Oxidation of Amino Acids PDF

Contents CONTENTS C H A P T E R 26 Introduction Amino Group Metabolism (=Metabolic Fates of Amino Groups) Nitrogen Excretion...

Contents CONTENTS C H A P T E R 26 Introduction Amino Group Metabolism (=Metabolic Fates of Amino Groups) Nitrogen Excretion The Urea Cycle The “Krebs Bicycle” Energetics of the Urea Cycle Genetic Defects in the Oxidation of Urea cycle Pathways of Amino Acid Catabolism Amino Acids Inborn Errors of Amino Acid Catabolism Alkaptonuria Albinism Phenylketonuria Maple Syrup Urine Disease INTRODUCTION A mino acids are the final class of biomolecules whose oxidation makes a significant contribution towards generation of metabolic energy. The fraction of metabolic energy derived from amino acids varies greatly with the type of organism and with the metabolic situation in which an organism finds itself. Carnivores may derive up to 90% of their energy requirements from amino acid oxidation. Herbivores, on the other hand, may obtain only a small fraction of their energy needs from this source. Most microorganisms can scavenge amino acids from their environment if they are available; these can be oxidized as fuel when the metabolic conditions so demand. Photosynthetic plants, on the contrary, rarely oxidize amino acids to provide energy. Instead they convert CO2 and H2O into the carbohydrate glucose that is used almost exclusively as an energy source. Amino acid metabolism does occur in plants, but it is generally concerned with the production of metabolites for other biosynthetic pathways. In animals, the amino acids can be oxidatively degraded in 3 different metabolic conditions: (a) During normal protein synthesis: Some of the Most of the ureotelic animals including amino acids released during protein breakdown man and shark secrete the excess will undergo oxidative degradation. ammonia as urea. (b) During protein-rich diet: The surplus may be catabolized and amino acids cannot be stored. (c) During starvation or in diabetes mellitus: Body proteins are used as fuel.  Contents 642 FUNDAMENTALS OF BIOCHEMISTRY Under these different circumstances, amino acids lose their amino groups, and the resulting α-keto acids may undergo oxidation to produce CO2 and H2O. Pathways leading to amino acid degradation are quite alike in most organisms. As is the case for sugar and fatty acid catabolic pathways, the processes of amino acid degradation converge on the central catabolic pathways for carbon metabolism. However, one major factor distinguishes amino acid degradation from the catabolic processes described till now, i.e., every amino acid contains an amino group. As such every degradative pathway passes through a key step in which α-amino group is separated from the carbon skeleton and shunted into the specialized pathways for amino group metabolism (Fig. 26–1). This biochemical fork in the road is the point around which this chapter is centered. Amino acids are needed for the synthesis of proteins and other biomolecules. The excess amount of amino acids, in contrast with glucose and fatty acids, cannot be stored; nor are they excreted. Rather surplus amino acids are used as metabolic fuel. The α-amino group of the amino acids is removed and the resulting carbon skeleton is converted into a major metabolic intermediate. Most of the amino groups of surplus amino acids are converted into urea whereas their carbon skeletons are transferred to acetyl-CoA, acetoacetyl-CoA, pyruvate, or one of the intermediates of the citric acid cycle. It follows that amino acids can form glucose, fatty acids and ketone bodies. The major site of amino acid degradation in mammals is the liver. The fate of the α-amino groups will be dealt with first, followed by that of the carbon skeleton. Fig. 26–1. An overview of the catabolism of amino acids The thick bifurcated arrow indicates the separate paths taken by the carbon skeleton and the amino groups. AMINO GROUP METABOLISM (= METABOLIC FATES OF AMINO GROUPS) Nitrogen is the fourth most important contributor (after carbon, hydrogen and oxygen) to the mass of living cells. Atmospheric nitrogen is abundant but is too inert for use in most biochemical processes. Only a few microorganisms have the capacity to convert into biologically useful forms (such as NH3) and as such amino groups are used with great economy in biological systems. The catabolism of ammonia and amino groups in vertebrates is presented in Fig. 26–2. Amino acids derived from dietary proteins are the source of most amino groups. Most of the amino groups  Contents OXIDATION OF AMINO ACIDS 643 are metabolized in the liver. Some of the ammonia that is generated is recycled and used in a variety of biosynthetic processes; the excess is either excreted directly or converted to uric acid or urea for excretion. Excess ammonia generated in extrahepatic (i.e., other than liver) tissues is transported to the liver in the form of amino groups, as described below, for conversion to the appropriate excreted form. The coenzyme pyridoxal phosphate (PLP or PALP) participates in these reactions. Two amino acids, glutamate and its amide form glutamine, play crucial roles in these pathways. Amino groups from amino acids are generally first transferred to a α-ketoglutarate in the cytosol of liver cells (= hepatocytes) to form glutamate. Glutamate is then transported into the mitochondria. In muscle, excess amino groups are generally transferred to pyruvate to form alanine. Alanine is another important molecule in the transport of amino groups, transporting them from muscle to the liver. LIVER Protein – COO COO– COO– — — — — — — + + H3N—C—H H N—C—H C O 3 R R R Amino acids a-keto acids Amino acids from ingested COO– COO– — — — — — — — — proteins + C O H3N— C H CH2 CH2 CH2 CH2 COO– COO– a-ketoglutarate Glutamate COO– — — — — NH +4 + H3N— C—H CH2 – – CH2 COO COO — — — — Alanine + Glutamine H3N— C H C O C from — from muscle muscle O NH2 and other CH3 CH3 tissue Alanine Pyruvate Glutamine Urea or uric acid Fig. 26–2. An overview of amino group catabolism in the vertebrate liver + Note that the excess NH 4 is excreted as urea or uric acid A. Transfer of Amino Groups to Glutamate The α-amino groups of the 20 l-amino acids, commonly found in proteins, are removed during the oxidative degradation of the amino acids. If not reused for the synthesis of new amino acids, these amino groups are channelled into a single excretory product (Fig. 26–3). Many aquatic organisms + simply release ammonia as NH4 into the surrounding medium. Most terrestrial vertebrates first convert ammonia into either urea (e.g., humans, other mammals and adult amphibians) or uric acid (e.g., reptiles, birds).  Contents 644 FUNDAMENTALS OF BIOCHEMISTRY Fig. 26.–3. Excretory forms of amino group nitrogen in different forms of life Note that the C atoms of urea and uric acid are at a high oxidation state. And the organism discards carbon only when it has obtained most of its available energy of oxidation. The first step in the catabolism of most of the L-amino acids is the removal of the α-amino group (i.e., transamination) by a group of enzymes called aminotransferases (= transaminases). In these reactions, the α-amino group is transferred to the α-carbon atom of α-ketoglutarate, leaving behind the corresponding α-keto acid analogue of the amino acid (Fig. 26–4). There is no net deamination in such reactions because the α-ketoglutarate becomes aminated as the α-amino acid is deaminated. The effect of transamination reactions is to collect the amino groups from many different amino acids in the form of only one, namely L-glutamate. Cells contain several different aminotransferases, many of which are specific for α ketoglutarate as the amino group acceptor. The amino-transferases differ in their specificity for the other substrate (i.e., the L-amino acid that donates the amino group) and are named for the amino group donor. The reactions catalyzed by the aminotransferases are freely reversible, having an equilibrium constant of about 1.0 (∆G°′ j 0 kJ/mol)). COO– COO– — — — — — — — — + C O COO– H3N— C—H COO– — — — — + PLP CH2 + H3N—C—H CH2 + C O aminotransferase CH2 R CH2 R COO– COO– a-ketoglutarate L-amino acid L-glutamate a-keto acid Fig. 26–4. The transamination (or the aminotransferase) reaction Note that in many aminotransferase reactions, α-ketoglutarate is the amino group acceptor. All aminotransferases have pyridoxal phosphate (PLP or PALP) as cofactor. All aminotransferases possess a common prosthetic group and have a common reaction mechanism. The prosthetic group is pyridoxal phosphate, which is the coenzyme form of pyridoxine or vitamin B6. Besides acting as a cofactor in the glycogen phosphorylase reaction, PALP also participates in the metabolism of molecules containing amino groups. PALP functions as an intermediate carrier of amino groups at the active site of aminotransferases. It undergoes reversible transformations between its aldehyde form (pyridoxal phosphate, PALP) which can accept an amino group, and its aminated form (pyridoxamine phosphate, PAMP) which can donate its amino group to an α-keto acid (Fig. 26–5a). PALP is generally bound covalently to the enzyme's active site through an imine (Schiff- base) linkage to the ε-amino group of a lysine (Lys) residue (Fig. 26–5b).  Contents OXIDATION OF AMINO ACIDS 647 3. The product Schiff base is then hydrolyzed. Fig. 26–7. Versatility of the pyridoxal phosphate enzymes PLP enzymes labilize one of the 3 bonds at the α-carbon atom of an amino acid substrate. For example, bond (a) is labilized by transaminases, bond (b) by decarboxylases, and bond (c) by aldolases. PLP enzymes also catalyze reactions at the β and γ carbon atoms of amino acids. B. Removal of Amino Groups from Glutamate Glutamate is transported from the cytosol to the mitochondria, where it undergoes oxidative + + deamination catalyzed by L-glutamate dehydrogenase (GD). GD can employ NAD or NADP as cofactor and is allosterically regulated by GTP and ADP. The combined action of the aminotransferases and GD is referred to as transdeamination. A few amino acids bypass the transdeamination pathway and undergo direct oxidative deamination. Glutamate dehydrogenase (Mr 330,000) is a complex allosteric enzyme and is present only in the mitochondrial matrix. The enzyme molecule consists of 6 identical subunits. It is influenced by the positive modulator ADP and by the negative modulator GTP. Whenever a hepatocyte needs fuel for the citric acid cycle, GD activity increases, making α-ketoglutarate available for the citric acid + cycle and releasing NH4 for excretion. On the contrary, whenever GTP accumulates in the mitochondria due to high activity of the citric acid cycle, oxidative deamination of glutamate is inhibited. C. Transport of Ammonia Through Glutamine to Liver In most animals excess ammonia, which is toxic to the animal tissues, is converted into a nontoxic compound before export from extrahepatic tissues into the blood and thence to the liver or kidneys. This transport function is accomplished by L-glutamine and not by glutamate which is so critical to amino group metabolism. In many tissues, ammonia enzymatically combines with glutamate to yield glutamine by the action of glutamine synthetase. The reaction, which requires ATP, takes place in 2 steps: I. First step: glutamate and ATP react to form ADP and γ-glutamyl phosphate  Contents 648 FUNDAMENTALS OF BIOCHEMISTRY II. Second step: γ-glutamyl phosphate reacts with ammonia to produce glutamine and inorganic phosphate. Glutamine is a nontoxic, neutral compound that can readily pass through cell membranes, whereas glutamate which bears a negative net charge, cannot. In most terrestrial animals, glutamine is carried through blood to the liver. The amide nitrogen of glutamine, like the amino group of glutamate, is released as ammonia only within liver mitochondria, where the enzyme glutaminase converts glutamine to glutamate and NH4+. Glutamine is, thus, a major transport form of ammonia. It is normally present in blood in much higher concentrations than other amino acids. D. Transport of Ammonia from Muscle to Liver Through Alanine (= Glucose—Alanine Cycle) Alanine also plays a special role in transporting amino groups to the liver in a nontoxic form by glucose— alanine cycle (Fig. 26–8). In muscle and certain other tissues that degrade amino acids for fuel, amino groups are collected in glutamate by transamination (refer Fig. 26–2). Glutamate may then either be converted to glutamine for transport to the liver, or it may transfer its α-amino group to pyruvate, a readily-available product of muscle glycolysis, by the action of alanine aminotransferase. Alanine passes into the blood and is carried to the liver. As in the case of glutamine, excess nitrogen carried to the liver as alanine is ultimately delivered as ammonia in the mitochondria. During a reversal of this alanine aminotransferase reaction, alanine transfers its amino group to α-ketoglutarate, forming glutamate in the cytosol. Some of this glutamate is transported into the mitochondria and acted upon + by glutamate dehydrogenase, releasing NH4. Alternatively, transamination with oxaloacetate moves amino groups from glutamate to aspartate, another nitrogen donor in urea synthesis. Vigorously contracting skeletal muscles operate anaerobically and produce not only ammonia from protein degradation but also large amounts of pyruvate from glycolysis. Both these products  Contents OXIDATION OF AMINO ACIDS 649 must find their way to the liver— ammonia for its conversion into urea for excretion and pyruvate for its Muscle protein incorporation into glucose and subsequent return to the muscles. The animals thus solve two problems with Amino acids one cycle (i.e., glucose—alanine cycle): (a) They move the carbon atoms of + NH4 pyruvate, as well as excess Glucose Pyruvate ammonia from muscle to liver Glycolysis Glutamate as alanine. Alanine (b) In the liver, alanine yields aminotransferase pyruvate, the starting material a-ketoglutarate for gluconeogenesis and Alanine + releases NH 4 for urea synthesis. Blood Blood The energetic burden of gluconeogenesis glucose alanine is, thus, imposed on the liver rather than on the muscle, so that the available ATP Alanine in the muscle can be devoted to muscle a-ketoglutarate contraction. Alanine Ammonia is toxic to animals and aminotransferase causes mental disorders, retarded Glutamate development and, in high amounts, coma Glucose Gluconeo- Pyruvate and death. The protonated form of genesis NH4 ammonia (ammonium ion) is a weak Urea Cycle acid, and the unprotonated form is a Urea strong base: + + NH4 Ö NH3 + H Most of the ammonia generated in + catabolic process is present as NH4 at neutral pH. Although most of the Fig. 26–8. The glucose—alanine cycle reactions that produce ammonia yield Alanine serves as a carrier of ammonia equivalents and of the + carbon skeleton of pyruvate from muscle to liver. The ammonia NH 4 a few reactions produce NH 3. Excessive amounts of ammonia cause is excreted, and the pyruvate is used to produce glucose, which is returned to the muscle. alkalization of cellular fluids, which has (Adapted from Lehninger, Nelson and Cox, 1993) multiple effects on cellular metabolism. NITROGEN EXCRETION The amino nitrogen is excreted in 3 different forms in various types of life-forms (Fig. 26–3). (a) as ammonia in most aquatic vertebrates, bony fishes and amphibian larvae (ammonotelic animals) (b) as urea in many terrestrial vertebrates including man, also sharks and adult amphibian (ureotelic animals) (c) as uric acid in reptiles and birds (uricotelic animals) Plants, however, recycle virtually all amino groups, and nitrogen excretion occurs only under highly unusual circumstances. There is no general pathway for nitrogen excretion in plants.  Contents 650 FUNDAMENTALS OF BIOCHEMISTRY In ureotelic organisms, the ammonia in the mitochondria of liver cells (= hepatocytes) is converted to urea via the urea cycle. This pathway was discovered by Hans Adolf Krebs and a medical student associate, Kurt Henseleit in 1932, five years before the elucidation of the citric acid cycle. In fact, the urea cycle was the first cyclic metabolic pathway to be discovered. They found that the rate of urea formation from ammonia was greatly accelerated by adding any one of the 3 α-amino acids: ornithine, citrulline or arginine. Their structure suggests that they might be related in a sequence. This finding led them to deduce that a cyclic process occurs (Fig. 26–9), in which ornithine plays a role resembling that of oxaloacetate in the citric acid cycle. A mole of ornithine combines with one mole of ammonia and one of CO2 to form citrulline. A second amino group is added to citrulline to form arginine. Arginine is then hydrolyzed to yield urea with concomitant regeneration of ornithine. Ureotelic animals have large amounts of the enzyme arginase in the liver. This enzyme catalyzes the irreversible hydrolysis of arginine to urea and ornithine. The ornithine is then ready for the next turn of the urea cycle. The urea is passed via the bloodstream to the kidneys and is excreted into the urine. Fig. 26–9. The urea cycle Note that ornithine and citrulline can serve as successive precursors of arginine. Ornithine and citrulline are nonstandard amino acids that are not found in proteins. A. Production of Urea from Ammonia: The Urea Cycle A moderately-active man consuming about 300 g of carbohydrate, 100 g of fat and 100 g of protein daily must excrete about 16.5 g of nitrogen daily. Ninety-five per cent is eliminated by the kidneys and the remaining 5% in the faeces. The major pathway of N2 excretion in humans is as urea which is synthesized in the liver, released into the blood, and cleared by the kidney. In humans eating an occidental diet, urea constitutes 80-90% of the nitrogen excreted. The urea cycle spans two cellular compartments (Figs 26–9 and 26–10). It begins inside the mitochondria of liver cells (= hepatocytes), but 3 of the steps occur in the cytosol. The first amino group to enter the urea cycle is derived from ammonia inside the mitochondria, arising by multiple pathways described above. Whatever its source, + – the NH4 generated in liver mitochondria is immediately used, together with HCO 3 produced by mitochondrial respiration, to form carbamoyl phosphate in the matrix. This ATP-dependent reaction is catalysed by carbamoyl phosphate synthetase I, a regulatory enzyme present in liver mitochondria of all ureotelic organisms including man. In bacteria, glutamine rather than ammonia serves as a substrate for carbamoyl phosphate synthesis.  NH3 — + – NH3 HN CH—NH—(CH2)3—CH—COO — – O R—CH—COO Amino acids O P—O— Transamination to O NH2 + — a-ketoglutarate PPi + NH3 N N Alanine (from CH2 — NH3 Glutamate O N N (a) extrahepatic CH3—CH —COO– ATP — – – 2a — — — — — — OOC—CH2—CH2—CH—COO tissues) H H H H Citrullyl-AMP — — CYTOSOL + OH OH intermediate NH3 Citrulline + O Aspartate — – NH3 — C—CH2—CH2—CH—COO + 2b —OCC—CH —CH—COO– H2N — Glutamine O NH3 2 — – AMP H2N—C—NH—(CH2)3—CH—COO Glutaminase 2 ATP Citrulline Argininosuccinate O 2ADP + Pi – + + – Pi – – HCO3 COO NH2 NH3 — — OOC—CH2—C—COO 1 – Carbamoyl – NH4+ OOC—CH2—CH—NH—C—NH—(CH2)3—CH—COO Oxaloacetate Glutamate Carbamoyl phosphate Aspartate Glutamate phosphate O O UREA 3 Fumarate aminotransferase dehydrogenase synthetase I – – a-keto- – CYCLE OOC—CH CH—COO Aspartate H2N—C—O—P—O glutarate Arginine To CAC — + Ornithine + NH3 O— + NH 2 NH3 — – – MITOCHONDRIAL — OOC—CH2—CH—COO MATRIX – Ornithine H2N—C—NH—(CH2)3—CH—COO + (b) 4 H 2O NH 3 — + – H3N—(CH2)3—CH—COO To step 2b UREA of the Urea Cycle O H2N—C—NH2 OXIDATION OF AMINO ACIDS Fig. 26–10. The urea cycle and the reactions that feed amino groups into it Note that one of the nitrogen atoms of the urea synthesized by this pathway is transferred from an amino acid, aspartate. The other nitrogen atom is derived from NH4+ 651 and the carbon and the carbon atom comes from CO2. Ornithine, a nonprotein amino acid, is the carrier of these carbon and nitrogen atoms. Also note that the enzymes catalyzing these reactions are distributed between the mitochondrial matrix and the cytosol. Contents  Contents 652 FUNDAMENTALS OF BIOCHEMISTRY The carbamoyl phosphate now enters the urea cycle, which itself consists of 4 enzymatic steps. These are: Step 1: Synthesis of citrulline Carbamoyl phosphate has a high transfer potential because of its anhydride bond. It, therefore, donates its carbamoyl group to ornithine to form citrulline and releases inorganic phosphate. The reaction is catalyzed by L-ornithine transcarbamoylase of liver mitochondria. The citrulline is released from the mitochondrion into the cytosol. Step 2: Synthesis of argininosuccinate The second amino group is introduced from aspartate (produced in the mitochondria by transamination and transported to the cytosol) by a condensation reaction between the amino group of aspartate and the ureido (= carbonyl) group of citrulline to form argininosuccinate. The reaction is catalyzed by argininosuccinate synthetase of the cytosol. It requires ATP which cleaves into AMP and pyrophosphate and proceeds through a citrullyl-AMP intermediate. Step 3: Cleavage of argininosuccinate to arginine and fumarate Argininosuccinate is then reversibly cleaved by argininosuccinate lyase (= argininosuccinase), a cold-labile enzyme of mammalian liver and kidney tissues, to form free arginine and fumarate, which enters the pool of citric acid cycle intermediates. These two reactions, which transfer the amino group of aspartate to form arginine, preserve the carbon skeleton of aspartate in the form of fumarate. Step 4: Cleavage of arginine to ornithine and urea The arginine so produced is cleaved by the cytosolic enzyme arginase, present in the livers of all ureotelic organisms, to yield urea and ornithine. Smaller quantities of arginase also occur in renal tissue, brain, mammary gland, testes and skin. Ornithine is, thus, regenerated and can be transported into the mitochondrion to initiate another round of the urea cycle. In the urea cycle, mitochondrial and cytosolic enzymes appear to be clustered and not randomly distributed within cellular compartments. The citrulline transported out of the mitochondria is not diluted into the general pool of metabolites in the cytosol. Instead, each mole of citrulline is passed directly into the active site of a molecule of argininosuccinate synthetase. This channeling continues for argininosuccinate, arginine and ornithine. Only the urea is released into the general pool within the cytosol. Thus, the compartmentation of the urea cycle and its associated reactions is noteworthy. + The formation of NH4 by glutamate dehydrogenase, its incorporation into carbamoyl phosphate, and the subsequent synthesis of citrulline occur in the mitochondrial matrix. In contrast, the next 3 reactions of the urea cycle, which lead to the formation of urea, takes place in the cytosol. A perusal of the urea cycle reveals that of the 6 amino acids involved in urea synthesis, one, N- acetylglutamate functions as an enzyme activator rather than as an intermediate. The remaining 5 amino acids — aspartate, arginine, ornithine, citrulline and argininosuccinate — all function as carriers of atoms which ultimately become urea. Two (aspartate and arginine) occur in proteins, while the remaining three (ornithine, citrulline and argininosuccinate) do not. The major metabolic roles of these latter 3 amino acids in mammals is urea synthesis. Note that urea formation is, in part, a cyclical process. The ornithine used in Step 1 is regenerated in Step 4. There is thus no net loss or gain of ornithine, citrulline, argininosuccinate or arginine during urea synthesis; however, ammonia, CO2, ATP and aspartate are consumed. B. The “Krebs Bicycle” The citric acid cycle and urea cycle both are linked together (Fig. 26-11). The fumarate produced  Contents OXIDATION OF AMINO ACIDS 653 in the cytosol by argininosuccinate lyase reaction is also an intermediate of the citric acid cycle. Fumarate enters the citric acid cycle in the the mitochondrion where it is first hydrated to malate by fumarase which, in turn, is oxidized to oxaloacetate by malate dehydrogenase. The oxaloacetate accepts an amino group from glutamate by transamination, and the aspartate thus formed leaves the mitochondrion and donates its amino group to the urea cycle in the argininosuccinate synthetase reaction; the other product of this transamination is α-ketoglutarate, another intermediate of the citric acid cycle. Because the reactions of the urea and citric acid cycles are inextricably interwined, cumulatively they have been called “Krebs bicycle”. C. Energetics of the Urea Cycle The urea cycle is energetically expensive. It brings together two amino groups and HCO3– to form a mole of urea which diffuses from the liver into the bloodstream. The overall reaction of the urea cycle is: Fig. 26–11. The Krebs bicycle It is composed of the urea cycle on the right, which meshes with the aspartate—argininosuccinate shunt of the citric acid cycle on the left. Note that the urea cycle, the citric acid cycle and the transamination of oxaloacetate are linked by fumarate and aspartate. Intermediates in the citric acid cycle are boxed 2NH4 + HCO3 + 3ATP + H2O → Urea + 2ADP + 4Pi + AMP + 5H + – 4– 3– 2– 2– + The synthesis of one mole of urea requires four high-energy phosphate groups. Two ATPs are required to make carbamoyl phosphate, and one ATP is required to make argininosuccinate. In the latter reaction, Carbamoyl phosphate is the official nomenclature for the –CO– however, the ATP undergoes a pyrophosphate cleavage to NH 2 group, but carbamyl is AMP and pyrophosphate which may be hydrolyzed to yield sometimes used. two Pi. D. Genetic Defects in the Urea Cycle The synthesis of urea in the liver is the major pathway of the removal of NH4+. A blockage of carbamoyl phosphate synthesis or any of the 4 steps of the urea cycle has serious consequences because there is + no alternative pathway for the synthesis of urea. They all lead to an elevated level of NH4 in the blood (hyperammonemia). Some of these genetic defects become evident a day or two after birth, when the afflicted infant becomes lethargic and vomits periodically. Coma and irreversible brain damage + may ensue. The high levels of NH4 are toxic probably because elevated levels of glutamine, formed + from NH4 and glutamate, lead directly to brain damage:  Contents 654 FUNDAMENTALS OF BIOCHEMISTRY NH4+ NH4+ a-ketoglutarate Glutamate Glutamine Glutamate Glutamate dehydraherase synthase People cannot tolerate a protein-rich diet because amino acids ingested in excess of the minimum daily requirements for protein synthesis would be deaminated in the liver, producing free ammonia in the blood. As we have seen, ammonia is toxic to humans. Human beings are incapable of synthesizing half of the 20 amino acids, and these essential amino acids (Table 26–1) must be provided in the diet. Table 26-1. Nonessential and essential amino acids for humans Nonessential amino acids Essential amino acids Name Abbreviation Name Abbreviation Alanine Ala Arginine Arg Asparagine Asn Histidine His Aspartate Asp Isoleucine Ile Cysteine Cys Leucine Leu Glutamate Glu Lysine Lys Glutamine Gln Methionine Met Glycine Gly Phenylalanine Phe Proline Pro Threonine Thr Serine Ser Tryptophan Trp Tyrosine Tyr Valine Val Patients with defects in the urea cycle are often treated by substituting in the diet the α-keto acid analogues of the essential amino acids, which are the indispensable parts of the amino acids. The α- keto acid analogues can then accept amino groups from excess nonessential amino acids by aminotransferase action (Fig. 26–12). Fig. 26–12. Transamination reaction for the synthesis of essential amino acids from the corresponding α-keto acids The dietary requirement for essential amino acids can, hence, be met by the α-keto acid skeletons.[RE and RN represent R groups of the essential and nonessential amino acids, respectively]. PATHWAYS OF AMINO ACID CATABOLISM Twenty standard amino acids, with a variety of carbon skeletons, go into the composition of proteins. As such, there are 20 different pathways for amino acid degradation. All these pathways taken together, in human beings, account for only 10-15% of the body’s energy production. Therefore, the individual amino acid degradative pathways are not nearly as active as glycolysis and fatty acid oxidation. Moreover, the activity of the catabolic pathways varies greatly from one amino acid to the other. For this reason, these will not be examined in detail. The 20 catabolic pathways converge to form only 5 products, all of which enter the citric acid cycle. From here, the carbons can be diverted to gluconeogenesis or ketogenesis, or they can be completely oxidized to CO2 and H2O (Fig. 26–13).  Contents OXIDATION OF AMINO ACIDS 655 All or part of the carbon skeletons of ten of the amino acids are finally broken down to yield acetyl-CoA. Five amino acids are converted into α-ketoglutarate, four into succinyl-CoA, two into fumarate and two into oxaloacetate. The individual pathways for the 20 amino acids will be summarized by means of flow diagrams, each leading to a specific point of entry into the citric acid cycle. Note that some amino acids appear more than once which means that their carbon skeleton is broken down into different fragments and each of which enters the citric acid cycle at a different point. The strategy of amino acid degradation is to form major metabolic intermediates that can be converted into glucose or be oxidized by the citric acid cycle. In fact, the carbon skeletons of the diverse set of 20 amino acids are funneled into only 7 molecules (refer Fig. 26–13), viz., pyruvate, acetyl-CoA, acetoacetyl-CoA, α-ketoglutarate, succinyl-CoA, fumarate and oxaloacetate. Thus, here we have an example of the remarkable economy of metabolic conversions. Fig. 26–13. Entry points of standard amino acids into the citric acid cycle This scheme represents the major catabolic pathways in vertebrates, but there are minor variations from one organism to another. Some amino acids are listed more than once, reflecting the fact that different parts of their carbon skeletons have different fates. The 7 molecules into which the carbon skeletons of the diverse sets of 20 amino acids are funneled are shown within thick-lined boxes. Based on their catabolic products, amino acids are classified as glucogenic or ketogenic (Table 26–2): (a) those amino acids that generate precursors of glucose, e.g., pyruvate or citric acid cycle intermediate (i.e., α-ketoglutarate, succinyl-CoA, fumarate or oxaloacetate), are referred to as glucogenic. Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Met, Pro, Ser, Thr and Val belong to this category. Net synthesis of glucose from these amino acids is feasible because these glucose precursors can be converted into phosphoenolpyruvate (PEP) and then into glucose. (b) those amino acids that are degraded to acetyl-CoA or acetoacetyl-CoA are termed as ketogenic because they give rise to ketone bodies. Their ability to form ketones is particularly evident  Contents 656 FUNDAMENTALS OF BIOCHEMISTRY in untreated diabetes mellitus, in which large amounts of ketones are produced by the liver, not only from fatty acids but from the ketogenic amino acids. Leucine (Leu) exclusively belongs to this category. The remaining 5 amino acids (Ile, Lys, Phe, Trp and Tyr) are both glucogenic and ketogenic. Some of their carbon atoms emerge in acetyl-CoA or acetoacetyl-CoA, whereas others appear in potential precursors of glucose. Thus, the division between glucogenic and ketogenic amino acids is not sharp. Whether an amino acid is regarded as being glucogenic, ketogenic or both depends partly on the eye of the beholder. Table 26–2. Classification of amino acids as glucogenic or ketogenic Glucogenic Ketogenic Glucogenic and ketogenic Alanine Glycine Leucine Isoleucine Arginine Histidine Lysine Asparagine Methionine Phenylalanine Aspartate Proline Tryptophan Cysteine Serine Tyrosine Glutamate Threonine Glutamine Valine Table 26–3 lists the catabolic end products of the 20 protein (or standard) amino acids. It may be seen that nearly all of the amino acids yield on breakdown either an intermediate of the citric acid cycle, pyruvate or acetyl-CoA. Five amino acids (Leu, Lys, Phe, Trp and Tyr) are exception to this since they give rise to acetoacetic acid. Since, however, this compound also forms acetyl-CoA, carbon skeletons of all of the amino acids are ultimately oxidized via the citric acid cycle. Table 26–3. End products of amino acid metabolism Amino acid(s) End product Alanine, Cysteine (Cystine), Glycine, Serine and Threonine (2) Pyruvic acid Leucine (2) Acetyl-CoA Leucine (4), Lysine (4), Phenylalanine (4), Tryptophan (4) and Tyrosine (4) Acetoacetic acid (or its CoA-ester) Arginine (5), Glutamic acid, Glutamine, Histidine (5) and Proline α-ketoglutaric acid Isoleucine (4), Methionine and Valine (4) Succinyl-CoA Phenylalanine (4) and Tyrosine (4) Fumarate Asparagine and Aspartic acid Oxaloacetic acid * The figures in parentheses specify the number of carbon atoms in the amino acid that are actually converted to the end product listed. A. Ten Amino Acids are Degraded to Acetyl-CoA. The carbon skeletons of 10 amino acids yield acetyl-CoA, which enters the citric acid cycle directly. Five of the ten are degraded to acetyl-CoA via pyruvate. Alanine, cysteine, glycine, serine and tryptophan belong to this category. In some organisms, threonine is also degraded to form acetyl- CoA as shown in Fig. 26–14; in men, it is degraded to succinyl-CoA, as described later. The other five amino acids are converted into acetyl-CoA and/or acetoacetyl-CoA which is then cleaved to form acetyl-CoA. Leucine, lysine, phenylalanine, tryptophan and tyrosine come under this category.