14.5 Nitrogen Metabolism: Nitrogen Fixation, Amino Acid Metabolism, and the Urea Cycle

14.5 Nitrogen Metabolism: Nitrogen Fixation, Amino Acid Metabolism, and the Urea Cycle

Quick Answer: Nitrogen metabolism (area G3, 6 items) lists nitrogen fixation, amino acid metabolism, and the urea cycle. Know nitrogenase stoichiometry, how transamination and glutamate dehydrogenase funnel amino groups into ammonium, every urea-cycle step with its compartment and cost, and the classic inborn errors.

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Biological Nitrogen Fixation

Only certain bacteria and archaea can reduce atmospheric $N_2$. Examples include free-living Azotobacter and cyanobacteria, and Rhizobium in legume root nodules.

$N_2 + 8H^+ + 8e^- + 16\ ATP \rightarrow 2NH_3 + H_2 + 16\ ADP + 16\ P_i$

• Nitrogenase has two parts: the Fe protein (reductase), which hydrolyses ATP and passes electrons on, and the MoFe protein, whose FeMo-cofactor binds and reduces $N_2$. Ferredoxin supplies the electrons.
• The enzyme is destroyed by oxygen. Legume nodules contain leghemoglobin, which binds $O_2$ and keeps its free concentration low while still supplying respiration.
• The industrial counterpart, the Haber-Bosch process, is covered in Section 4.1.

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Assimilating Ammonia

• Glutamine synthetase: glutamate + $NH_4^+$ + ATP gives glutamine + ADP + $P_i$. This is the main entry point of fixed nitrogen in bacteria and plants and a key ammonia-detoxifying step in animal tissues.
• Glutamate synthase (GOGAT) in bacteria and plants: glutamine + $\alpha$-ketoglutarate + NADPH gives 2 glutamate.
• Glutamate dehydrogenase: $\alpha$-ketoglutarate + $NH_4^+$ + NAD(P)H $\rightleftharpoons$ glutamate. The reaction runs in either direction depending on conditions.

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Amino Acid Catabolism

Transamination

Aminotransferases (transaminases) use pyridoxal phosphate to move an amino group from an amino acid to $\alpha$-ketoglutarate:

• ALT: alanine + $\alpha$-ketoglutarate $\rightleftharpoons$ pyruvate + glutamate
• AST: aspartate + $\alpha$-ketoglutarate $\rightleftharpoons$ oxaloacetate + glutamate

Raised blood ALT and AST indicate liver or muscle damage. Transamination does not remove nitrogen; it collects it on glutamate.

Oxidative Deamination and Nitrogen Transport

In liver mitochondria, glutamate dehydrogenase releases the nitrogen as $NH_4^+$ and regenerates $\alpha$-ketoglutarate. Free ammonia is toxic, so other tissues send nitrogen to the liver in safer forms:

• Glutamine carries two nitrogens in blood from most tissues; glutaminase releases $NH_4^+$ in the liver and kidney.
• The glucose-alanine cycle: muscle transaminates pyruvate to alanine, and the liver converts alanine back to pyruvate for gluconeogenesis.

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The Urea Cycle

Citrulline leaves the mitochondrion, and ornithine returns to it.

Overall:

$NH_4^+ + HCO_3^- + \text{aspartate} + 3\ ATP + H_2O \rightarrow \text{urea} + \text{fumarate} + 2\ ADP + 2\ P_i + AMP + PP_i$

• Sources of urea's atoms: one nitrogen from $NH_4^+$ through carbamoyl phosphate, the other from aspartate; the carbon from $HCO_3^-$.
• Cost: 3 ATP, but 4 high-energy phosphate bonds, because $PP_i$ is hydrolysed to $2P_i$.
• Link to the citric acid cycle (aspartate-argininosuccinate shunt): fumarate is hydrated to malate and oxidized to oxaloacetate, which is transaminated back to aspartate. The NADH from this step partly offsets the cycle's energy cost.
• Regulation: CPS I is inactive without N-acetylglutamate, made from acetyl-CoA and glutamate. Arginine stimulates its synthesis, so a high-protein meal speeds the cycle. Long-term, cycle enzymes are induced by high-protein diets and fasting.

Hyperammonemia: urea-cycle defects cause ammonia to build up, with lethargy, vomiting, and encephalopathy. OTC deficiency, which is X-linked, is the most common. Ammonia may deplete $\alpha$-ketoglutarate through glutamate formation, starving the brain's citric acid cycle.

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Fates of the Carbon Skeletons

The nine essential amino acids for humans are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

Inborn Errors of Amino Acid Metabolism

Amino Acids as Precursors

Glycine and succinyl-CoA form heme (via ALA synthase). Tyrosine gives dopamine, noradrenaline, adrenaline, thyroid hormones, and melanin. Tryptophan gives serotonin, melatonin, and niacin. Histidine gives histamine, arginine gives nitric oxide, and glutamate gives GABA.

Nitrogen Excretion

Animals excrete nitrogen as ammonia (ammonotelic, most aquatic animals), urea (ureotelic, mammals), or uric acid (uricotelic, birds and reptiles).