BCM 2 exam 2 study guide final

Question: What is the coenzyme involved in transaminase reactions? Answer: Pyridoxal phosphate (PLP), the coenzyme form of vitamin B6.

Question: What is the underlying role of PLP in transamination? Answer: PLP acts as an intermediate carrier of amino groups at the active site of aminotransferases. Its aminated form is pyridoxamine phosphate (PMP).

Question: What is the overall mechanism of a PLP-dependent transamination? Answer: Amino acid + α-ketoglutarate ⇌ α-keto acid + glutamate. PLP accepts the amino group from the amino acid to become PMP, then PMP transfers that amino group to α-ketoglutarate, regenerating PLP.

Question: What other reactions can PLP facilitate besides transamination? Answer: Racemization and decarboxylation.

Question: What is the function of N-acetylglutamate? Answer: N-acetylglutamate is the essential allosteric activator of carbamoyl phosphate synthetase I (CPS I).

Question: How does N-acetylglutamate regulate the urea cycle? Answer: It activates CPS I, the enzyme that catalyzes formation of carbamoyl phosphate and controls entry of NH4+ into the urea cycle.

Question: How is N-acetylglutamate produced and how does it regulate the urea cycle? Answer: Glutamate + acetyl-CoA → N-acetylglutamate, catalyzed by N-acetylglutamate synthase. Arginine activates N-acetylglutamate synthase → ↑ N-acetylglutamate → activation of CPS I → ↑ urea-cycle flux.

Question: What determines steady-state N-acetylglutamate levels in mammals? Answer: Glutamate, acetyl-CoA, and arginine. Arginine activates N-acetylglutamate synthase and therefore indirectly activates the urea cycle.

Question: What processes are associated with the glucose-alanine cycle? Answer: Muscle exports nitrogen and pyruvate as alanine to the liver; the liver disposes of the nitrogen as urea and returns the carbon as glucose.

Question: What is the purpose of the glucose-alanine cycle? Answer: It transports amino nitrogen from skeletal muscle to the liver while allowing the pyruvate carbon skeleton to be recycled into glucose.

Question: What is the pathway of the glucose-alanine cycle? Answer: Muscle: amino acids → glutamate; glutamate + pyruvate ⇌ α-ketoglutarate + alanine via alanine aminotransferase → alanine enters blood → liver: alanine + α-ketoglutarate ⇌ pyruvate + glutamate → glutamate releases NH4+ for urea synthesis; pyruvate → gluconeogenesis → glucose → blood → muscle.

Question: Which two major metabolic processes are coupled by the glucose-alanine cycle? Answer: Amino acid catabolism/nitrogen disposal and gluconeogenesis.

Question: What is the function of glutamate dehydrogenase in amino acid metabolism? Answer: It reversibly converts glutamate to α-ketoglutarate and NH4+, linking amino-group metabolism to the citric acid cycle.

Question: Why is glutamate dehydrogenase important for nitrogen disposal? Answer: Transamination collects amino groups in glutamate, and GDH releases glutamate's amino group as NH4+ in liver mitochondria for urea synthesis.

Question: What reaction is catalyzed by glutamate dehydrogenase? Answer: Glutamate + NAD(P)+ + H2O ⇌ α-ketoglutarate + NH4+ + NAD(P)H + H+. GDH operates in the mitochondrial matrix and can use NAD+ or NADP+.

Question: How is glutamate dehydrogenase regulated? Answer: ADP positively modulates GDH, whereas GTP negatively modulates it. The α-ketoglutarate produced can enter the citric acid cycle or be used for glucose synthesis. Ch18 Candas Lecture (1)

Question: How is the energy demand of the urea cycle compensated? Answer: Fumarate produced by the urea cycle is converted to malate and then oxaloacetate, generating NADH that can yield ATP through oxidative phosphorylation.

Question: Why is the energetic cost of the urea cycle lower than its ATP consumption alone suggests? Answer: The aspartate-argininosuccinate shunt links the urea and citric acid cycles, and oxidation of malate to oxaloacetate produces NADH, recovering some of the energy spent by the urea cycle.

Question: How does the aspartate-argininosuccinate shunt compensate for urea-cycle energy use? Answer: Argininosuccinate → arginine + fumarate → malate → oxaloacetate. Malate dehydrogenase converts malate + NAD+ → oxaloacetate + NADH + H+; oxaloacetate can then be transaminated to aspartate and return to the urea cycle.

Question: How much energy does the urea cycle consume directly? Answer: 3 ATP molecules are consumed, but 4 high-energy phosphate bonds are used because one ATP is converted to AMP + PPi. The textbook notes that cycle interconnections reduce the energetic cost. Chapter 18 textbook(1)

Question: What compounds are excreted for the elimination of nitrogen in mammals? Answer: Urea is the major nitrogenous excretory product in mammals.

Question: Why do mammals primarily convert ammonia to urea? Answer: Free ammonia is toxic, so ureotelic mammals detoxify amino nitrogen by converting it into relatively nontoxic urea.

Question: What is the general route for nitrogen excretion in mammals? Answer: Amino acids → amino groups collected largely as glutamate, glutamine, or alanine → liver → NH4+ → carbamoyl phosphate → urea cycle → urea → blood → kidneys → urine.

Question: How do the major nitrogenous waste strategies differ among animals? Answer: Ammonotelic animals excrete ammonia, ureotelic animals such as mammals excrete urea, and uricotelic animals excrete uric acid. Water availability is a major determinant. Ch18 Candas Lecture (1)

Question: What is phenylketonuria (PKU)? Answer: PKU is an inherited defect in conversion of phenylalanine to tyrosine, usually caused by phenylalanine hydroxylase deficiency.

Question: What metabolic reaction is defective in classical phenylketonuria? Answer: Phenylalanine → tyrosine is impaired because phenylalanine hydroxylase is deficient.

Question: What is the normal phenylalanine hydroxylase reaction? Answer: Phenylalanine + O2 + tetrahydrobiopterin (BH4) → tyrosine + H2O + dihydrobiopterin, catalyzed by phenylalanine hydroxylase.

Question: Why does phenylalanine accumulate in PKU? Answer: Loss of phenylalanine hydroxylase activity prevents normal conversion of phenylalanine to tyrosine, causing phenylalanine to accumulate.

Question: How does the urea cycle support the Krebs cycle? Answer: The urea cycle produces fumarate, which can be converted to malate and oxaloacetate, both citric acid cycle intermediates.

Question: What is the metabolic connection between the urea cycle and the citric acid cycle? Answer: The aspartate-argininosuccinate shunt connects the cycles through fumarate, malate, oxaloacetate, and aspartate.

Question: Trace the connection between the urea cycle and Krebs cycle. Answer: Argininosuccinate → arginine + fumarate → fumarate → malate → oxaloacetate → aspartate; aspartate reenters the urea cycle by combining with citrulline → argininosuccinate.

Question: What useful products arise from the fumarate generated by the urea cycle? Answer: Fumarate supplies a citric acid cycle intermediate, and its conversion through malate to oxaloacetate generates NADH and regenerates oxaloacetate for aspartate formation. Chapter 18 textbook(1)

Question: Which compound directly donates a nitrogen atom for urea formation during the urea cycle? Answer: Aspartate directly donates the second nitrogen of urea.

Question: Where do the two nitrogen atoms of urea originate? Answer: One nitrogen comes from NH4+ and the second comes from aspartate.

Question: How do the two nitrogens enter the urea cycle? Answer: NH4+ → carbamoyl phosphate via CPS I → citrulline; aspartate then combines with citrulline → argininosuccinate. Both nitrogens are ultimately incorporated into urea.

Question: At what step does aspartate donate its nitrogen to the urea cycle? Answer: Citrulline + aspartate + ATP → argininosuccinate + AMP + PPi, catalyzed by argininosuccinate synthetase. Chapter 18 textbook(1)

Question: What is the metabolic defect in maple syrup urine disease? Answer: Deficiency of the branched-chain α-keto acid dehydrogenase complex, impairing degradation of leucine, isoleucine, and valine.

Question: Why does branched-chain α-keto acid dehydrogenase deficiency cause maple syrup urine disease? Answer: The branched-chain amino acids are transaminated, but their resulting α-keto acids cannot undergo normal oxidative decarboxylation.

Question: Where does the defective step occur in branched-chain amino acid catabolism in MSUD? Answer: Leucine/isoleucine/valine → corresponding branched-chain α-keto acids by transamination → ✕ branched-chain α-keto acid dehydrogenase complex → downstream acyl-CoA derivatives.

Question: Which three amino acids are improperly degraded in maple syrup urine disease? Answer: Leucine, isoleucine, and valine.

Question: Where does urea synthesis take place in mammals? Answer: In the liver, with the first two urea-cycle reactions in mitochondria and the remaining reactions in the cytosol.

Question: Why does the urea cycle span two cellular compartments? Answer: Carbamoyl phosphate and citrulline are produced in the mitochondrial matrix, after which citrulline is transported to the cytosol for the remaining reactions.

Question: What is the compartmental organization of the urea cycle? Answer: Mitochondria: NH4+ + HCO3− → carbamoyl phosphate → citrulline. Citrulline exits to cytosol. Cytosol: citrulline → argininosuccinate → arginine → urea + ornithine. Ornithine returns to mitochondria.

Question: Which organ is specialized for converting excess amino nitrogen into urea? Answer: The liver.

Question: Catabolism of which amino acids yields pyruvate? Answer: Alanine, cysteine, glycine, serine, threonine, and tryptophan.

Question: Why are amino acids that yield pyruvate considered glucogenic? Answer: Pyruvate can be converted to oxaloacetate and used for gluconeogenesis, allowing their carbon skeletons to contribute to glucose synthesis.

Question: What is the pathway by which pyruvate-producing amino acids can contribute to glucose? Answer: Amino acid → pyruvate → oxaloacetate → phosphoenolpyruvate → gluconeogenesis → glucose.

Question: Are leucine and lysine able to contribute net carbon to gluconeogenesis? Answer: No. Leucine and lysine are exclusively ketogenic.

Question: In amino acid catabolism, what is the first reaction and cofactor for many amino acids? Answer: Transamination, using pyridoxal phosphate (PLP).

Question: What happens during the initial transamination step of amino acid catabolism? Answer: The α-amino group is transferred from an amino acid to α-ketoglutarate, producing glutamate and the corresponding α-keto acid.

Question: What is the general transamination reaction? Answer: L-amino acid + α-ketoglutarate ⇌ α-keto acid + L-glutamate, catalyzed by an aminotransferase using PLP.

Question: Why is glutamate central to amino acid catabolism? Answer: Transamination funnels amino groups from many different amino acids into glutamate, which can subsequently release NH4+ through glutamate dehydrogenase.

Question: Which amino acid transports amino groups from muscle to the liver in a nontoxic form? Answer: Alanine.

Question: Why is alanine suited for transporting muscle nitrogen? Answer: Muscle transfers amino groups to pyruvate to form alanine, allowing nitrogen and the pyruvate carbon skeleton to travel to the liver.

Question: How is alanine formed and used in the glucose-alanine cycle? Answer: Muscle: glutamate + pyruvate ⇌ α-ketoglutarate + alanine via alanine aminotransferase → blood → liver → alanine + α-ketoglutarate ⇌ pyruvate + glutamate → NH4+ → urea; pyruvate → glucose.

Question: What happens to the carbon skeleton of alanine after it reaches the liver? Answer: It becomes pyruvate, which is used to produce glucose; the glucose is returned to muscle. Ch18 Candas Lecture (1)

Question: What is the function of tetrahydrofolate and its derivatives in metabolism? Answer: Tetrahydrofolate (THF) carries and transfers one-carbon units in several oxidation states.

Question: What types of groups are transferred by tetrahydrofolate derivatives? Answer: One-carbon units, carried primarily at the N5 and/or N10 positions of tetrahydrofolate.

Question: How does tetrahydrofolate participate in one-carbon metabolism? Answer: One-carbon units enter the THF pool → are carried in forms such as N5,N10-methylene-THF and N5-methyl-THF → donated to reactions including nucleotide and methionine biosynthesis.

Question: Why must tetrahydrofolate be regenerated? Answer: THF must be regenerated so that it can continue accepting and transferring one-carbon units in metabolism.

Question: Which enzyme is critical in activating protein-digesting zymogens in the small intestine? Answer: Trypsin is the central activating protease; enteropeptidase initiates the cascade by converting trypsinogen to trypsin.

Question: Why is trypsin central to pancreatic zymogen activation? Answer: Trypsin activates additional trypsinogen as well as chymotrypsinogen, procarboxypeptidases, and proelastase.

Question: What is the zymogen activation cascade in the small intestine? Answer: Enteropeptidase: trypsinogen → trypsin → additional trypsinogen → trypsin; trypsin also activates chymotrypsinogen, procarboxypeptidases, and proelastase.

Question: Why are pancreatic proteases synthesized as zymogens? Answer: Inactive precursors protect the pancreas from self-digestion; pancreatic trypsin inhibitor provides additional protection.

Question: What substrate is used to synthesize methionine by methionine synthase? Answer: Homocysteine.

Question: What does methionine synthase accomplish? Answer: It transfers a methyl group to homocysteine, producing methionine.

Question: What is the methionine synthase reaction? Answer: N5-methyl-THF + homocysteine → THF + methionine, catalyzed by methionine synthase with vitamin B12 participating in methyl transfer.

Question: Why are folate and vitamin B12 metabolism connected to methionine synthesis? Answer: Methionine synthase transfers the methyl group of N5-methyl-THF to homocysteine through a vitamin B12-dependent reaction.

Question: How many ATP are used in urea formation? Answer: 3 ATP molecules are used, corresponding to 4 high-energy phosphate bonds.

Question: Why does the urea cycle use four high-energy phosphate bonds despite consuming only three ATP? Answer: CPS I uses 2 ATP → 2 ADP, while argininosuccinate synthetase uses 1 ATP → AMP + PPi, equivalent to two high-energy phosphate bonds.

Question: Where is ATP consumed during the urea cycle? Answer: CPS I: NH4+ + HCO3− + 2 ATP → carbamoyl phosphate. Argininosuccinate synthetase: citrulline + aspartate + ATP → argininosuccinate + AMP + PPi.

Question: What is the energetic accounting for one urea molecule? Answer: 3 ATP molecules are consumed, but 4 high-energy phosphate bonds are expended. The energetic cost is partially offset by NADH generation through the fumarate → malate → oxaloacetate connection.

Question: Which two amino acids are exclusively ketogenic? Answer: Leucine and lysine.

Question: What does exclusively ketogenic mean? Answer: Their carbon skeletons yield acetyl-CoA and/or acetoacetate and cannot contribute net carbon to glucose synthesis.

Question: What is the metabolic fate of exclusively ketogenic amino acids? Answer: Leucine and lysine → acetyl-CoA and/or acetoacetate → ketone-body or lipid metabolism, rather than net gluconeogenesis.

Question: Which amino acids cannot contribute to gluconeogenesis? Answer: Leucine and lysine. All other amino acids can contribute to gluconeogenesis when needed. Ch18 Candas Lecture (1)

Question: What coenzyme is required for all transamination reactions? Answer: Pyridoxal phosphate (PLP), derived from vitamin B6.

Question: Why is PLP required for transamination? Answer: PLP accepts an amino group to become pyridoxamine phosphate (PMP), which then donates that amino group to an α-keto acid.

Question: What are the two functional forms involved in PLP-dependent transamination? Answer: PLP (aldehyde form) accepts an amino group → PMP (aminated form); PMP donates its amino group to an α-keto acid → PLP is regenerated.

Question: How is PLP associated with an aminotransferase active site? Answer: PLP is a prosthetic group used by all aminotransferases and carries amino groups at the active site. Ch18 Candas Lecture (1)

Question: What signals are associated with secretion of gastrin and secretin? Answer: Dietary protein in the stomach stimulates gastrin secretion; low pH in the small intestine stimulates secretin secretion.

Question: What is the physiological distinction between gastrin and secretin signaling? Answer: Gastrin responds to dietary protein in the stomach, whereas secretin responds to acidic gastric contents reaching the duodenum.

Question: What are the downstream responses associated with gastrin and secretin? Answer: Dietary protein → gastrin → gastric glands secrete HCl and pepsinogen. Low pH in duodenum → secretin → pancreas secretes bicarbonate + water → neutralization of gastric acid.

Question: What is the purpose of secretin-stimulated bicarbonate secretion? Answer: It neutralizes gastric acid in the small intestine and maintains an optimal pH for digestion. Ch18 Candas Lecture (1)

Question: Which amino acid metabolism is associated with serotonin production? Answer: Tryptophan.

Question: What is the relationship between tryptophan and serotonin? Answer: Tryptophan is a precursor of serotonin. The textbook identifies serotonin as one of the biomolecules produced from tryptophan metabolism. Chapter 18 textbook(1)

Question: What is the pathway from tryptophan to serotonin? Answer: Tryptophan + O2 + BH4 → 5-hydroxytryptophan + H2O + BH2, catalyzed by tryptophan hydroxylase; 5-hydroxytryptophan → serotonin + CO2, catalyzed by aromatic L-amino acid decarboxylase using PLP. [Outside detail: the uploaded sources establish tryptophan → serotonin and BH4 dependence of tryptophan hydroxylase, but do not fully spell out this reaction sequence.]

Question: What important cofactor is used by tryptophan hydroxylase? Answer: Tetrahydrobiopterin (BH4). The slides identify BH4 as an essential cofactor for tryptophan hydroxylase.

Question: Which amino acid is used to make phosphocreatine? Answer: Creatine is synthesized from glycine, arginine, and methionine and then phosphorylated to phosphocreatine.

Question: What is the metabolic role of phosphocreatine? Answer: Phosphocreatine serves as a high-energy phosphate reserve that can rapidly regenerate ATP.

Question: What is the pathway for creatine and phosphocreatine biosynthesis? Answer: Arginine + glycine → guanidinoacetate + ornithine; guanidinoacetate + S-adenosylmethionine (SAM) → creatine + S-adenosylhomocysteine; creatine + ATP ⇌ phosphocreatine + ADP, catalyzed in the final step by creatine kinase.

Question: Which three amino acids contribute to creatine biosynthesis? Answer: Glycine, arginine, and methionine. Chapter 22 textbook(1)

Question: Which compound is required for the synthesis of methionine? Answer: N5-methyltetrahydrofolate (N5-methyl-THF) provides the methyl group required to convert homocysteine to methionine.

Question: Why is N5-methyltetrahydrofolate required for methionine synthesis? Answer: It supplies the one-carbon methyl group transferred to homocysteine by methionine synthase.

Question: What is the folate-dependent pathway for methionine synthesis? Answer: N5-methyl-THF + homocysteine → THF + methionine, catalyzed by methionine synthase with vitamin B12 participating in methyl transfer.

Question: What vitamin is closely linked to folate during methionine synthesis? Answer: Vitamin B12.

Question: What are the bile pigments? Answer: Biliverdin and bilirubin.

Question: Where do bile pigments come from? Answer: They arise from degradation of heme.

Question: What is the pathway for bile-pigment production? Answer: Heme + 3 O2 + 3 NADPH + 3 H+ → biliverdin + Fe2+ + CO + 3 NADP+ + 3 H2O via heme oxygenase; biliverdin + NADPH + H+ → bilirubin + NADP+ via biliverdin reductase.

Question: What is bilirubin's relationship to heme metabolism? Answer: Bilirubin is a bile pigment produced by reduction of biliverdin during heme degradation.

Question: What is glutathione? Answer: Glutathione (GSH) is a tripeptide derived from glutamate, cysteine, and glycine that functions as a cellular redox buffer.

Question: Why is glutathione important? Answer: It functions as a redox buffer, with its cysteine thiol participating in oxidation-reduction reactions.

Question: How is glutathione synthesized and oxidized? Answer: Glutamate + cysteine + ATP → γ-glutamylcysteine; γ-glutamylcysteine + glycine + ATP → glutathione (GSH). Oxidation of two GSH molecules produces glutathione disulfide (GSSG) containing a disulfide bond.

Question: What unusual bond is present in glutathione? Answer: The γ-carboxyl group of glutamate forms the peptide linkage to cysteine, rather than the usual α-carboxyl group. Chapter 22 textbook(1)

Question: Which amino acid is used to make the plant hormone indole-3-acetate (auxin)? Answer: Tryptophan.

Question: What is indole-3-acetate? Answer: Indoleacetate is a plant growth factor derived from tryptophan. Chapter 18 textbook(1)

Question: What is the biosynthetic relationship between tryptophan and indole-3-acetate? Answer: Tryptophan → indole-3-pyruvate → indole-3-acetaldehyde → indole-3-acetate (IAA/auxin).

Question: What other important compounds arise from tryptophan metabolism? Answer: Serotonin, indoleacetate, and nicotinate, with nicotinate serving as a precursor of NAD and NADP in animals. Chapter 18 textbook(1)

Question: What is the precursor to phenylalanine? Answer: Prephenate is the branch-specific precursor leading from chorismate toward phenylalanine.

Question: Where does the phenylalanine precursor arise? Answer: Prephenate arises from chorismate in the aromatic amino acid biosynthetic pathway.

Question: What is the pathway leading toward phenylalanine? Answer: Erythrose 4-phosphate + phosphoenolpyruvate (PEP) → shikimate → chorismate → prephenate → phenylalanine.

Question: Which three aromatic amino acids arise from the chorismate pathway? Answer: Phenylalanine, tyrosine, and tryptophan. Chorismate branches toward tryptophan on one side and phenylalanine/tyrosine on the other.

Question: Which reaction step in the synthesis of proline is nonenzymatic? Answer: The spontaneous cyclization of glutamate γ-semialdehyde to Δ1-pyrroline-5-carboxylate (P5C).

Question: What happens during the nonenzymatic step of proline synthesis? Answer: Glutamate γ-semialdehyde spontaneously cyclizes to Δ1-pyrroline-5-carboxylate (P5C). 3- Ch22 Candas Lecture (1)(3)

Question: What is the pathway for proline synthesis from glutamate? Answer: Glutamate + ATP → γ-glutamyl phosphate + ADP; γ-glutamyl phosphate + NAD(P)H + H+ → glutamate γ-semialdehyde + Pi + NAD(P)+; glutamate γ-semialdehyde → spontaneously Δ1-pyrroline-5-carboxylate (P5C); P5C + NAD(P)H + H+ → proline + NAD(P)+.

Question: What is the direct cyclic intermediate immediately preceding proline? Answer: Δ1-Pyrroline-5-carboxylate (P5C). The textbook specifically notes rapid, reversible cyclization of the γ-semialdehyde to P5C. Chapter 22 textbook(1)

Question: What enzymes are involved in assimilation of inorganic nitrogen into organic molecules? Answer: Glutamine synthetase and glutamate synthase (GOGAT) form the major pathway of ammonium assimilation.

Question: Why are glutamine and glutamate central to nitrogen assimilation? Answer: They are the critical entry points through which NH4+ is incorporated into amino acids and other nitrogen-containing biomolecules.

Question: How do glutamine synthetase and glutamate synthase assimilate ammonium? Answer: GS: glutamate + NH4+ + ATP → glutamine + ADP + Pi + H+. GOGAT: α-ketoglutarate + glutamine + NAD(P)H + H+ → 2 glutamate + NAD(P)+.

Question: What other enzyme can directly incorporate ammonium into glutamate? Answer: Glutamate dehydrogenase: α-ketoglutarate + NH4+ + NADPH + H+ → glutamate + NADP+ + H2O. The textbook notes that GDH can use NAD(P)H, while specifically stating that reducing power for ammonium assimilation is furnished by NADPH. Chapter 22 textbook(1)

Question: How is nitrogen fixation regulated? Answer: Nitrogen fixation is regulated by fixed-nitrogen availability and by protection of nitrogenase from O2.

Question: Why must nitrogenase activity be regulated? Answer: N2 reduction requires 16 ATP per N2, and nitrogenase is highly sensitive to oxygen, so fixation is restricted to conditions where fixed nitrogen is needed and nitrogenase can function.

Question: What is the overall nitrogen-fixation reaction? Answer: N2 + 10 H+ + 8 e− + 16 ATP → 2 NH4+ + H2 + 16 ADP + 16 Pi.

Question: How can nitrogen-fixing organisms protect nitrogenase from oxygen? Answer: They maintain a low-O2 environment around nitrogenase; in legume root nodules, leghemoglobin binds O2 and helps maintain a sufficiently low free-O2 concentration.

Question: How do glutamine synthetase and glutamate synthase work together? Answer: Glutamine synthetase incorporates NH4+ into glutamine; glutamate synthase transfers glutamine's amide nitrogen to α-ketoglutarate, producing two glutamates.

Question: What is the overall purpose of the GS-GOGAT pathway? Answer: It incorporates inorganic NH4+ into organic nitrogen, producing glutamate that can donate amino groups for biosynthesis.

Question: What are the specific reactions of the GS-GOGAT pathway? Answer: GS: glutamate + NH4+ + ATP → glutamine + ADP + Pi + H+. GOGAT: α-ketoglutarate + glutamine + NAD(P)H + H+ → 2 glutamate + NAD(P)+. The slides give the net reaction as α-ketoglutarate + NH4+ + NAD(P)H + ATP → glutamate + NAD(P)+ + ADP + Pi and state that the pathway uses 1 ATP and 1 NADPH. 3- Ch22 Candas Lecture (1)(3)

Question: What electron donors can glutamate synthase use? Answer: NADPH can supply the reducing electrons; plants also possess a form of glutamate synthase that uses reduced ferredoxin instead of NADPH. Chapter 22 textbook(1)

Question: Which amino acid gives rise to the biological messenger nitric oxide? Answer: Arginine.

Question: What is nitric oxide in amino acid metabolism? Answer: Nitric oxide (NO) is a biological signaling molecule synthesized from arginine by nitric oxide synthase (NOS).

Question: What is the pathway for nitric oxide synthesis? Answer: Arginine + NADPH + H+ + 2 O2 → citrulline + NO + NADP+ + 2 H2O, catalyzed by nitric oxide synthase (NOS) and requiring tetrahydrobiopterin (BH4). [Outside detail: the uploaded slides identify arginine, NOS, and BH4, but the fully balanced overall reaction is added for pathway completeness.]

Question: What important cofactor is required by nitric oxide synthase? Answer: Tetrahydrobiopterin (BH4).

Question: Biosynthesis of which amino acid will be crippled if a cell cannot obtain tetrahydrofolate? Answer: Methionine biosynthesis is impaired because N5-methyl-THF supplies the methyl group used to convert homocysteine to methionine.

Question: Why does methionine biosynthesis depend on tetrahydrofolate? Answer: N5-methyl-THF carries the methyl group transferred to homocysteine in the methionine synthase reaction.

Question: What is the THF-dependent methionine synthesis reaction? Answer: N5-methyl-THF + homocysteine → THF + methionine, catalyzed by methionine synthase with vitamin B12 participating in methyl transfer.

Question: What is the broader metabolic function of tetrahydrofolate that explains this dependence? Answer: THF derivatives carry and transfer one-carbon units in metabolism.

Question: What reversible covalent modification regulates glutamine synthetase? Answer: Adenylylation and deadenylylation of a Tyr residue.

Question: How does adenylylation affect glutamine synthetase? Answer: Adenylylation decreases glutamine synthetase activity, whereas deadenylylation increases its activity.

Question: What regulatory cascade controls glutamine synthetase adenylylation? Answer: PII regulatory protein → adenylyltransferase (AT) → adenylylation/deadenylylation of glutamine synthetase. PII itself is regulated by uridylylation through uridylyltransferase (UT).

Question: What is notable about regulation of bacterial glutamine synthetase? Answer: It is regulated at multiple levels, including allosteric regulation, reversible covalent modification, and regulation of gene expression. Chapter 22 textbook(1)

Question: Which amino acid is used to make the hormones epinephrine and norepinephrine? Answer: Tyrosine.

Question: What is the relationship between tyrosine and catecholamines? Answer: Tyrosine is the amino acid precursor of dopamine, norepinephrine, and epinephrine.

Question: What is the pathway from tyrosine to epinephrine? Answer: Tyrosine → L-DOPA → dopamine → norepinephrine → epinephrine. Tyrosine hydroxylase uses BH4; aromatic L-amino acid decarboxylase uses PLP; dopamine β-hydroxylase converts dopamine to norepinephrine; phenylethanolamine N-methyltransferase uses S-adenosylmethionine (SAM) to convert norepinephrine to epinephrine.

Question: Which catecholamine is the immediate precursor of epinephrine? Answer: Norepinephrine.

Question: What is shikimate and where does it occur? Answer: Shikimate is a seven-carbon intermediate in aromatic amino acid biosynthesis in bacteria, fungi, and plants.

Question: Why is shikimate important? Answer: It is an intermediate in the pathway that produces the aromatic amino acids tryptophan, phenylalanine, and tyrosine.

Question: How is shikimate related to chorismate? Answer: Erythrose 4-phosphate + phosphoenolpyruvate → first four steps → shikimate → three additional steps, including addition of three carbons from another phosphoenolpyruvate → chorismate.

Question: Do animals use the shikimate pathway to synthesize aromatic amino acids? Answer: No. The pathway described in the textbook occurs in bacteria, fungi, and plants. Chapter 22 textbook(1)

Question: What is chorismate and where does it occur? Answer: Chorismate is the first branch-point intermediate in aromatic amino acid biosynthesis in bacteria, fungi, and plants.

Question: What is the importance of chorismate? Answer: One branch from chorismate leads to tryptophan, while another leads to phenylalanine and tyrosine.

Question: What is the pathway leading to and branching from chorismate? Answer: Erythrose 4-phosphate + PEP → shikimate → chorismate → tryptophan branch OR prephenate → phenylalanine/tyrosine branch.

Question: How is chorismate related to tryptophan biosynthesis? Answer: Chorismate → anthranilate → ribosylphosphate-containing intermediates → indole-3-glycerol phosphate → tryptophan.

Question: Which amino acid provides the nitrogen atom in the indole ring of tryptophan? Answer: Glutamine.

Question: How does glutamine contribute nitrogen to tryptophan biosynthesis? Answer: Glutamine donates its amide nitrogen during formation of anthranilate from chorismate, and this nitrogen ultimately becomes the indole nitrogen of tryptophan.

Question: What is the pathway from chorismate to tryptophan? Answer: Chorismate + glutamine → anthranilate → N-(5′-phosphoribosyl)-anthranilate → subsequent intermediates → indole-3-glycerol phosphate → indole → tryptophan. Tryptophan synthase catalyzes the terminal reactions and its β reaction requires PLP.

Question: What enzyme complex catalyzes the final stages of tryptophan synthesis? Answer: Tryptophan synthase, an α2β2 complex; the β-subunit reaction requires PLP. The lecture slides specifically identify the α2β2 structure and PLP requirement. 3- Ch22 Candas Lecture (1)(3)

Question: What is the anammox reaction? Answer: Anaerobic ammonium oxidation converts nitrite and ammonium ions into nitrogen gas and water.

Question: What is the biological significance of anammox? Answer: It is an anaerobic microbial nitrogen-cycle process that produces N2 and is important in natural environments and wastewater treatment.

Question: What is the overall anammox reaction? Answer: NH4+ + NO2− → N2 + 2 H2O.

Question: What are ladderane lipids and why are they associated with anammox? Answer: They are unusual membrane lipids containing linearly concatenated cyclobutane rings and are enriched in the anammoxosome of anammox bacteria. 3- Ch22 Candas Lecture (1)(3)

Question: What enzymes are involved in incorporating ammonium into metabolism? Answer: Glutamine synthetase, glutamate synthase, and glutamate dehydrogenase are the principal enzymes discussed for incorporation of NH4+ into organic metabolism.

Question: Through which molecules does ammonium primarily enter biosynthetic metabolism? Answer: Glutamate and glutamine are the critical entry points for incorporation of NH4+ into amino acids and other nitrogen-containing biomolecules.

Question: What are the major reactions for incorporation of NH4+ into metabolism? Answer: Glutamine synthetase: glutamate + NH4+ + ATP → glutamine + ADP + Pi + H+. Glutamate synthase: α-ketoglutarate + glutamine + NAD(P)H + H+ → 2 glutamate + NAD(P)+. Glutamate dehydrogenase: α-ketoglutarate + NH4+ + NADPH + H+ → glutamate + NADP+ + H2O. 3- Ch22 Candas Lecture (1)(3) Chapter 22 textbook(1)

Question: What additional reaction uses ammonium in mammalian nitrogen metabolism? Answer: Carbamoyl phosphate synthetase I converts NH4+ and HCO3− into carbamoyl phosphate using 2 ATP in the mitochondrial matrix, providing the first nitrogen for urea synthesis.

Question: Which cofactor or functional group in the nitrate reductase electron-transfer chain has the highest reduction potential? Answer: The molybdenum cofactor (MoCo), the final electron carrier before nitrate.

Question: Why does MoCo receive electrons late in the nitrate reductase electron-transfer chain? Answer: Electrons are transferred sequentially through the enzyme's redox centers until MoCo transfers them to the substrate nitrate, reducing NO3− to NO2−.

Question: What is the electron-transfer pathway through nitrate reductase? Answer: NADH → cysteine −SH groups → FAD → cytochrome b557 → molybdenum cofactor (MoCo) → NO3− → NO2−. The textbook explicitly gives this sequence. Chapter 22 textbook(1)

Question: What is the overall first step of nitrate assimilation? Answer: NO3− → NO2− is a two-electron reduction catalyzed by nitrate reductase. Electrons originate from NADH and pass through cysteine −SH groups → FAD → cytochrome b557 → MoCo → nitrate.