Lecture: Amino Acid catabolism: Nitrogen-The Urea cycle
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1 BIOC 423: Introductory Biochemistry Biochemistry Education Department of Biochemistry & Molecular Biology University of New Mexico Lecture: Amino Acid catabolism: Nitrogen-The Urea cycle OBJECTIVES Describe the role of glutamic acid, pyridoxal phosphate, and glutamate dehydrogenase in the processing of amino acid nitrogen. Draw the biochemically functional part of pyridoxal phosphate in the aldehyde and amine structures. Describe the steps between removal of nitrogen from the amino acid in a peripheral tissue until it is excreted in the urine Compare and contrast the Cori cycle with the Alanine cycle Write the reactions in which ammonium ion is fixed into an organic form. Draw the chemical structures, and name the enzymes and cofactors of the various intermediates in the urea cycle. Describe the subcellular locations of the urea cycle enzymes. OUTLINE Enzymes of Nitrogen Metabolism Glutaminase / Glutamine synthetase Glutamate dehydrogenase Transaminase (Pyridoxyl Phosphate function) Nitrogen Transport Glutamine - Glutamate cycle Alanine Cycle Nitrogen Detoxification (Urea Cycle)
2 LECTURE By this point in the course you should start seeing some similarities in the metabolism of most compounds. The oxidant in these reactions is generally NAD + or FAD. The metabolism of protein presents us with a problem which we have not yet encountered and that problem is nitrogen. When an individual s diet is the Atkins or South Beach diet the problem is significantly magnified because of the nitrogen content. The first step in the metabolism of protein is to convert that protein into amino acids. The method of breaking down proteins depends on the origin of the protein. In the protein is dietary, digestion starts in the stomach with the actions of the pepsin, a relatively non-specific acid protease. Protein digestion is continued in the small intestine with a variety of proteases including trypsin, chymotrypsin and amino and carboxypeptidases. Amino acids are absorbed by the intestinal epithelial cells and transported usually to the liver or other tissue using amino acids for fuel. A second situation in which protein is used for fuel is during starvation. In this case there are two important catabolic products of protein. One destination is for the production of energy but the second equally important destination is for the production of glucose to fuel the brain and RBCs. During starvation, and normal cellular turnover, cellular proteins are tagged with ubiquitin to target them to the proteasome. The proteasome will then degrade the protein to amino acid. Like dietary digestion, cellular digestion liberates amino acids into the blood. The first step in the oxidation of most amino acids is the removal of the nitrogen atom from the remainder of the amino acid carbon skeleton. Herein is the problem. In some chemical forms (ammonium ion) nitrogen is toxic. Consequently, the method for removing nitrogen must end with the nitrogen in a non-toxic form. Also, we cannot move nitrogen from one tissue to the other in the form of ammonium ion. When we consider nitrogen catabolism there are basically two different issues. Movement of nitrogen from peripheral tissue to the liver Detoxification of nitrogen in the liver (urea production). The kidneys ultimately remove waste nitrogen (urea) from the body. Moving nitrogen from peripheral tissue to the liver To shuttle nitrogen from cells using amino acid as fuel to the liver for detoxification requires 4 different enzymes. Glutamine Synthetase: is probably one of the most highly regulated enzymes in the body. The reaction is shown below.
3 We will discuss the regulation of this enzyme when we discuss amino acid synthesis. You can think of gln as the source of synthetic nitrogen. Note that this reaction, which fixes toxic nitrogen in a nontoxic form, is irreversible due to the hydrolysis of ATP. Glutaminase: The second reaction is the reverse of glutamine synthetase. We will reverse this reaction with another enzyme just like we did when we reversed the irreversible steps of glycolysis for gluconeogenesis. The enzyme in this case is a glutamine hydrolyase or glutaminase. Glu/Gln Transport system: Given only the above two enzymes we can create a nitrogen transport system. This system is illustrated in the figure below. Using this system ammonium nitrogen, produced in the tissues, can be detoxified and transported to the liver for detoxification and eventual disposal. The problem with the system is that It costs an ATP for every amino acid. If the amino acid is being catabolized to supply energy needs, this transport system will be at a disadvantage because much of the energy will need to be used simply to transport ammonia nitrogen.
4 Transaminase (aminotransferase) transport system: There is an energy inexpensive alternative to the Glu/Gln transport system. This second system, to which we were introduced last lecture, depends on the transfer of an amino group from any amino acid to an α-keto acid. The two most abundant α-keto acids are pyruvate and α- ketoglutarate; consequently, the transaminase transport system usually involves one of these amino acids. A transaminase reaction that moves an amino group from Val to pyruvate is illustrated in the following reaction: Pyridoxal phosphate (PLP or PyP) is a cofactor for the reaction: The transaminase reaction requires the enzyme as part of it s catalytic cycle to temporarily hold the nitrogen atom. This activity needs the help of the cofactor pyridoxal phosphate (PLP) which is derived from vitamin B6. In this reaction the aldehyde of the PLP initially forms a Schiff base with the ε amino group of a Lys residue at the active site of the enzyme. When the amino acid enters the site the Schiff base is rearranged to involve the PLP and amino acid. The bonding structure of the Schiff base rearranges again and can be hydrolyzed with water leaving the nitrogen atom on PLP (now pyridoxamine). This hydrolysis reaction results in the former amino acid becoming an α-keto acid and it exits the active site of the enzyme. This set of reactions is reversed when another α-keto acid enters the active site. Most biochemistry textbooks illustrate the mechanism of this reaction in detail. The reaction can also be illustrated using a type of kinetic analysis called Cleland Kinetics, shown below. The line at the bottom represents different states or modification to the enzyme during the course of the reaction. The arrows indicate substrates or products entering or leaving the active site of the enzyme.
5 Alanine Glucose cycle or Transaminase Transport System: This system is complex and needs several steps. All of the steps are catalyzed by a transaminase enzyme. None of the steps require ATP. In a peripheral tissue using amino acid for fuel that depends on this system (muscle) the oxidation of amino acid takes place in the matrix of the mitochondria. 1. The available α-keto acid is α-ketoglutarate. The nitrogen is moved from the generic amino acid to α-ketoglutarate generating Glu. 2. Glu is transported into the cytoplasm leaving the CAC deficient in intermediates. 3. To replace CAC intermediates the nitrogen on Glu, via a transamination is moved to pyruvate. Pyruvate is readily available from blood glucose via glycolysis. 4. The Ala generated in the above reaction exits the cell and is transported to the liver. 5. In the liver, nitrogen, via a transaminase, if transferred to α-ketoglutarate forming Glu and pyruvate. Pyruvate is used to make glucose to replace the glucose taken from the blood in the initial steps of this transport process. 6. In order to regenerate α-ketoglutarate from Glu we need a new enzyme. That enzyme is glutamate dehydrogenase. With these two enzymes we can now assemble the Alanine Glucose cycle. You should note the similarity between this cycle (when amino acid is used as fuel) and the Cori cycle we studied previously (when carbohydrate is used as fuel).
6 Ammonium Toxicity: As stated earlier, ammonium ion is toxic. Toxicity can come from interference with reactions involving other cations and in interference with catecholamine transport and metabolism. However, a major part of the toxicity involves the enzyme glutamate dehydrogenase. The reaction as illustrated earlier is shown as irreversible. The reason for this lack of reversibility is the low concentrations of cytoplasmic NH 4 + and NADH. If ammonium levels increase the enzyme uses NADPH (which is abundant in the cell) to catalyze the reverse reaction. This is one of the only enzymes of metabolism that can use either NAD+ or NADPH. If this reverse reaction is forced to proceed, ATP levels rapidly fall. The CAC is compromised because of a lack of intermediates (α-ketoglutarate is being consumed to make glutamate) and glycolysis is compromised because glucose 6- phosphate is being sent to the pentose phosphate pathway to regenerate NADPH.
7 Ammonia is detoxified by converting it to urea Urea is produced from ammonia in five enzymatic steps Carbamoyl phosphate synthetase I: The first amino group to enter the urea cycle is derived from ammonia in liver mitochondria, which joins with respirationproduced carbon dioxide (as bicarbonate) to make carbamoyl phosphate in an ATP-dependent reaction catalyzed by carbamoyl phosphate synthetase I 1. The carbamoyl phosphate now enters the urea cycle proper; it donates its carbamoyl group to ornithine to form citrulline, with the release of Pi (catalyzed by ornithine transcarbamoylase) Note that ornithine plays a role similar to oxaloacetate in the CAC, accepting material at the beginning of the cycle. 2. The citrulline now passes from the mitochondrion to the cytosol. 3. The second amino group is introduced from aspartate (made in the matrix by transamination, transported to the cytosol) by a condensation reaction between the amino group of aspartate and the carbonyl group of citrulline, forming argininosuccinate. The cytosolic reaction, catalyzed by argininosuccinate synthetase, requires ATP. 4. Argininosuccinate is cleaved by argininosuccinate lyase to form free arginine and fumarate. 5. Fumarate enters the matrix to become part of the pool of citric acid cycle intermediates. 6. Arginine is cleaved to yield urea and regenerate ornithine. Arginase is the enzyme, urea is the end product and ornithine is transported back into the matrix ready to start again. The reactions and enzymes of the urea cycle are summarized below. You are responsible for knowing and understanding the urea cycle and should be able to reproduce it on an examination. Using the reaction pathway below you should be able to fill in the structures of arginine, ornithine and citrulline
8 NH 4 + CO ATP CPS 1 H 2 N O C O - P Urea Fumarate Arginine arginosuccinate lyase arginase Ornithine Pi ornithine transcarbamoylase O HO C HC N CH 2 HO C O NH 2 C NH CH 2 CH 2 arginosuccinate synthetase AMP PPi ATP Aspartate Citrulline HO C O CH 2 C NH 2 H Regulation of the urea cycle Long term: The long term regulation of the urea cycle is through gene expression. All five enzymes are synthesized at higher rates in starving animals and in those on very high protein diets. Short-term: allosteric regulation of carbamoyl phosphate synthetase I (CPS-1). CPS-1 is allosterically activated by N-acetylglutamate. The synthesis of N- acetylglutamate requires Glu and acetyl-scoa. The enzyme is activated by high levels of acetyl-scoa and Glu. This makes sense. Amino acids are being oxidized, producing ammonia, when glucose levels are low. The hormone glucacon is mobilizing fatty acid (high acetyl-scoa) and activating protein breakdown (high Glu). As a consequence you have all the reactants necessary to make N-acetylglutamate. Links between the urea cycle and the CAC Asparate-argininosuccinate shunt: In matrix of the mitochondria, Asp (oxaloacetate) and fumarate are common intermediates of both the Urea cycle and the CAC (TCA).
9 Note! It takes energy to make urea! It is important enough to get rid of toxic ammonia that the body spends ATP on the process. 2 ATPs are needed to make carbamoyl phosphate, and one ATP to make argininosuccinate, but this ATP is cleaved to AMP and PPi 2NH HCO ATP + H2O urea + 2 ADP + 4 Pi + AMP + 5H+ However, the urea cycle also causes a net conversion of OAA to fumarate (via aspartate), and fumarate returns to the CAC, where it will generate an NADH as it proceeds to OAA again. Remember NADH equals ATP, so the reaction although expensive is not quite as expensive as gluconeogenesis.
10 PROBLEMS What reaction(s) take(s) place in the mitochondrial matrix? What (is) are the source(s) of the nitrogens in urea? () Free NH 4 + () can be formed directly from A. Glutamic Acid B. Serine C. Fumarate D. Tryptophan Name the α-keto acids that are formed by transamination of alanine, glutamic acid and aspartic acid. Trace the reactions of the α-amino nitrogen atom in serine from the amino acid to the excretion products.
11 Urea production, as a process to eliminate ammonia: A. Is not necessary during periods of starvation because not much protein is taken in via the diet B. Is a catabolic, energy-generating process C. Necessitates transport of carbamoyl phosphate across the mitochondrial membrane D. A and C E. None of the above All of the following statements regarding the urea cycle are true EXCEPT A. The supply of carbamoyl phosphate to the urea cycle enzymes is regulated by N-acetyl-glutamate B. The immediate precursor of urea in the cycle is ornithine C. The formation of carbamoyl phosphate requires the expenditure of two molecules of ATP per molecule of ammonia incorporated D. Fumarate is formed in the urea cycle E. Aspartate used in the urea cycle can arise from oxaloacetate via a transamination reaction Which of the following are true concerning amino acid metabolism? A. Extra amino acids beyond what the cell immediately needs can be incorporated into storage proteins analogous to glycogen and triacylglycerols B. The major site of amino acid degradation in the human is the liver C. The nitrogen atoms of amino acids are recycled via anaplerotic reactions D. Transamination reactions have large negative free energy changes E. All of the above
12 The citric acid cycle and the urea cycle overlap to form what has sometimes been called the "Kreb's bicycle." Which of the following statements describes the interactions between these two metabolic cycles? A. The citric acid intermediate oxaloacetate is converted to aspartate B. Aspartate is used in the urea cycle to make arginosuccinate in the cytoplasm C. Arginosuccinate yields fumarate for the citric acid cycle and arginine for the urea cycle, thus connecting the two cycles D. Fumarate is a citric acid cycle intermediate E. All of the above are true Since the reactions of the urea cycle occur in two different cellular compartments, which urea cycle intermediates must be transported across the inner mitochondrial membrane? A. Arginosuccinate B. Citrulline C. Ornithine D. A and C E. B and C
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