Unit 6: Metabolism III

BTY501 — Biomolecules And Metabolism 7 min read

Amino acids and nucleotides carry the bulk of the body's nitrogen, and because there is no dedicated storage form for excess nitrogen, its removal, recycling, and safe excretion govern this unit. The reactions below explain how the α-amino group is stripped from amino acids, how the residual carbon skeletons feed either glucose or ketone-body synthesis, how toxic ammonia is converted to urea, and how purine and pyrimidine nucleotides are built and dismantled.

Defining features carried through the unit:

Nitrogen has no store: surplus amino acids are catabolised, not stockpiled; their nitrogen ends up in urea, their carbon in energy pathways.
Ammonia is neurotoxic: free NH₃/NH₄⁺ must be trapped (as glutamate/glutamine) and disposed of via the urea cycle.
PLP is the workhorse cofactor: pyridoxal-5′-phosphate (vitamin B₆ derivative) mediates most amino-transfer chemistry.
Glutamate is the nitrogen hub: it collects amino groups by transamination and releases them by oxidative deamination.
Convergence: carbon skeletons funnel into ~7 common intermediates (pyruvate, acetyl-CoA, acetoacetyl-CoA, α-ketoglutarate, succinyl-CoA, fumarate, oxaloacetate).

II. Removal of the α-Amino Group

How nitrogen is detached from amino acids and collected on glutamate.

Amino acid catabolism begins by separating nitrogen from carbon; two coupled reaction types achieve this.

A. Transamination reactions

Transamination transfers an α-amino group from an amino acid to α-ketoglutarate, producing a new α-keto acid and glutamate, without net loss of nitrogen.

General reaction: catalysed by aminotransferases (transaminases), fully reversible.
TEXT
```
amino acid + α-ketoglutarate ⇌ α-keto acid + glutamate
```
Cofactor mechanism: PLP forms a Schiff base (aldimine) with the substrate; the amino group is held transiently as pyridoxamine phosphate (PMP) before being handed to α-ketoglutarate.
Key enzymes and diagnostic value:
- ALT (alanine aminotransferase): alanine + α-KG ⇌ pyruvate + glutamate; raised in hepatocellular injury.
- AST (aspartate aminotransferase): aspartate + α-KG ⇌ oxaloacetate + glutamate; raised in myocardial and liver damage.
Energetics: ΔG ≈ 0, so flow direction depends on substrate concentrations — this reversibility lets transamination both degrade and synthesise non-essential amino acids.
Note: lysine and threonine do not undergo transamination.

B. Oxidative deamination reaction

Oxidative deamination liberates the collected nitrogen as free ammonia, regenerating α-ketoglutarate so transamination can continue.

Central reaction — glutamate dehydrogenase (GDH): located in the mitochondrial matrix, uses NAD⁺ or NADP⁺.
TEXT
```
glutamate + H₂O + NAD(P)⁺ ⇌ α-ketoglutarate + NH₄⁺ + NAD(P)H + H⁺
```
Regulation: allosterically activated by ADP/GDP (low energy → burn amino acids) and inhibited by ATP/GTP.
Coupling with transamination (transdeamination): transaminases channel all amino groups onto glutamate; GDH then releases them, making glutamate the single exit point for nitrogen.
Accessory route: amino acid oxidases (L- and D-, FMN/FAD-dependent) deaminate directly, producing H₂O₂ detoxified by catalase; minor quantitatively.

III. Fate of the Carbon Skeletons

Where the leftover α-keto acids go — glucose or fat.

Once deaminated, the carbon skeleton is classified by the metabolic intermediate it yields.

A. Glucogenic amino acids

Glucogenic amino acids degrade to pyruvate or a citric-acid-cycle intermediate that can be converted to oxaloacetate and hence to glucose.

Definition: any amino acid whose skeleton enters gluconeogenesis via pyruvate, α-ketoglutarate, succinyl-CoA, fumarate, or oxaloacetate.
Examples and entry points:
- → pyruvate: alanine, glycine, serine, cysteine.
- → α-ketoglutarate: glutamate, glutamine, proline, arginine, histidine.
- → succinyl-CoA: methionine, valine, threonine.
- → fumarate: part of phenylalanine and tyrosine.
- → oxaloacetate: aspartate, asparagine.
Significance: the sole amino-acid source of glucose during fasting; acetyl-CoA cannot be converted to glucose, which is why only these skeletons qualify.

B. Ketogenic amino acids

Ketogenic amino acids degrade to acetyl-CoA or acetoacetyl-CoA, feeding ketone-body and lipid synthesis but never glucose.

Definition: skeleton yields acetoacetyl-CoA/acetyl-CoA, which cannot be netted into glucose because the pyruvate dehydrogenase step is irreversible.
Purely ketogenic (only two): leucine and lysine.
Both glucogenic and ketogenic: isoleucine, phenylalanine, tyrosine, tryptophan, threonine (part of each skeleton goes each way).
Worked distinction — phenylalanine: hydroxylated to tyrosine, then split into fumarate (glucogenic) and acetoacetate (ketogenic), illustrating the dual class.

IV. The Urea Cycle

Conversion of toxic ammonia into excretable urea.

The urea cycle (Krebs–Henseleit cycle, 1932) fixes two nitrogen atoms and one carbon into urea, spanning mitochondrion and cytosol of hepatocytes.

A. Reactions of the cycle

The cycle consumes one NH₄⁺, one aspartate, one CO₂, and 4 ATP-equivalents per urea molecule.

Step 0 — activation (mitochondrion): carbamoyl phosphate synthetase I (CPS-I), the committed and rate-limiting step, needs N-acetylglutamate (NAG) as obligatory allosteric activator.
TEXT
```
NH₄⁺ + CO₂ + 2ATP → carbamoyl phosphate + 2ADP + Pi
```
The five cyclic enzymes:
1. Ornithine transcarbamoylase: ornithine + carbamoyl phosphate → citrulline (mitochondrion; citrulline exported).
2. Argininosuccinate synthetase: citrulline + aspartate + ATP → argininosuccinate (ATP → AMP + PPi, i.e. 2 high-energy bonds).
3. Argininosuccinase: argininosuccinate → arginine + fumarate.
4. Arginase: arginine + H₂O → urea + ornithine (ornithine re-enters).
Nitrogen sources: one N from free NH₄⁺ (via GDH), the second from aspartate (via AST), so both amino-group routes converge here.

B. Urea cycle and its significance

The cycle is the principal detoxification and nitrogen-excretion pathway, integrated with the citric-acid cycle.

Detoxification: removes ~90% of waste nitrogen as urea (~30 g/day in adults); protects the CNS from ammonia.
Krebs bicycle link: the fumarate released in step 3 is oxidised to oxaloacetate, transaminated back to aspartate — coupling the urea and citric-acid cycles.
Energetic cost: 4 ATP-equivalents consumed, partly offset by NADH from the fumarate→oxaloacetate arm.
Clinical relevance: enzyme deficiencies (e.g. OTC deficiency, X-linked) cause hyperammonemia; the pathway also explains protein-restricted diets in liver failure.

V. Biosynthesis of Nucleotides

De novo assembly of purine and pyrimidine ribonucleotides.

Nucleotides are built either de novo from small precursors or salvaged from free bases; both routes require PRPP (5-phosphoribosyl-1-pyrophosphate).

A. Purine biosynthesis

Purines are built directly onto the ribose-5-phosphate scaffold, atom by atom, giving IMP as the first complete nucleotide.

Precursor atoms: glycine, glutamine (2 N), aspartate, CO₂, and N¹⁰-formyl-THF (2 C).
Committed step: glutamine-PRPP amidotransferase converts PRPP → phosphoribosylamine; inhibited by AMP, GMP, IMP (feedback).
Branch from IMP:
1. → AMP: needs GTP + aspartate (adenylosuccinate intermediate).
2. → GMP: needs ATP + glutamine (via XMP).
  - Reciprocal control: GTP drives AMP synthesis, ATP drives GMP synthesis, balancing the pools.
Salvage: HGPRT and APRT reattach free bases to PRPP; HGPRT loss causes Lesch–Nyhan syndrome.

B. Pyrimidine biosynthesis

The pyrimidine ring is completed first as free orotate, then attached to ribose-phosphate.

Precursor atoms: glutamine, CO₂ (via cytosolic CPS-II), and aspartate.
Rate-limiting step: CPS-II forms carbamoyl phosphate; activated by ATP/PRPP, inhibited by UTP.
Ring completion: carbamoyl phosphate + aspartate → carbamoyl aspartate → dihydroorotate → orotate → (with PRPP) OMP → UMP.
Downstream: UMP → UTP → CTP (glutamine-dependent amination); dUMP → dTMP via thymidylate synthase using N⁵,N¹⁰-methylene-THF — the target of 5-fluorouracil and methotrexate.

VI. Degradation of Nucleotides

Catabolism of purines to uric acid and pyrimidines to soluble products.

Degradation strips phosphate and sugar, then dismantles the base; the two ring types diverge sharply in their end products.

A. Purine degradation

Purines converge on uric acid, a poorly soluble excretory product in humans.

Pathway: AMP/GMP → (nucleotidase, deaminase) → hypoxanthine/xanthine → xanthine oxidase → uric acid.
TEXT
```
hypoxanthine → xanthine → uric acid   (both by xanthine oxidase, O₂-dependent)
```
Species note: humans lack urate oxidase, so uric acid is the terminal product; most mammals excrete allantoin.
Clinical link: urate overproduction/underexcretion causes gout; treated with allopurinol, a xanthine-oxidase inhibitor.

B. Pyrimidine degradation

Pyrimidines break down to highly soluble compounds requiring no special excretory handling.

Cytosine/uracil → β-alanine; thymine → β-aminoisobutyrate.
Ring opening: dihydropyrimidine dehydrogenase reduces the ring, which is then hydrolysed.
End products: β-alanine and β-aminoisobutyrate are further degraded to CO₂, NH₃, and water, the nitrogen entering the urea cycle — closing the loop with Section IV.