25.4 How Do Organisms Synthesize Amino Acids? 803 + H 2 O P R 1 H 2 C P P H O HH O HO OH H P P NH 2 N HC N N N P P P H 2 C H HH O HO OH H N C H N NN R P P P 2 P P H 2 C H HH O HO OH H N C H N NN R P HN 3 H 2 C H HH O HO OH H N C H N NN R P R P H 2 N H O 4 N NN H 2 N HN O CH C C HH C O C OHH C OHH CH 2 P N 1 -5-Phosphoribulosylformimino- 5-aminoimidazole-4- carboxamide ribonucleotide 5 NN R P H 2 N O C NH 2 C OHH C OHH CH 2 GlutamateGlutamine C HC H N CH N H 2 O H 2 O H 2 O H 2 O 6 CH 2 C CH 2 C HC H N CH N O Glutamate 7 NH 3 + CH 2 CH 2 C HC H N CH N HC 8 P NH 3 + CH 2 H 2 COH C HC H N CH HC 9, 10 + + 3 H + 2 NADH 2 NAD + NH 3 + CH 2 COO – C HC H N CH N HC O P O P O HN P O O P O P O P O N 5-Phosphoribosyl- ␣-pyrophosphate (PRPP) N 1 -5-Phosphoribosyl-ATP N 1 -5-Phosphoribosyl-AMP N 1 -5-Phosphoribosylformimino- 5-aminoimidazole-4- carboxamide ribonucleotide 5-Aminoimidazole-4- carboxamide ribonucleotide To purine biosynthesis Imidazole glycerol phosphate Imidazole acetol phosphate ␣-Ketoglutarate L-Histidinol phosphate L-Histidinol Histidine ATP FIGURE 25.40 The pathway of histidine biosynthesis.The enzymes are (1) ATP-phosphoribosyl transferase, (2) pyrophosphohydrolase, (3) phosphoribosyl-AMP cyclohydrolase, (4) phosphoribosylformimino-5- aminoimidazole carboxamide ribonucleotide isomerase,(5) imidazole glycerol phosphate synthase, (6) imidazole glycerol-P dehydratase, (7) L-histidinol phosphate aminotransferase, (8) histidinol phosphate phosphatase, and (9) histidinol dehydrogenase. 804 Chapter 25 Nitrogen Acquisition and Amino Acid Metabolism (Figure 25.40). Five carbon atoms from PRPP and one from ATP end up in histi- dine. Step 5 involves some novel chemistry: The substrate, phosphoribulosylformimino- 5-aminoimidazole-4-carboxamide ribonucleotide, picks up an amino group (from the amide of glutamine) in a reaction accompanied by cleavage and ring closure to yield two imidazole compounds—the histidine precursor, imidazole glycerol phosphate, and a purine nucleotide precursor, 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR). Note that AICAR as a purine nucleotide precursor can ultimately re- plenish the ATP consumed in reaction 1. Nine enzymes act in histidine’s ten syn- thetic steps. Reactions 9 and 10, the successive NAD ϩ -dependent oxidations of an alcohol to an aldehyde and then to a carboxylic acid, are catalyzed by the same dehydrogenase. 25.5 How Does Amino Acid Catabolism Lead into Pathways of Energy Production? In normal human adults, close to 90% of the energy requirement is met by oxi- dation of carbohydrates and fats; the remainder comes from oxidation of the car- bon skeletons of amino acids. The primary physiological purpose of amino acids is to serve as the building blocks for protein biosynthesis. The dietary amount of free amino acids is trivial under most circumstances. However, if excess protein is con- sumed in the diet or if the amount of amino acids released during normal turnover of cellular proteins exceeds the requirements for new protein synthesis, the amino acid surplus must be catabolized. Also, if carbohydrate intake is insufficient (as dur- ing fasting or starvation) or if carbohydrates cannot be appropriately metabolized due to disease (as in diabetes mellitus), body protein becomes an important fuel for metabolic energy. The 20 Common Amino Acids Are Degraded by 20 Different Pathways That Converge to Just 7 Metabolic Intermediates Because the 20 common amino acids of proteins are distinctive in terms of their car- bon skeletons, each amino acid requires its own unique degradative pathway. Be- cause amino acid degradation normally supplies only 10% of the body’s energy, then, on average, degradation of any given amino acid will satisfy less than 1% of energy needs. Therefore, we will not discuss these pathways in detail. It so happens, however, that degradation of the carbon skeletons of the 20 common ␣-amino acids converges to just 7 metabolic intermediates: acetyl-CoA, succinyl-CoA, pyruvate, ␣-ketoglutarate, fumarate, oxaloacetate, and acetoacetate. Because succinyl-CoA, pyru- vate, ␣-ketoglutarate, fumarate, and oxaloacetate can serve as precursors for glucose synthesis, amino acids giving rise to these intermediates are termed glucogenic. Those degraded to yield acetyl-CoA or acetoacetate are termed ketogenic, because these substances can be used to synthesize fatty acids or ketone bodies. Some amino acids are both glucogenic and ketogenic (Figure 25.41). The C-3 Family of Amino Acids: Alanine, Serine, and Cysteine The carbon skele- tons of alanine, serine, and cysteine all converge to pyruvate (Figure 25.42). Transamination of alanine yields pyruvate: Alanine ϩ ␣-ketoglutarate 34 pyruvate ϩ glutamate (25.10) Deamination of serine by serine dehydratase also yields pyruvate. Cysteine is con- verted to pyruvate via a number of paths. The carbon skeletons of three other amino acids also become pyruvate. Glycine is convertible to serine and thus to pyruvate. The three carbon atoms of tryptophan that are not part of its indole ring appear as alanine (and, hence, pyruvate) upon Trp degradation. Threonine by one of its degradation routes is cleaved to glycine and acetaldehyde. The glycine is then converted to pyruvate via serine; the acetaldehyde is oxidized to acetyl-CoA (Figure 25.42). 805 Oxaloacetate Fumarate Succinyl-CoA ␣-Ketoglutarate Isocitrate Citrate Citric acid cycle Acetyl-CoA Acetoacetate Pyruvate Glucose Ile Leu Thr Trp Leu Lys Phe Tyr Arg Gln Glu Pro His Ile Met Val Asp Phe Tyr Asp Arg CO 2 CO 2 CO 2 Ala Ser Cys Gly Thr Trp FIGURE 25.41 Metabolic degradation of the common amino acids. Glucogenic amino acids are shown in pink, ketogenic in blue. CH 2 C COO – H + NH 3 CH 3 C COO – O HSCH 3 C COO – H + NH 3 HOCH 2 C COO – H + NH 3 Indole ring products CH 2 C COO – H + NH 3 N H THF N 5 ,N 10 -Methylene THF H 2 C COO – + NH 3 H 3 C CH O C COO – H + NH 3 C H HO H 3 C Pyruvate CysteineAlanine Serine Tryptophan Glycine Acetaldehyde Threonine FIGURE 25.42 Formation of pyruvate from alanine, serine, cysteine, glycine, tryptophan, or threonine. 806 Chapter 25 Nitrogen Acquisition and Amino Acid Metabolism The C-4 Family of Amino Acids: Aspartate and Asparagine Transamination of aspartate gives oxaloacetate: Aspartate ϩ ␣-ketoglutarate 34 oxaloacetate ϩ glutamate (25.11) Hydrolysis of asparagine by asparaginase yields aspartate and NH 4 ϩ . Alternatively, aspartate degradation via the urea cycle leads to a different citric acid cycle inter- mediate, namely, fumarate (Figure 25.23). The C-5 Family of Amino Acids Is Converted to ␣-Ketoglutarate Via Glutamate The five-carbon citric acid cycle intermediate ␣-ketoglutarate is always a product of transamination reactions involving glutamate. Thus, glutamate and any amino acid convertible to glutamate are classified within the C-5 family. These amino acids include glutamine, proline, arginine, and histidine (Figure 25.43). A DEEPER LOOK Histidine—A Clue to Understanding Early Evolution? Histidine residues in the active sites of enzymes often act directly in the enzyme’s catalytic mechanism. Catalytic participation by the imidazole group of His and the presence of imidazole as part of the purine ring system support a current speculation that life before the full evolution of protein molecules must have been RNA based. This notion correlates with the discovery that RNA molecules can have catalytic activity, an idea captured in the term ribozyme (see Chapter 13). H 2 O CH 2 C COO – CH 2 C O H H + NH 3 H N COOH CH 2 C COO – CH 2 C H + NH 3 H 2 N O CH 2 C COO – CH 2 H + NH 3 + H 3 N CH 2 C COO – CH 2 H + NH 3 H 2 NCH 2 NHC + NH 2 C O H 2 NNH 2 Urea CH 2 Glutamate-␥-semialdehyde Proline Glutamine Ornithine Arginine CH 2 C COO – Histidine H + NH 3 + NH 3 54 3 CHC NH C H N 21 CH 2 C COO – CH 2 C O – O H 1234 5 CH 2 C COO – CH 2 C O – O ␣-Ketoglutarate Glutamate O FIGURE 25.43 The degradation of the C-5 family of amino acids leads to ␣-ketoglutarate via glutamate. The histidine carbons, numbered 1 through 5, become carbons 1 through 5 of glutamate, as indicated. 25.5 How Does Amino Acid Catabolism Lead into Pathways of Energy Production? 807 Degradation of Valine, Isoleucine, and Methionine Leads to Succinyl-CoA The breakdown of valine, isoleucine, and methionine converges at propionyl-CoA (Figure 25.44). Methionine first becomes S-adenosylmethionine and then homocysteine (see Figure 25.28). The carboxyl groups from all three are lost as CO 2 . The two dis- tal carbon atoms of leucine become acetyl-CoA. Propionyl-CoA is subsequently con- verted to methylmalonyl-CoA and thence to succinyl-CoA via the same reactions me- diating the oxidation of fatty acids that have odd numbers of carbon atoms (see Chapter 23). Leucine Is Degraded to Acetyl-CoA and Acetoacetate Leucine is one of only two purely ketogenic amino acids; the other is lysine. Deamination of leucine via a transamination reaction yields ␣-ketoisocaproate, which is oxidatively decarboxylated to isovaleryl-CoA (Figure 25.45). Subsequent reactions, one of which is a biotin- dependent carboxylation, give -hydroxy--methylglutaryl-CoA, which is then cleaved to yield acetyl-CoA and acetoacetate, a ketone body (see Figure 23.26). Neither of these products is convertible to glucose. The initial steps in valine, leucine, and isoleucine degradation are identical. All three are first deaminated to ␣-keto acids by the branched-chain amino acid aminotrans- A DEEPER LOOK The Serine Dehydratase Reaction—A -Elimination The degradation of serine to pyruvate (see Figure 25.42) is an ex- ample of a pyridoxal phosphate–catalyzed -elimination reaction. -Eliminations mediated by PLP yield products that have under- gone a two-electron oxidation at C ␣ . Serine is thus oxidized to pyru- vate, with release of ammonium ion (see accompanying figure). At first, this looks like a transaminase half-reaction, but there is an im- portant difference. In each transaminase half-reaction, PLP under- goes a net two-electron reduction or oxidation (depending on the direction), whereas -eliminations occur with no net oxidation or reduction of PLP. Note too that the aminoacrylate released from PLP is unstable in aqueous solution. It rapidly tautomerizes to the preferred imine form, which is spontaneously hydrolyzed to yield the ␣-keto acid product—pyruvate in this case. + H CH 2 C COO – H NH 3 + HO O N C + CH 3 N + 2– O 3 PO H H 2 C C COO – B H H + C N C CH 3 N H 2– O 3 PO H COO – H 2 C + C COO – H 2 C NH 3 + C COO – H 3 C NH 2 + + CH 3 COO – C O NH 4 + + H 2 O H 2 O + E – H O – H O – E • PLP complex Water removal step Aminoacrylate (unstable) E • PLP Com p lex Schiff base Elimination of  OH group -elimination intermediate ᮡ The serine dehydratase reaction mechanism—an example of a PLP-dependent -elimination reaction. 808 Chapter 25 Nitrogen Acquisition and Amino Acid Metabolism ferase, a mitochondrial enzyme. The resulting ␣-keto acids are then oxidatively decar- boxylated by the CoA-dependent branched-chain ␣-keto acid dehydrogenase complex (BCKAD complex) to form CoA derivatives. Maple syrup urine disease is a hereditary defect in the oxidative decarboxylation of these branched-chain ␣-keto acids. The meta- bolic block created by this defect leads to elevated levels of valine, leucine, and H 3 + N CH COO – – OOC CH 2 CH 2 C S O – OOC CH 2 C S O CH 3 + CH 3 CH 2 C S O CH CH 3 H 3 C H 3 + N CH 2 COO – CH CH 2 S CH 3 H 3 + N CH COO – CH CH 2 H 3 C CH 3 CH 3 C S O CoA CoA CoA CoA ATP ADP H 2 O, CO 2 , P i Succinyl-CoA Propionyl-CoA carboxylase Propionyl-CoA ValineMethionine Isoleucine FIGURE 25.44 Valine, isoleucine, and methionine are converted via propionyl-CoA to succinyl-CoA for entry into the citric acid cycle.The shaded carbon atoms of the three amino acids give rise to propionyl-CoA. CH H 3 CCH 3 CH 2 CH COO – + H 3 N CH H 3 CCH 3 CH 2 C COO – O CH H 3 CCH 3 CH 2 C SCoA O C H 3 CCH 2 CH 2 C O COO – OH CH 3 C O CH 2 COO – + CH 3 C O SCoA SCoA Leucine ␣-Ketoisocaproate Isovaleryl-CoA -Hydroxy-- methylglutaryl-CoA Acetoacetate Acetyl-CoA FIGURE 25.45 Leucine is degraded to acetyl-CoA and acetoacetate. 25.5 How Does Amino Acid Catabolism Lead into Pathways of Energy Production? 809 isoleucine (and their corresponding branched-chain ␣-keto acids) in the blood and urine. The urine of individuals with this disease smells like maple syrup. The defect is fatal unless dietary intake of these amino acids is greatly restricted early in life. Lysine Degradation Lysine degradation proceeds by several pathways, but the saccharopine pathway found in liver predominates (Figure 25.46). This degradative route proceeds backward along the lysine biosynthetic pathway through saccharopine and ␣-aminoadipate to ␣-ketoadipate (see Figure 25.24). Next, ␣-ketoadipate under- goes oxidative decarboxylation to glutaryl-CoA, which is then transformed into acetoacetyl-CoA and ultimately into the ketone body, acetoacetate. As indicated earlier, degradation of the nonindole carbons of tryptophan yields pyruvate. The indole ring of Trp is converted by a series of reactions to ␣-ketoadipate and ultimately acetoacetate by these same reactions of Lys degradation. Phenylalanine and Tyrosine Are Degraded to Acetoacetate and Fumarate The first reaction in phenylalanine degradation is the hydroxylation reaction of tyrosine biosyn- thesis (see Figure 25.38). Both these amino acids thus share a common degradative pathway. Transamination of Tyr yields the ␣-keto acid p-hydroxyphenylpyruvate (Figure 25.47, reaction 1). p-Hydroxyphenylpyruvate dioxygenase, a vitamin C–dependent CH 2 + H 3 N CH 2 CH 2 CH 2 CH + H 3 N COO – CH 2 CH 2 CH 2 CO COO – CH 2 CH 2 CH 2 C SCoA CO 2 CO 2 O CH 3 C CH 2 C SCoA O O CH 3 C CH 2 COO – O COO – COO – Lysine ␣-Ketoadipate Glutaryl-CoA Acetoacetyl-CoA Acetoacetate FIGURE 25.46 Lysine degradation via the saccharopine, ␣-ketoadipate path- way culminates in the formation of the ketone body, acetoacetate. + O 2 O 2 CO 2 H 2 O + 1 OH CH 2 CH COO – H 3 N Glu OH CH 2 C COO – O Ascorbate 2 Dehydroascorbate ++ OH OH H 2 C – OOC 3 CH 2 – OOC C O CH 2 C O CH CH – OOC 4 COO – HC C O CH 2 C O CH 2 CH – OOC 5 HC COO – CH – OOC COO – CH 3 C O CH 2 + ␣-KG Tyrosine p-Hydroxy- phenylpyruvate Homogentisate 4-Maleylacetoacetate 4-Fumarylacetoacetate FumarateAcetoacetate FIGURE 25.47 Phenylalanine and tyrosine degradation. 810 Chapter 25 Nitrogen Acquisition and Amino Acid Metabolism enzyme, then carries out a ring hydroxylation–oxidative decarboxylation to yield homogentisate (Figure 25.47, reaction 2). Ring opening and isomerization (Figure 25.47, reactions 3 and 4) give 4-fumaryl-acetoacetate, which is hydrolyzed to acetoacetate and fumarate (reaction 6). Animals Differ in the Form of Nitrogen That They Excrete Animals often enjoy a dietary surplus of nitrogen. Excess nitrogen liberated upon metabolic degradation of amino acids is excreted by animals in three different ways, in accord with the availability of water. Aquatic animals simply release free ammonia to the surrounding water; such animals are termed ammonotelic (from the Greek telos, meaning “end”). On the other hand, terrestrial and aerial species employ mech- anisms that convert ammonium to less toxic waste compounds that require little H 2 O for excretion. Many terrestrial vertebrates, including humans, are ureotelic, meaning that they excrete excess N as urea, a highly water-soluble nonionic substance. Urea is formed by ureoteles via the urea cycle (see Figure 25.23). The uricotelic organisms are those animals using the third means of N excretion, conversion to uric acid, a rather insoluble purine analog. Birds and reptiles are uricoteles. Uric acid metabo- lism is discussed in the next chapter. Some animals can switch from ammonotelic to ureotelic to uricotelic metabolism, depending on water availability. HUMAN BIOCHEMISTRY Hereditary Defects in Phe Catabolism Underlie Alkaptonuria and Phenylketonuria Alkaptonuria and phenylketonuria are two human genetic dis- eases arising from specific enzyme defects in phenylalanine degradation. Alkaptonuria is characterized by urinary excretion of large amounts of homogentisate and results from a deficiency in homogentisate dioxygenase (step 3, Figure 25.47). Air oxida- tion of homogentisate causes urine to turn dark on standing, but the only malady suffered by carriers of this disease is a tendency toward arthritis later in life. In contrast, phenylketonurics, whose urine contains excessive phenylpyruvate (see accompanying figure), suffer severe mental re- tardation if the defect is not recognized immediately after birth and treated by putting the victim on a diet low in phenylalanine. These individuals are deficient in phenylalanine hydroxylase (Fig- ure 25.38), and the excess Phe that accumulates is transaminated to phenylpyruvate and excreted. CH 2 C COO – O Phenylpyruvate ᮡ The structure of phenylpyruvate. SUMMARY 25.1 Which Metabolic Pathways Allow Organisms to Live on Inorganic Forms of Nitrogen? Nitrogen, an element essential to life, occurs in the environment principally as atmospheric N 2 and as NO 3 Ϫ ions in so- lution in soils and water. The metabolic pathways of nitrogen fixation and nitrate assimilation reduce these oxidized forms of nitrogen to the metabolically useful form, ammonium. Nitrate assimilation is a two- enzyme pathway: nitrate reductase and nitrite reductase. Nitrate reduc- tase is a molybdenum cofactor-dependent flavohemoprotein. Nitrite reductase catalyzes the six-electron reduction of NO 2 Ϫ to NH 4 ϩ via a siroheme-dependent reaction. Nitrogen fixation is carried out by the ni- trogenase system; biological reduction of N 2 to 2 NH 4 ϩ is an ATP- dependent eight-electron transfer reaction, with H 2 as an obligatory by- product. Nitrogenase is a metal-rich enzyme having an 8Fe-7S cluster as well as a 7Fe-1Mo-9S cluster known as the FeMo-cofactor. Nitrogenase is regulated in two ways: Its activity is inhibited by ADP, and its synthesis is repressed by NH 4 ϩ . 25.2 What Is the Metabolic Fate of Ammonium? Despite the great diversity of organic nitrogenous compounds found in cells, only a limited set of reactions incorporate ammonium ions into organic linkage: (1) glutamate dehydrogenase (GDH), (2) glutamine synthetase (GS), and (3) carbamoyl-P synthetase. Of these, the first two are quantitatively more important. Glutamate dehdyrogenase, by adding NH 4 ϩ to the citric acid cycle intermediate ␣-ketoglutarate, sits at the interface between nitrogen metabolism and carbohydrate (and energy) metabolism. Glutamine synthetase catalyzes the ATP-dependent amidation of the ␥-carboxyl group of Glu. Glutamine is the major donor of ONH 2 groups for the synthesis of many nitrogen-containing organic compounds, in- cluding purines, pyrimidines, and other amino acids. As such, its activity is tightly regulated. Most ammonium assimilation into organic linkage proceeds by one of two routes, depending on NH 4 ϩ availability: the GDH–GS route when ammonium is abundant and the glutamate syn- thase (GOGAT)–GS route when [NH 4 ϩ ] is limiting. Problems 811 25.3 What Regulatory Mechanisms Act on Escherichia coli Glutamine Synthetase? Glutamine synthetase is a paradigm of enzyme regulation, because its activity can be modulated at three different levels: (1) allo- steric regulation by feedback inhibition, (2) covalent modification through adenylylation of Tyr 397 in each of the 12 GS polypeptide chains, and (3) regulation of gene expression by the phosphorylated form of the transcriptional enhancer NR I . Allosteric inhibitors of GS include five amino acids (Gly, Ser, Ala, His, and Trp), two nucleotides (one purine [AMP] and one pyrimidine [CTP]), one aminosugar (glucosamine-6-P), and carbamoyl-P. Adenylylation of GS converts it from a more active, allo- sterically unresponsive form to a less active, allosterically sensitive form. The ratio of adenylylated GS to deadenylylated GS is ultimately deter- mined by the [Gln]/[␣-KG] ratio, with a low ratio favoring the deadeny- lylated state and thus greater synthesis of glutamine. 25.4 How Do Organisms Synthesize Amino Acids? In many cases, amino acid biosynthesis is a matter of synthesizing the appropriate ␣-keto acid carbon skeleton for the amino acid and then transaminating this ␣-keto acid using Glu as amino donor by action of an aminotrans- ferase reaction. Mammals have retained the ability to synthesize the ␣-keto acid analog for 10 of the 20 common amino acids (the so-called nonessential amino acids), but the ability to make the other 10 ␣-keto acid analogs has been lost over evolutionary time, rendering these 10 amino acids as essential in the diet. The common amino acids can be grouped into families on the basis of the metabolic progenitor that serves as their precursor: The ␣-ketoglutarate family includes Glu, Gln, Pro, Arg, and (sometimes) Lys; the pyruvate family includes Ala, Val, and Leu; the aspartate family includes Asp, Asn, Met, Thr, Ile, and (some- times) Lys; the 3-phosphoglycerate family includes Ser, Gly, and Cys; and the PEP and erythrose-4-P family includes the aromatic amino acids Phe, Tyr, and Trp. Histidine is a special case—it is formed from PRPP and ATP. AICAR is a byproduct. 25.5 How Does Amino Acid Catabolism Lead into Pathways of Energy Production? The 20 common amino acids are degraded by 20 differ- ent pathways that converge to just 7 metabolic intermediates: pyruvate, acetyl-CoA, acetoacetate, oxaloacetate, ␣-ketoglutarate, succinyl-CoA, and fumarate. All seven of these compounds are intermediates in or readily feed into the pathways of energy production (citric acid cycle and oxidative phosphorylation). PROBLEMS Preparing for an exam? Create your own study path for this chapter at www.cengage.com/login. 1. What is the oxidation number of N in nitrate, nitrite, NO, N 2 O, and N 2 ? 2. How many ATP equivalents are consumed per N atom of ammo- nium formed by (a) the nitrate assimilation pathway and (b) the nitrogen fixation pathway? (Assume for this problem NADH, NADPH, and reduced ferredoxin are each worth 3 ATPs.) 3. Suppose at certain specific metabolite concentrations in vivo the cyclic cascade regulating E. coli glutamine synthetase has reached a dynamic equilibrium where the average state of GS adenylylation is poised at n ϭ 6. Predict what change in n will occur if: a. [ATP] increases. b. P IIA /P IID increases. c. [␣-KG]/[Gln] increases. d. [P i ] decreases. 4. How many ATP equivalents are consumed in the production of 1 equivalent of urea by the urea cycle? 5. Why are persons on a high-protein diet (such as the Atkins diet) advised to drink lots of water? 6. How many ATP equivalents are consumed in the biosynthesis of lysine from aspartate by the pathway shown in Figure 25.27? 7. If PEP labeled with 14 C in the 2-position serves as the precursor to chorismate synthesis, which C atom in chorismate is radioactive? 8. (Integrates with Chapter 22.) Write a balanced equation for the syn- thesis of glucose (by gluconeogenesis) from aspartate. 9. For each of the 20 common amino acids, give the name of the enzyme that catalyzes the reaction providing its ␣-amino group. 10. Which vitamin is central in amino acid metabolism? Why? 11. Vitamins B 6 , B 12 , and folate may be recommended for individuals with high blood serum levels of homocysteine (a condition called hyperhomocysteinemia). How might these vitamins ameliorate homo- cysteinemia? 12. (Integrates with Chapter 19.) On the basis of the following informa- tion, predict a reaction mechanism for the mammalian branched- chain ␣-keto acid dehydrogenase complex (the BCKAD complex). This complex carries out the oxidative decarboxylation of the ␣-keto acids derived from valine, leucine, and isoleucine. a. One form of maple syrup urine disease responds well to adminis- tration of thiamine. b. Lipoic acid is an essential coenzyme. c. The enzyme complex contains a flavoprotein. 13. People with phenylketonuria must avoid foods containing the low- calorie sweetener Aspartame, also known as NutraSweet. Find the structure of Aspartame in the Merck Index (or other scientific source) and state why these people must avoid this substance. 14. Glyphosate (otherwise known as RoundUp) is an analog of PEP. It acts as a noncompetitive inhibitor of 3-enolpyruvylshikimate-5-P synthase; it has the following structure in its fully protonated state: HOOCOCH 2 ONHOCH 2 OPO 3 H 2 Consult Figures 25.35 and 25.36 and construct a list of the diverse metabolic consequences that might be experienced by a plant cell exposed to glyphosate. 15. (Integrates with Chapter 18.) When cells convert glucose to glycine, which carbon atoms of glucose are represented in glycine? 16. Although serine is a nonessential amino acid, serine deficiency syn- drome has been observed in humans. One such form of the syn- drome is traceable to a deficiency in 3-phosphoglycerate dehydro- genase (see Figure 25.31). Individuals with this syndrome not only are serine-deficient but also are impaired in their ability to synthe- size another common amino acid, as well as a class of lipids. De- scribe why. 17. Go to www.pdb.org and examine the pdb file 1LM1 for glutamate synthase. Find its iron–sulfur cluster and FMN prosthetic group. Discover how this enzyme is organized into an N-terminal domain that functions in ammonia removal from glutamine (the glutam- inase domain) and the ␣-ketoglutarate–binding site near the Fe/S and flavin prosthetic groups. Consult van den Heuvel, R. H. H., et al., 2002. Structural studies on the synchronization of catalytic cen- ters in glutamate synthase. Journal of Biological Chemistry 277: 24579–24583, to see how these two sites are connected by a tunnel for passage of ammonia from glutamine to ␣-ketoglutarate. 18. The thermic effect of food is a term used to describe the energy cost of processing the food we eat, digesting it, and either turning it into precursors for needed biosynthesis, usable energy in the form of ATP, or storing the excess intake as fat. The thermic effect is usually approximated at 10% of the total calories consumed, but the ther- mic effect of fat is only 2% to 3% of total fat calories and the ther- mic effect of protein is 30% or more of calories consumed as pro- tein. Why do you suppose dietary protein has a much higher thermic effect than either dietary carbohydrate or fat? 812 Chapter 25 Nitrogen Acquisition and Amino Acid Metabolism Preparing for the MCAT Exam 19. From the dodecameric (␣ 12 ) structure of glutamine synthetase shown in Figure 25.14, predict the relative enzymatic activity of GS monomers (isolated ␣-subunits). 20. Consider the synthesis and degradation of tyrosine as shown in Figures 25.37, 25.38, and 25.47 to determine where the carbon atoms in PEP and erythrose-4-P would end up in acetoacetate and fumarate. FURTHER READING Nitrate Assimilation and Nitrogen Fixation Brewin, A. J., and Legocki, A. B., 1996. Biological nitrogen fixation for sustainable agriculture. Trends in Microbiology 4:476–477. Burris, R. H., 1991. Nitrogenases. Journal of Biological Chemistry 266: 9339–9342. Campbell, W. H., and Kinghorn, J. R., 1990. Functional domains of as- similatory nitrate reductases and nitrite reductases. Trends in Bio- chemical Sciences 15:315–319. Crawford, N. M., and Arst, H. N., Jr., 1993. The molecular genetics of ni- trate assimilation in fungi and plants. Annual Review of Genetics 27:115–146. Lin, J. T., and Stewart, V., 1998. Nitrate assimilation in bacteria. Advances in Microbial Physiology 39:1–30. Mortenson, L. E., Seefeldt, L. C., Morgan, T. V., and Bolin, J. T., 1993. The role of metal clsuters and MgATP in nitrogenase catalysis. Ad- vances in Enzymology 67:299–374. Peters, J. W., and Szilagyi, R. K., 2006. Exploring new frontiers of nitro- genase structure and mechanism. Current Opinion in Chemical Biology 10:101–108. Rees, D. C., et al., 2005. Structural basis of nitrogen fixation. 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