Chapter 28 Specific Catabolic Pathways: Carbohydrate, Lipid, and Protein Metabolism

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1 28.1 According to Table 28.2 the ATP yield from stearic acid is 146 ATP. This makes 146/18 = 8.1 ATP/carbon atom. For lauric acid (C 12 ): Step 1 Activation -2 ATP Step 2 Dehydrogenation five times 10 ATP Step 3 Dehydrogenation five times 15 ATP Six C 2 fragments in common pathway 72 ATP Total 95 ATP 95/12 = 7.9 ATP per carbon atom for lauric acid. Thus stearic acid yields more ATP/C atom. This will be generally true for all the fatty acids. The longer the fatty acid, the higher the ATP per carbon atom as the initial input of -2 ATP is a constant for the process Fats in the diet are triglycerides (esters of fatty acids and glycerol). Lipases catalyze the hydrolysis of the ester bonds yielding long-chain fatty acids and glycerol The major use of amino acids is in the synthesis of proteins. Proteins from ingested food are hydrolyzed and the amino acids are used to rebuild proteins that the body constantly degrades. We cannot store amino acids so we need a constant supply in our diet Before degradation of a molecule can begin, it is often necessary to activate the compound. Glucose is activated by the addition of a phosphate group (from ATP) by the action of an enzyme, hexokinase. We must invest some energy to prime the glycolysis process The step referred to is # 4, the aldolase-catalyzed cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. Glyceraldehyde 3- phosphate metabolism continues immediately in glycolysis (Step # 5), but the dihydroxyacetone phosphate must first be isomerized to glyceraldehyde 3-phosphate by an isomerase. Glyceraldehyde 3-phosphate and dihydroxyacetone phosphate are in equilibrium and removal of glyceraldehyde 3-phosphate by glycolysis drives the isomerization reaction The kinases listed below are shown in Figure Step 1: hexokinase (glucokinase) Step 3: phosphofructokinase Step 6: phosphoglycerate kinase Step 9: pyruvate kinase 28.7 (a) The steps in glycolysis that need ATP are # 1, phosphorylation of glucose and # 3, the phosphorylation of fructose 6-phosphate. 298

2 (b) The steps that yield ATP are # 6, catalyzed by phosphoglycerate kinase and # 9, catalyzed by pyruvate kinase The first oxidation step in glycolysis is # 5, the conversion of glyceraldehyde 3- phosphate to 1,3-bisphosphoglycerate. Note that the substrate is oxidized, carbon 1 is converted from an aldehyde to a carboxylic acid, and the coenzyme NAD is reduced to NADH. The NADH represents a source of energy when its equivalent is used to enter the electron transport chain ATP is a negative modulator for the allosteric, regulatory enzyme phosphofructokinase, Step # 3, as well as for the enzyme pyruvate kinase, step # The process that converts pyruvate to acetyl CoA is chemically defined as an oxidative decarboxylation. Pyruvate is decarboxylated and what was a keto group is oxidized to the level of a carboxylic acid. NADH is produced confirming the redox process The oxidation of glucose 6-phosphate by the pentose phosphate pathway produces NADPH. This reduced cofactor is necessary for many biosynthetic pathways, but especially for the synthesis of essential fatty acids, and as a defense against oxidative damage (a) The reduction of pyruvate to lactate uses an energy-rich coenzyme, NADH, so this reaction consumes energy. (b) The conversion of pyruvate to acetyl CoA generates energy in the form of NADH The anaerobic degradation of a mole of glucose leads to two moles of lactate. Therefore, three moles of glucose produce six moles of lactate (a) Glucose to acetyl CoA: Each mole of glucose is converted to two moles of glyceraldehyde 3-phosphate, so there is a total of two moles of NADH produced at step 5 and two moles of NADH produced during the conversion of two moles of pyruvate to two moles of acetyl CoA. Therefore, one mole of glucose yields a grand total of four moles of NADH. (b) Glucose to lactate: Each mole of glucose produces two moles of NADH at step 5. Those two moles, however, are used during the reduction of pyruvate to lactate. Therefore, the total, net yield of NADH is zero Using the data in Table 28.1, a net yield of 2 ATPs are directly produced by the glycolysis of glucose (glucose to pyruvate). There is the initial expenditure of two ATPs in the first three steps of glycolysis. Then steps 6 and 9 produce 4 ATPs, for a net yield of 2. Most of the ATP from glucose degradation comes from oxidation of the reduced cofactors, NADH and FADH 2, linked to respiration and the common pathway. 299

3 28.16 (a) Glucose to pyruvate: according to Table 28.1 and Figure 27.4, there are only two molecules of ATP produced from each glucose converted to pyruvate in the glycolysis process. (b) Pyruvate to acetyl CoA: six ATPs are produced in this step, as each pyruvate yields one NADH for a total of two with each one yielding 3 ATPs when the NADH is reoxidized by the electron transport chain. (c) Glucose to carbon dioxide and water: Table 28.1 shows how 36 ATP molecules are produced from the complete oxidation of a glucose molecule (a) Fructose catabolism by glycolysis in the liver yields two ATPs just like glucose. (b) Glycolytic breakdown of fructose in muscle also yields two ATPs per fructose Both statements are correct so there is no discrepancy. In step 5, a single glyceraldehyde 3-phosphate is being oxidized to produce one NADH. However, each glucose entering the pathway yields two molecules of glyceraldehyde 3-phosphate. Table 28.1 calculates NADH yield from each glucose molecule Enzymes that catalyze the phosphorylation of substrates using ATP are called kinases. Therefore, the enzyme that transforms glycerol to glycerol 1-phosphate is called glycerol kinase The hydrolysis of ATP to ADP and P i cleaves one phosphate anhydride bond, which releases 7.3 kcal/mole (Section 27.3). Glycerol 1-phosphate has a phosphate ester bond that is hydrolyzed. The energy released is equivalent to the energy from the hydrolysis of AMP, which in Section 27.3 was given as 3.4 kcal/mole. Much more energy is released from ATP than glycerol 1-phosphate. In some cases ATP is hydrolyzed to AMP PP i, but the PP i is almost immediately hydrolyzed to 2 P i. In this case the energy released is doubled (a) The enzymes are thiokinase and thiolase. (b) Thio refers to the presence of the element sulfur. (c) Both of these enzymes use Coenzyme A that contains a reactive thiol group, SH, as a substrate (a) The enzymes for β-oxidation are present in the mitochondrial matrix. (b) Transfer of fatty acids from the cytoplasm to the mitochondria is done by the small molecule, carnitine, and an enzyme system, carnitine acyltransferase Each turn of fatty acid β-oxidation yields one C-2 fragment (acetyl CoA), one FADH 2, and one NADH. Therefore, the total yield from three turns is three acetyl CoA, three FADH 2, and three NADH. There is still a six-carbon portion of lauric acid left, hexanoyl CoA. 300

4 28.24 The catabolism of a small fatty acid is just as efficient as that of a long-chain fatty acid once the oxidation process begins. However, there is an initial input of energy for the activation to be taken into account. Therefore, the longer the fatty acid, the more ATPs are produced compared to the ATP input in the activation step Using the data from Table 28.2, the yield from the oxidation of one mole of myristic acid is 112 moles of ATP. The process requires six turns of β oxidation and produces 7 moles of acetyl CoA More energy is produced from β-oxidation of the saturated acid, stearic acid than from oleic acid. Oleate, which already has a double bond, will skip a step in β-oxidation that produces the reduced cofactor, FADH 2 (acyl CoA dehydrogenase). That will lead to less ATP produced. This makes sense when we consider the two fatty acid structures. Because oleate has a double bond, it is already partially oxidized and a step closer to complete oxidation than stearate Under normal conditions, the body preferentially uses glucose as an energy source. When a person is well fed (balance of carbohydrates and fats and proteins), fatty acid oxidation is slowed and the acids are linked to glycerol and are stored in fat cells for use in times of special need. Fatty acid oxidation becomes important when glucose supplies begin to be depleted, for example, during extensive physical exercise or fasting or starvation More energy is released per weight from the oxidation of fats than the oxidation of carbohydrates. Using energy from glucose as representing carbohydrates, glucose yields 6 ATPs for each carbon atom. The oxidation of stearic acid yields about 8 ATPs per carbon atom. In addition, when glycerol obtained from fat degradation is metabolized, another 6.7 ATP molecules are generated per carbon atom of glycerol. Therefore, fats have a higher caloric value than carbohydrates The transformation of acetoacetate to β-hydroxybutyrate is a redox reaction using the cofactor, NADH. Acetone is produced by the spontaneous decarboxylation of acetoacetate Yes, ketone body catabolism may be used as a source of energy. Ketone bodies are made in the liver and distributed to the brain and heart for emergency needs. Ketone bodies in brain or heart cells are degraded to acetyl CoA. The acetyl CoA enters the citric acid cycle and oxidative phosphorylation for complete oxidation to carbon dioxide and water Oxaloacetate produced from the carboxylation of PEP normally enters the citric acid cycle at Step 1. As we will learn in the next chapter, oxaloacetate may also be used to synthesize glucose. 301

5 28.32 The reaction shown is a transamination, which involves transfer of an amino group from an amino acid to an α-ketoacid. The process is an initial step in preparing amino acids for degradation. The α-keto acid carbon skeleton remaining from the amino acid may enter the citric acid cycle for use in energy production or biosynthesis of glucose Oxidative deamination of alanine: CH 3 CH NAD H 2 O CH 3 C NADH H NH 4 NH 3 O Alanine Pyruvate Ammonia and the ammonium ion are both toxic to humans; therefore, it must be converted to the form of urea. The urea, a condensed form of ammonia, is water soluble and easily eliminated from the body. As urea, it will not change the ph of the blood while it is being filtered out by the kidneys One of the nitrogen atoms in urea comes originally from an ammonium ion through the intermediate carbamoyl phosphate (steps 1 and 2 in the urea cycle). The ammonium ion was probably released from an amino acid by oxidative deamination. The other nitrogen atom of urea comes from aspartate that enters the urea cycle at step The compound fumarate is an intermediate in both the citric acid cycle and the urea cycle. Aspartate is a pseudo intermediate in both as it is an intermediate in the urea cycle and becomes oxaloacetate via transamination. Oxaloacetate is an intermediate in the citric acid cycle (a) The toxic product from the oxidative deamination of Glu is the ammonium ion. (b) The ammonium ion is converted to urea by the urea cycle and eliminated in the urine Most of the toxic ammonium ion is removed from the body by conversion to urea, but it may also be detoxified by reductive amidation, which is the reverse reaction of oxidative deamination, and by the ATP dependent amidation of glutamate to yield glutamine (Section 28.8) Tyrosine is considered a glucogenic amino acid because pyruvate can be converted to glucose when the body needs it. Any amino acid with an easy pathway to pyruvate will be considered glucogenic Bilirubin is a product of heme degradation. Bilirubin is removed from the blood by the liver. A high concentration of the chemical in the blood indicates that the liver is not functioning properly and perhaps the cells are diseased. 302

6 28.41 During initial hemoglobin catabolism, the heme group and globin proteins are separated. The globins are hydrolyzed to free amino acids that are recycled and the iron is removed from the porphyrin ring and saved in the iron-storage protein, ferritin, for later use Functional groups in biliverdin that are from oxidation: two carbon atoms at the top are oxidized from hydrocarbons to carbonyl groups. The carbon atom removed is oxidized to carbon monoxide. Functional groups reduced: some nitrogen atoms are reduced to N-H During exercise, normal glucose catabolism shifts to a greater production of lactate rather than conversion of pyruvate to acetyl CoA and entry into the citric acid cycle. This shift in metabolism is a result of a depletion of oxygen supplies. A build-up of lactate in muscle leads to a lowering of ph which effects myosin and actin action Epinephrine acting as a hormone begins the signal transduction process (Section 24.5) by enhancing the synthesis of the secondary messenger, cyclic AMP, in muscle cells. The cyclic AMP stimulates the action of protein kinase A which phosphorylates and thus activates glycogen phosphorylase. The action of glycogen phosphorylase is to degrade glycogen to glucose 1-phosphate which is converted to glucose 6-phosphate and degraded by glycolysis for energy The acidic nature of the ketone bodies lowers blood ph. This increase in proton concentration is neutralized by the bicarbonate/carbonic acid buffer system present in blood (Section 9.11D and Chemical Connections 9D) The nurse could perhaps suspect dehydration from observing skin characteristics, blood pressure, and pulse. The nurse could also smell the patient s breath for the odor of volatile acetone, one of the ketone bodies. However, ketone bodies are also produced by individuals who are fasting, starving, or on a low-carbohydrate diet. No definitive diagnosis for diabetes can be made until blood and urine tests are completed It is necessary to tag proteins for destruction so that the ones that are no longer needed can be turned over without degrading proteins that are needed Ubiquitin carries out the important function of tagging proteins for destruction. In comparing the sequence of ubiquitin from many species, it has been found that the sequence of ubiquitin is very similar across all species that have ubiquitin Ubiquitin is linked to targeted proteins by forming an amide bond between the carboxyl terminus of ubiquitin (Gly) to a side-chain amino group on a lysine residue of the doomed protein. 303

7 28.50 The protein portion of damaged hemoglobin (globin) is marked for destruction with ubiquitin as described in Problem above. The labeled globin is attacked by a proteosome and degraded to free amino acids When phenylalanine accumulates, it is converted to phenylpyruvate via transamination: CH-NH 3 C= O α-ketoglutarate C=O CH-NH 3 Phenylalanine Phenylpyruvate Glutamate The yellow coloration of jaundice is caused by accumulation of the heme degradation product bilirubin (Figure 28.10) The presence of a high concentration of ketone bodies in the urine of a patient is usually indicative of diabetes. However, before the disease can be confirmed, other, more detailed tests must be completed as fasting or starvation or special dieting can also increase ketone bodies The color changes observed in bruises represent the redox reactions in heme degradation. Black and blue colors are due to congealed blood, green to the biliverdin, and yellow to bilirubin (Figure 28.10) (a) NAD participates in step # 5, the oxidation of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate and step # 12, the oxidation of pyruvate to acetyl CoA. (b) NADH participates in steps # 10 and # 11, reduction of pyruvate to ethanol and lactate, respectively. (c) If one considers the path from glucose to lactate, then there is no net gain of the cofactors. If one considers the path from glucose to pyruvate, then there is a gain of two NADH per glucose. Pyruvate to acetyl CoA would add another two NADH per glucose The production of ethanol from glucose in yeast, called anaerobic glycolysis, is similar to the conversion of glucose to lactate in humans. There is no net production of reduced coenzymes for recycling. Only two moles of ATP are produced in the conversion of one mole of glucose to ethanol. 304

8 28.57 The amino acids Ala, Gly, and Ser are glucogenic; that is, their carbon atoms may be used to synthesize glucose, thus relieving hypoglycemia (low blood sugar) The pentose phosphate pathway is used to produce ribose from glucose. Glucose 6- phosphate entering the pathway is oxidized to form ribulose 5-phosphate and NADPH. Ribulose 5-phosphate can then be converted to ribose 5-phosphate and then to ribose Products of the transamination reaction of Ala and oxaloacetate: CH-NH 3 C=O C=O CH 3 Alanine Oxaloacetate CH 3 Pyruvate CH-NH 3 Aspartate Step 9 in glycolysis, PEP ADP react to form pyruvate ATP, confirms that PEP has more energy than ATP. Otherwise there would not be enough energy to drive the reaction toward formation of the product ATP A number of metabolic processes could occur with the radioactive fatty acid so different molecules should be analyzed. Some of the radioactive fatty acid could be stored in triglycerides in fat tissue; some radioactivity would be in acetyl CoA after β oxidation of the fatty acids; and some would be in carbon dioxide (released from citric acid cycle) Structure of carbamoyl phosphate: an amide an anhydride O O H 2 N-C-O-P-O - O - Carbamoyl phosphate The urea cycle is an energy-consuming pathway as it requires 3 molecules of ATP (four phosphate anhydride bonds) to produce a single urea from carbon dioxide and two ammonium ions. 305

9 28.64 Phosphoenolpyruvate may be converted to pyruvate (pyruvate kinase) and the pyruvate carboxylated to oxaloacetate (a) The β-oxidation of lauric acid (12 carbons) requires 5 turns. (b) Palmitic acid (16 carbons) requires 7 turns Table 28.1 refers to the complete oxidation of glucose to carbon dioxide and water. Glycolysis is only the beginning of the complete process The conversion of pyruvate the acetyl CoA is part of aerobic metabolism. The other two possibilities, conversion to lactate or (in some organisms) to ethanol are anaerobic The conversion of pyruvate to lactate regenerates NAD in anaerobic metabolism. Lactate is a dead end metabolite in the muscle, but it can be sent to the liver in the bloodstream and reconverted to glucose When people are on severely restricted diets, they use up their carbohydrate stores quickly. When a person is metabolizing fats and not carbohydrates, ketone bodies will be produced Amino acids yield citric acid cycle intermediates on degradation, thus providing energy The nitrogen portion of amino acids tends to be excreted, but carbon skeletons are degraded to yield energy or, alternatively, to serve as building blocks for biosynthetic processes Catabolism Oxidative Energy-yielding Anabolism Reductive Energy-requiring Energy is required to form amide bonds. This process is the opposite of the first step in the digestion of proteins In photosynthesis, carbon dioxide and water combine to produce glucose and oxygen. In aerobic metabolism, glucose and oxygen combine to form carbon dioxide and water. On that level, the two processes are the exact opposite of one another. However, photosynthesis requires light energy from the sun, and glucose breakdown yields energy. The overall pathways are also quite different with respect to the intermediate steps All catabolic pathways produce compounds that eventually enter the citric acid cycle. Many intermediates of the citric acid cycle are starting points for biosynthetic pathways. 306

10 28.76 Fats require more oxidation steps to produce carbon dioxide and water than is the case with carbohydrates. The oxidation reactions yield energy in the form of ATP, so fats provide more energy than carbohydrates on a per carbon atom basis Citric acid is an excellent nutrient, since it can be completely degraded to carbon dioxide and water. It enters the mitochondrion easily The phosphate group on glycolytic intermediates is charged. Since glycolysis takes place in the cytoplasm, the charge is an advantage because it will make these compounds less likely to pass through the cell membrane. The mitochondrion is surrounded by a double membrane, so its contents are less likely to leak out. 307