three carbons in pyruvate. NADH is formed from reduction of NAD+ by the hydride ion from dehydrogenation of pyruvate. - The Krebs cycle (also TCA of citric acid cycle) begins by combining acetyl-CoA (2C) with oxaloacetate (4C) to form citric acid (6C). Throughout the rest of the cycle, two carbon dioxide molecules are formed, ergo reforming oxaloacetate (keep in mind that one molecule of pyruvate leads to the production of 3 CO2 (one from PDH and two from Krebs cycle)). Furthermore, the Krebs cycle produces 3 NADH, 1 FADH2, and 1 ATP (first isGTP, but is immediately converted). - The Krebs cycle both receives and provides small carbon skeletons. Amino acids can be used to make ATP, or parts of the Krebs cycle can be used to make amino acids. Different intermediates form different amino acids, and vice versa.- NAD+/NADH oxidation and reduction:- When NADH reaches the mitochondria, it gives its electrons to complex I. The electrons then travel to complex III, then complex IV, and finally meet with oxygen and hydrogen NAD+ is aromatic while NADH is not. Therefore, NAD+ is the preferred form due to resonance stabilization, and as a result, moving from NADH to NAD+ releases a lot of energy.to form water. FADH2 gives it electrons to complex II, which then continues to complex IIIand so on. NADH  NAD+ + H+ + 2e-2e- + 2H+ + ½ O2  H2O- ATP and acetyl-CoA have favorable free energy values of -7 and -8 kcal/mol respectively. On the other hand, NADH and FADH2 both have free energy values close to -50 kcal/mol.Each NADH produces approximately 3 ATP while FADH2 produces 2 ATP. - Factors that favor ATP hydrolysis:1. Decrease in repulsion between negatively charged phosphate groups. 2. Increased resonance stabilization on phosphate. 3. Increased solubility in water due to neutral pKa of hydrogen. - ATP is thermodynamically unstable, but kinetically stable. In other words, ATP would like to separate into ADP and Pi, but the energy barrier is so large that without a catalyst, thereaction takes years. - In a carboxylic acid, there are extended pi cloud interactions between the carbonyl oxygen, the carbonyl carbon, and the alcohol oxygen. Although acetyl-CoA has a very similar structure and sulfur is right below oxygen in the periodic stable, the p orbitals of sulfur are much larger than those of oxygen, therefore disrupting the pi cloud in acetyl-CoA.- Going back to thermodynamics, the bond energy of a reaction can be calculated by subtracting the energy of the reactants from the products. A larger bond energy meant that the reaction was favorable. Furthermore, calculations revealed that polar moleculesare more stable than nonpolar molecules. - When looking at keto-enol tautomerization, the bond energy of the keto form is slightly higher than the bond energy of the enol form, making the keto form the more stable of the two. - Brown fat, found in newborns and hibernating animals, contains a protein called thermogenin. This protein is able to form a channel through the inner membrane of the mitochondria, allowing H+ to flows down its gradient without producing ATP. However, the movement of the protons produces heat, which keeps newborns and hibernating animals warm. - In addition to being used for DNA formation, pyrophosphate and its irreversible hydrolysis also drives the farnesylation of proteins to produce a nonpolar anchor.- Another irreversible reaction is the formation of carbon dioxide because it is entropically favored. The PDH reaction and two reactions in the Krebs cycle are irreversible because they result in the release


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UB BIO 205 - Exam 4 Study Guide

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