Lecture 13: Overview of Metabolism PDF

BioC 3021 Notes 1 Robert Roon Lecture 13: Overview of Metabolism Slide 1. Overview of Metabolism In this lecture, we will consider the general features of metabolism in living organisms. We will focus on the storage and transfer of energy. Slide 2. Naked Gr...

BioC 3021 Notes 1 Robert Roon Lecture 13: Overview of Metabolism Slide 1. Overview of Metabolism In this lecture, we will consider the general features of metabolism in living organisms. We will focus on the storage and transfer of energy. Slide 2. Naked Greek Guys Running These Greek guys have been running for about 2400 years. If their pace is about 8 miles per hour and they are expending about 130 Calories per mile, how many Calories have they burned??? Slide 3. Lehninger Quote Dr Albert Lehninger said that, “Living things are composed of lifeless molecules.”... And I say that we will never totally understand the miracle of life by studying biochemistry, but we have to start somewhere. Slide 4. Enzyme Catalysis Almost every reaction that occurs in living cells is catalyzed by an enzyme. -Most enzymes are proteins (a few are nucleic acids). -Enzymes speed the rates of biological reactions. -They channel reactions to form specific products. -They avoid the formation of unwanted side products. -The activity of enzymes is highly regulated. Slide 5. Metabolism We will soon be examining the details of metabolic pathways. However, before we do that, it is important to have an overall perspective on what these metabolic pathways actually accomplish. This lecture will provide an overview of metabolism, so that when we study individual pathways, such as glycolysis or the TCA cycle or fatty acid biosynthesis, we have some idea of how these BioC 3021 Notes 2 Robert Roon processes relate to the overall pattern of metabolism. The term metabolism covers all the individual enzyme catalyzed reactions and pathways that occur in living cells. Metabolism can be divided into two components—Catabolism and Anabolism. Catabolism refers to metabolic pathways that convert complex biomolecules or polymers into simpler products such as carbon dioxide, water, and urea. Catabolic pathways are degradative, generally involve oxidation, and often produce energy. Most catabolic pathways for biomolecules containing a high percentage of carbon (such as carbohydrates, proteins, and lipids) ultimately release energy. On the other hand, the catabolic pathways for biomolecules with a high percentage of nitrogen (such as the purines and pyrimidines) produce little or no energy. The term anabolism relates to metabolic pathways that produce complex biomolecules or polymers from simpler building blocks. The biosynthesis of proteins, lipids, or nucleic acids is accomplished by anabolic pathways. Anabolic pathways are synthetic, often involve reduction, and use significant amounts of energy. Slide 6. Central Themes in Metabolism A few central themes are at the core of all biochemical knowledge: -The focus of catabolic pathways is the synthesis of energy rich intermediates (ATP and the reduced nucleotides, NADH and NADPH). -ATP is generated during the catabolism of reduced organic compounds such as lipids, carbohydrates and proteins. -NADH is also generated during the oxidative catabolism of reduced organic compounds, and is used to produce ATP by the oxidative phosphorylation system. BioC 3021 Notes 3 Robert Roon -NADPH is generated by the pentose phosphate pathway, and is used as the major reductant in anabolic pathways. -All biomolecules can be synthesized from a few simple building blocks. -Degradative oxidative pathways and biosynthetic anabolic pathways that connect the same compounds are always distinct. Slide 7. Summary of Catabolic Pathways -Catabolic pathways use reduced organic compounds—lipids, carbohydrates, and amino acids, as starting materials. -They yield products such as pyruvate, acetylCoA, and carbon dioxide that are more oxidized than the starting materials. -They use molecular oxygen as the oxidizing agent. -A central focus of catabolism is the net production of energy. -Much of that energy produced in catabolic reactions is released as heat. -Some of the energy is used directly to produce ATP by substrate level phosphorylation. -Some of the energy is used to synthesize NADH, which then is converted to ATP by means of oxidative phosphorylation. -Some of the energy is use to synthesize NADPH, which then is used as a reducing agent in anabolic reactions. Slide 8. Summary of Anabolic Pathways -Anabolic pathways synthesize complex end products such as lipids, carbohydrates, and proteins from simple starting materials -They yield products that are more reduced than the starting materials. -They use NADPH as the reducing agent. -Most anabolic pathways employ ATP as a source of energy to drive thermodynamically unfavorable reactions. -They result in the net release of energy as heat (same as catabolic pathways). In fact, every pathway and every reaction within that pathway has to release some heat, or the reaction would be running backwards. BioC 3021 Notes 4 Robert Roon Slide 9. ATP Stores Chemical Energy -Catabolic pathways release energy by oxidizing reduced organic compounds. -Some of the energy released from the oxidation of reduced organic compounds is stored as ATP. -The outer two phosphate residues of ATP are linked by phosphoanhydride bonds. -The energy from catabolic pathways is used to synthesize the phosphoanhydride bonds of ATP. -The hydrolysis of these phosphoanhydride bonds is used to energize thermodynamically unfavorable reactions. Slide 10. Phosphoanhydride and Phosphoester Bonds in ATP When adenosine triphosphate (ATP) is used as a cofactor, the two terminal phosphates (γ and β phosphates) release high amounts of energy upon hydrolysis. These phosphates are linked to each other and to the α phosphate by phosphoanhydride bonds, which release approximately 7.3 kcal per mole upon hydrolysis. The inner α phosphate, which is linked to a carbon atom by a phosphoester bond, releases much less energy upon hydrolysis and is not generally coupled to energy requiring reactions. Slide 11. Hydrolysis and Synthesis of ATP The hydrolysis of ATP results in energy output, and ATP hydrolysis serves as a source of energy input for other biochemical reactions. Conversely, the synthesis of ATP requires energy input, and is coupled to energy output from other catabolic reactions. Slide 12. Coupled Reactions A thermodynamically unfavorable reaction (with a positive ΔG) can be made to occur if it is coupled with a thermodynamically favorable reaction (with a negative ΔG). Coupled reactions involve shared intermediates. BioC 3021 Notes 5 Robert Roon Slide 13. Glucose Phosphorylation Is a Coupled Reaction The ATP-dependent phosphorylation of glucose exemplifies the coupling of an unfavorable reaction to a favorable reaction. The reaction of glucose plus Pi to form glucose-6-P is unfavorable with a positive ΔG of 13.9 kJ/mol. The hydrolysis of ATP to ADP has a negative ΔG of -30.5 kJ/mol. When the two reactions are combined, and ATP transfers its γ phosphate to glucose, the overall reaction has a negative ΔG of -16.6 kJ/mol. Slide 14. Hexokinase Chemistry It turns out that our coupled reaction example, the ATP-dependent phosphorylation of glucose to form glucose-6-P, is the first reaction of glycolysis. It is catalyzed by the enzyme hexokinase. The phosphate group is transferred from the phosphoanhydride bond in ATP to a lower energy phosphoester bond in glucose 6- phosphate. Slide 15. NADH and NADPH NAD+ is reduced to NADH during many oxidative reactions of catabolism. In its conversion to NADH, the NAD+ collects electrons released during catabolism. The NADH is a form of stored chemical energy. It can be oxidized in aerobic cells, and this oxidation provides the energy for the reaction: ADP + Pi --> ATP. NADPH is a stored form of reducing power. It is used to drive the reductive biosynthetic reactions of anabolic pathways. Slide 16. Nicotinamide Adenine Dinucleotide (NAD+) Nicotinamide Adenine Dinucleotide (NAD+) functions in oxidation reactions as an acceptor of hydrogen and electrons. Its phosphorylated variant Nicotinamide Adenine Dinucleotide BioC 3021 Notes 6 Robert Roon Phosphate (NADP+) functions in its reduced form as a donor of protons and electrons in reduction reactions. Slide 17. Reduction of NAD+ to NADH plus H+ The Nicotinamide ring of NAD+ (and NADP+) is the site of enzymatic activity, and it can exist in a reduced or oxidized state. The riboses, phosphates, and the adenine base of these compounds are involved in binding to enzyme active sites. When NAD+ acts as an oxidant, the nicotinamide ring gains two electrons and a proton, with another proton going into the solvent. The substrate that is being oxidized loses two electrons and two protons. Slide 18. Role of NADH in Oxidative Phosphorylation When we study the function of the electron transport system in oxidative phosphorylation, we will see that NADH is the major electron donor. High energy electrons received from NADH will pass through the electron transport system and ultimately end up reacting with oxygen and protons to produce water. The passage of high energy electrons through the electron transport system is coupled to the translocation of protons from the mitochondrial matrix to the intermembrane space. The proton gradient produced by this process is used by the ATPase, hydrogen ion pump to drive the synthesis of ATP. Slide 19. Compare NAD+ and NADP+ The structure of NADP+ is the same as that of NAD+, only there is a phosphate on the number two carbon of the lower ribose ring. The extra phosphate changes the binding properties of these cofactors. Enzymes that recognize one cofactor do not generally recognize the other. NAD+ is usually an oxidant for catabolic reactions, and NADPH generally functions as a reductant for anabolic reactions. Slide 20. Structure of NADP+ BioC 3021 Notes 7 Robert Roon Here, we see the structure of NADP+ with the extra phosphate residue on C-2’ of the lower ribose ring. Slide 21. Oxidation and Reduction As we have seen, metabolism consists of catabolism in which reduced compounds are oxidized to produce chemical energy, and anabolism in which smaller oxidized compounds are reduced to synthesize larger biochemical intermediates and complex macromolecules. Slide 22. Oxidation Levels of Carbon The production of energy by catabolic pathways in most organisms involves an oxidative process, in which highly hydrogenated compounds are oxidized in a stepwise manner into carbon dioxide. This figure shows the sequential oxidation of a carbon atom from the most reduced (highly hydrogenated) alkane on the left to the most oxidized (highly oxygenated) carbon dioxide on the right. Conversely, energy is often used in anabolic pathways that involve the sequential reduction of oxidized compounds, such as carbon dioxide, to more reduced compounds, such as alkanes. The information on this small figure is extremely important, because it forms the basis of metabolic pathways and energy transfer. Slide 23. Combustion of Glucose If we were to burn one mole of glucose completely to carbon dioxide, the process would release about 687 kcal (2870 kJ) of energy as heat. That is the maximum amount of energy that can be produced by combining glucose and oxygen. Slide 24. Oxidation of Glucose in a Bomb Calorimeter The amount of energy released as heat by oxidizing glucose to carbon dioxide can be measured in a bomb calorimeter. Slide 25. Oxidation of Glucose in a Living Organism The amount of energy released by oxidizing glucose to carbon BioC 3021 Notes 8 Robert Roon dioxide in a living organism would be exactly the same as that measured in a calorimeter. However, a significant portion of that energy would be captured as chemical energy, and a proportionately reduced amount of heat would be produced. That is the genius of living organisms—they can siphon off the energy from oxidation and trap it as chemical energy in ATP. The exact amount of energy that organisms can trap as ATP will vary, but a good estimate would be about 30 percent. Slide 26. Fuel Reserves in Humans In addition to the daily intake of food, humans depend on energy reserves. The energy reserves of an average human are about: -1500 kcal of carbohydrate as glycogen (less than a one day energy supply). -135,000 kcal as fat (enough for a month or two) -25,000 kcal as protein (enough for 15 or 20 days) The major reserves of carbohydrate are found as glycogen in liver and muscle. Reserves of lipid are found as triglycerols, mainly in adipose tissue. Proteins are not present in humans as storage material, but working proteins (eg. muscle protein) can be scavenged during starvation. Slide 27. Daily Input and Output of Energy The average human uses 1500-2500 kcal per day depending on the amount of exercise. Someone running a marathon (26.2 miles) might burn an additional 3500 kcal. An athlete running for 24 hours in an ultra-marathon might expend 24,000 kcal. You must burn about 3500 kcal to lose a pound of body weight. The major input sources for energy production in humans are carbohydrate, fat, protein—and don’t forget oxygen! The major output products of energy production are carbon dioxide, water, and urea. (urea is used by humans to get rid of excess nitrogen) BioC 3021 Notes 9 Robert Roon Slide 28. The Major Catabolic Pathways This figure shows the central catabolic pathways that are found in most organisms. -Carbohydrates are funneled into the glycolysis pathway, which converts glucose to pyruvate. Under aerobic conditions, the pyruvate is then converted to acetylCoA. -Stored fats (triacylglycerols) are hydrolyzed to fatty acids and glycerol. The glycerol is integrated into glycolysis, and the fatty acids are oxidized to acetylCoA. -Proteins are first hydrolyzed into amino acids. The amino acids can be converted into pyruvate, acetylCoA, or intermediates of the TCA cycle. -You can see that most of these catabolic pathways ultimately converge on acetylCoA. The acetylCoA is oxidized to carbon dioxide in the TCA cycle. -The primary energy rich product of the TCA cycle is NADH. NADH donates electrons to the oxidative phosphorylation system. Energy from those electrons is used to create a proton gradient, which in turn is used to drive the formation of ATP. Slide 29. Metabolic Profiles of Major Organs I -Adipose tissue serves as a storehouse for fat in the form of triacylglycerols. -The liver converts lactic acid to glucose, stores carbohydrate as glycogen, interconverts various forms of fat, releases energy rich metabolites into the blood, and regulates the blood level of these intermediates. Slide 30. Metabolic Profiles of Major Organs II BioC 3021 Notes 10 Robert Roon -The brain uses high levels of glucose for metabolism and nerve transmission, and is totally dependent on blood glucose as an energy source. -Muscle tissue uses fats and carbohydrates to produce work. About 75% of human carbohydrate reserves are stored in muscle as glycogen. Slide 31. Regulation of Metabolic Activity Metabolic activity is highly regulated by a variety of mechanisms: -With allosteric regulation, various metabolites can directly activate or inhibit the level of enzyme activity. Enzyme activity is also directly regulated by covalent modification of proteins. -Mechanisms that regulate the level of gene expression cause changes in enzyme levels depending on the metabolic needs of the cell. -Cellular compartmentalization permits certain metabolic activities to be expressed in specific areas of the cell. -Organ specialization allows for the expression of metabolic activities in certain tissues. Slide 32. Maximum Running Velocity at Different Distances The total ATP equivalents available from various sources vary from about 223 mmol from ATP itself to 4,000,000 mmol from stored fatty acids. The rates at which these equivalents can be utilized for energy production are almost inversely proportional to their quantity. This is reflected in the world record rates for running various distances that vary from approximately 25 miles/hour in a short sprint (which burns mostly ATP and creatine phosphate) to about 13 miles per hour in a marathon (in which the aerobic metabolism of glucose and fatty acids serves as the primary energy source). Slide 33. Creatine Kinase. BioC 3021 Notes 11 Robert Roon Phosphocreatine serves as a backup storage form of high energy phosphate. When there is an immediate need for ATP energy, the high energy phosphate from phosphocreatine can be transferred to ADP, effectively prolonging the availability of ATP energy. The transfer of high energy phosphate between phosphocreatine and ATP is catalyzed by creatine kinase. Slide 34. Naked Greek Guys Still Running So here we are 30 minutes later, and the Greek guys are still running. How may kcal have they used up in the past half an hour?