Nitrogen MetabolismFigure 26-67X-Ray structure of the A. vinelandii nitrogenase in complex with ADP · AlF4 -.(a) reduced P-cluster.Figure 26-69The flow of electrons in the nitrogenase-catalyzed reduction of N2.The Nitrogen CycleAmino Acid CatabolismTransaminationPLP role in transaminationBond orientation in a PLP–amino acid Schiff base. (a) The -orbital framework of a PLP–amino acid Schiff base.Figure 26-4The oxidative deamination of glutamate by glutamate dehydrogenase in the mitochondria .Figure 26-3The glucose–alanine cycle.The Urea CycleFigure 26-7The urea cycle.Figure 26-7 The urea cycle.Degradation of amino acid carbon skeletons to one of seven common metabolic intermediates.Some catabolic pathways are very simpleSome are idiosyncratic: Serine dehydrataseFigure 26-14The reactions catalyzed by the glycine cleavage system, a multienzyme complex.Most are long and complicatedSee, I told you!Arg, Glu, Gln, His, and Pro to -ketoglutarate.Folic acid and S-adenosyl methionine are important cofactors in amino acid metabolism.Figure 26-47Tetrahydrofolate (THF).Figure 26-48The two-stage reduction of folate to THF.Table 26-1Oxidation Levels of C1 Groups Carried by THF.Figure 26-49Interconversion of the C1 units carried by THF.Amino acid decarboxylation can produce potent biomoleculesGlutamine Synthetase is the Main Regulatory Enzyme of Nitrogen MetabolismGlutamine synthetase is regulated allosterically.Glutamine synthetase is also regulated by covalent modification – via adenylationTable 26-2Essential and Nonessential Amino Acids in Humans.Synthesis of Serine and Glycine from 3PGFigure 26-54The syntheses of alanine, aspartate, asparagine, glutamate, and glutamine.Figure 26-57The biosynthesis of the “glutamate family” of amino acids: arginine, ornithine, and proline.Figure 26-62The biosynthesis of chorismate, the aromatic amino acid precursor.Figure 26-63The biosynthesis of phenylalanine, tryptophan, and tyrosine from chorismate.Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.Last TimeVoet Biochemistry 3e© 2004 John Wiley & Sons, Inc.Nitrogen MetabolismNitrogen is a biologically important element, behind C, H, and O in mass. It is a key component of proteins and nucleic acids, vitamins, and energy transfer moleculesAir is 80% N2, but the triple bond is very stable and the cost of crossing the transition state barriers is high. Only a few diazotrophic bacteria can reduce N2to NH3; for example, Rhizobium live in legume plant root nodules and “fix” nitrogen.The overall reaction, catalyzed by nitrogenase, is:N2+ 8H++ 16 ATP + 8e-Æ 2NH3+ H2+ 16 ADP + 16 PiInterestingly, the reduction of N2+ 3 H2Æ 2 NH3is favorable: ∆G0’ = -34 KJ (not as good as burning H2in O2, but OK). The problem is the transition state barrier.Electrons for nitrogenase must come from ETS or photosynthesis.NH3 from nitrogenase can be oxidized by soil bacteria to nitrite or nitrate, and must be re-reduced by reductases for use in biological molecules.Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.Figure 26-67 X-Ray structure of the A. vinelandiinitrogenase in complex with ADP · AlF4 −.Page 1046N2+ 8 H++ 8e-+ 16 ATP --> 2 NH3+ H2+ 16 ADP + 16 PiN=N Æ H-N=N-H Æ H2N-NH2Æ 2 NH3(γ2)-β−α−α−β-(γ2)Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.(a) reduced P-cluster.Page 1047Figure 26-68a The prosthetic groups of the nitrogenase MoFe-protein.(b) 2-electron-oxidized(c) The A. vinelandii FeMo-cofactor.[4Fe-3S][3Fe-3S-Mo][4Fe-3S] [4Fe-3S][S][N]Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.Figure 26-69 The flow of electrons in the nitrogenase-catalyzed reduction of N2.Page 1048N2+ 8 H++ 8e-+ 16 ATP --> 2 NH3+ H2+ 16 ADP + 16 Pi2 ATP / e-Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.The Nitrogen CycleSoil anaerobes use nitrate as e- acceptor in metabolism2NH4++ 3O2Æ 4H++ 2 NO2-; ∆G0’= -550 KJ = -46KJ/e-2NO2-+ O2Æ 2NO3-; ∆G0’= -148 KJ = -37KJ/e-Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.Amino Acid CatabolismIngested protein must be catabolized. In addition, cellular proteins all turn over; the half life for PEP carboxykinase is 5 hours while hemeoglobin is 2800 hours. Most degraded proteins, amino acids, are salvaged and reused. However, we destroy, and must replace, about 50 – 100 grams of “protein” per day.The catabolism of amino acids can be broken into 2 main areas:1. Gathering and removal of ammonia (transamination, and deamination)2. The breakdown of the carbon skeleton. (Can be used for energy; lions exist on protein and rarely eat potatoes.)Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.TransaminationIn this process the α-amino group from a wide variety of amino acids can be transferred to an α-keto acid carrier, commonly αKG. The new α-keto acid is routed to carbohydrate machinery, and Glu is a “standarized” ammonia carrier for transfer to other systems or for oxidative deamination which breaks the N-C bond. Most transamination occurs in cytoplasm, but specialized reactions occur in mitochondria.The amino transferases, or transaminases, use the PLP cofactor.Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.PLP role in transaminationIn this scenario, an amino acid transfers its amine group to PLP, releasing the corresponding α-ketoacid. Next αKG binds and the process “reverses” to generate Glu.Note the loss of the αH in this mechanism at the arrow.Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.Bond orientation in a PLP–amino acid Schiff base. (a) The π-orbital framework of a PLP–amino acid Schiff base.PLP is an unusually versatile cofactor for amino acid metabolism. Once the α-amino group has formed a Schiff base, any of the 3 substituents can be rotated so that its bond is parallel to the PLP π system. This makes that group labile, since the carbanionproduct is resonant stabilized by the cofactor. In transamination, the αHdeparts, but later we will see that the carboxylate or side chain may leave in other mechanisms.Voet Biochemistry 3e© 2004 John Wiley & Sons, Inc.Figure 26-4 The oxidative deamination of glutamate by glutamate dehydrogenase in the mitochondria .Page 989The enzyme glutamate dehydrogenase oxidatively removes ammonia from glutamate (which accumulates from transamination of many amino acids). It is mostly found in liver and kidney GluDH is unusual in that it can use either NAD or NADP.GluDH is activated by NAD or