Transamination and delamination

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Transamination and Deamination

These two reactions are the primary ways the body removes nitrogen from amino acids, and they work sequentially - transamination first funnels nitrogen into glutamate, then deamination releases it as free ammonia.

1. Transamination

Definition: The transfer of an amino (-NH₂) group from an amino acid to an α-keto acid, converting the donor into its corresponding α-keto acid while the acceptor becomes an amino acid.

Transamination reaction showing amino acid and α-keto acid pairs with PLP as cofactor

Key Features

Feature	Detail
Enzyme	Aminotransferases (transaminases)
Cofactor	Pyridoxal phosphate (PLP) - derived from Vitamin B6
Common acceptor	α-Ketoglutarate → glutamate
Reversibility	Freely reversible (equilibrium constant ~1)
Mechanism	"Ping-pong" (alternating substrate addition and product release)
Exceptions	Lysine and threonine do NOT undergo transamination (Harper's also adds proline and hydroxyproline)

Prototypical Reactions

Aspartate aminotransferase (AST / GOT): Aspartate + α-Ketoglutarate ⇌ Oxaloacetate + Glutamate
Alanine aminotransferase (ALT / GPT): Alanine + α-Ketoglutarate ⇌ Pyruvate + Glutamate

Why α-Ketoglutarate/Glutamate is Central

Because virtually all aminotransferases use α-ketoglutarate as the nitrogen acceptor, the amino groups from most amino acids ultimately concentrate in glutamate. This is physiologically critical: glutamate is the only amino acid that undergoes oxidative deamination at an appreciable rate, linking transamination to ammonia production.

Mechanism (PLP as Nitrogen Carrier)

PLP sits at the active site covalently bound to the enzyme's lysine residue (as a Schiff base). During transamination:

The amino acid displaces lysine, forming a Schiff base with PLP (external aldimine).
The Schiff base rearranges (tautomerization) to a ketimine.
Hydrolysis releases the α-keto acid and leaves PLP in the pyridoxamine phosphate (PMP) form (now carrying the amino group).
An α-keto acid (usually α-ketoglutarate) reacts with PMP, reverses the steps, picks up the NH₂ group, and is released as glutamate - regenerating enzyme-bound PLP.

Clinical Relevance

AST and ALT are released into the blood when liver or cardiac cells are injured. Elevated serum levels are key markers of hepatocellular damage (hepatitis, cirrhosis) and myocardial infarction.

2. Deamination (Oxidative Deamination)

Definition: The removal of an amino group from glutamate as free ammonia (NH₃), with simultaneous oxidation of the carbon skeleton back to α-ketoglutarate. This is the main step that liberates nitrogen as free ammonia for urea synthesis.

Combined transamination + oxidative deamination (amino acid disposal) and reductive amination (amino acid synthesis)

Glutamate Dehydrogenase (GDH) - The Key Enzyme

Feature	Detail
Substrate	L-Glutamate
Location	Mitochondrial matrix (liver and kidney primarily)
Coenzyme	NAD⁺ (oxidative deamination) or NADPH (reductive amination) - unique dual specificity
Products	α-Ketoglutarate + NH₃ + NADH (or NADPH)
Activator	ADP (low energy signal)
Inhibitor	GTP (high energy signal)

Reaction: Glutamate + NAD⁺ → α-Ketoglutarate + NH₃ + NADH

Direction of Reaction

Condition	Direction
After protein meal (high glutamate)	Forward → amino acid degradation → NH₃ production
High ammonia levels	Reverse → reductive amination → glutamate synthesis
Low energy (high ADP)	Forward (ADP activates GDH)
High energy (high GTP)	Reverse inhibited (GTP inhibits GDH)

D-Amino Acid Oxidase (DAO)

A secondary deamination pathway in peroxisomes of liver and kidney:

Acts on D-amino acids (from diet, not used in mammalian proteins)
Flavin adenine dinucleotide (FAD)-dependent
Produces α-keto acid + NH₃ + H₂O₂
Increased DAO activity has been linked to susceptibility to schizophrenia (degrades D-serine, a modulator of NMDA receptors)

3. The Link Between Transamination and Deamination (Transdeamination)

These two processes act in sequence - a pathway sometimes called transdeamination:

Most amino acids
        ↓  (Aminotransferase + PLP)
    Glutamate  +  α-keto acid
        ↓  (GDH + NAD⁺)
α-Ketoglutarate  +  NH₃  →  enters urea cycle

This two-step sequence allows the amino nitrogen from virtually all amino acids (not just glutamate) to be funneled into the urea cycle. α-Ketoglutarate is regenerated in the second step and is recycled back into the first, making the whole system catalytic.

4. Ammonia Transport to the Liver

Since ammonia is toxic (especially to the brain), peripheral tissues do not release it directly. Two mechanisms carry nitrogen safely to the liver:

Glutamine shuttle: Glutamine synthetase combines NH₃ + glutamate → glutamine (non-toxic). In the liver, glutaminase cleaves it back to glutamate + NH₃, which then enters GDH.
Glucose-alanine cycle: Muscle transamination produces alanine from pyruvate. Alanine travels to the liver, ALT converts it back to pyruvate + glutamate; GDH then deaminates glutamate to release NH₃ for the urea cycle. The pyruvate is used for gluconeogenesis.

5. Summary Comparison

Feature	Transamination	Oxidative Deamination
Nitrogen fate	Transferred to another α-keto acid	Released as free NH₃
Enzyme	Aminotransferases	Glutamate dehydrogenase (GDH)
Cofactor	PLP (Vitamin B6)	NAD⁺ / NADPH
Location	Cytoplasm and mitochondria	Mitochondrial matrix
Reversibility	Freely reversible	Reversible (direction regulated by energy status)
Net result	No nitrogen loss; interconverts amino acids	Nitrogen leaves amino acid pool as NH₃
Role	Funnels nitrogen into glutamate	Releases that nitrogen for urea synthesis

Sources:

Basic Medical Biochemistry: A Clinical Approach, 6e, pp. 1313-1315
Lippincott's Illustrated Reviews: Biochemistry, 8e, pp. 706-710
Harper's Illustrated Biochemistry, 32e, pp. 293-295

How does the urea cycle capture ammonia from GDH?

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How the Urea Cycle Captures Ammonia from GDH

The handoff from GDH to the urea cycle is elegant - both processes share the same compartment (the mitochondrial matrix), so ammonia never has to travel far or enter the blood.

The Two Nitrogen Sources of Urea

Each urea molecule carries two nitrogen atoms. They come from different sources:

Nitrogen atom	Source	Route
N-1	Free NH₃ from GDH	→ Carbamoyl phosphate → citrulline
N-2	Amino group of aspartate	→ Argininosuccinate → arginine

Glutamate is the immediate precursor of both - it donates NH₃ via GDH (N-1) and donates its amino group to oxaloacetate via AST to make aspartate (N-2).

Step-by-Step: GDH → Urea Cycle

Here is the full cycle diagram showing exactly where and how ammonia enters:

Urea cycle - showing mitochondrial entry of ammonia via CPS-I and cytosolic steps

Step 1 - Carbamoyl Phosphate Synthesis (Mitochondrial Matrix)

GDH releases NH₃ → CPS-I immediately captures it.

NH₃  +  HCO₃⁻  +  2 ATP  ──CPS-I──→  Carbamoyl phosphate  +  2 ADP  +  Pi

Enzyme: Carbamoyl Phosphate Synthetase I (CPS-I) - located in the mitochondrial matrix, co-localised with GDH
Energy cost: 2 ATP hydrolysed (one per phosphorylation step)
Absolute requirement for allosteric activator: N-acetylglutamate (NAG)
The ammonia incorporated here becomes one of the two nitrogens in urea

Why CPS-I and not CPS-II? CPS-II is the cytosolic isoform used for pyrimidine synthesis. It uses glutamine as the nitrogen source (not free NH₃) and does not require NAG. CPS-I is exclusively for the urea cycle.

Step 2 - Citrulline Formation (Still in Mitochondria)

Carbamoyl phosphate  +  Ornithine  ──OTC──→  Citrulline  +  Pi

Enzyme: Ornithine transcarbamylase (OTC) - mitochondrial
The carbamoyl group (carrying GDH-derived nitrogen) is transferred to ornithine
Citrulline is then exported to the cytosol via an antiporter that simultaneously imports ornithine

Steps 3-5 - Cytosolic Reactions (Adding the Second Nitrogen)

Citrulline  +  Aspartate  ──Argininosuccinate synthetase──→  Argininosuccinate  (costs ATP → AMP + PPi)
Argininosuccinate  ──Argininosuccinate lyase──→  Arginine  +  Fumarate
Arginine  ──Arginase-I──→  Urea  +  Ornithine

Aspartate donates the second nitrogen (from its amino group) to form argininosuccinate, then arginine
Arginase-I cleaves arginine, releasing urea (H₂N-CO-NH₂) and regenerating ornithine
Ornithine is shuttled back into the mitochondria to start another round

The NAG "Throttle" on Ammonia Entry

The key regulatory point is CPS-I, controlled by N-acetylglutamate (NAG):

Glutamate  +  Acetyl-CoA  ──NAG synthase──→  NAG
                                ↑
                           Stimulated by Arginine

NAG is synthesized specifically to activate CPS-I - it has no other known function in mammals
Arginine (which builds up when amino acid catabolism is high) stimulates NAG synthesis, activating CPS-I AND producing more ornithine via arginase - a feed-forward amplification loop
The overall cycle is regulated by substrate availability: the more NH₃ produced by GDH, the faster CPS-I runs

The "Krebs Bi-Cycle" Connection

The urea cycle and TCA cycle are physically linked via shared intermediates in the cytosol - sometimes called the Krebs bi-cycle:

Fumarate released from argininosuccinate lyase → converted by fumarase to malate → oxidised to oxaloacetate
Oxaloacetate is transaminated by AST to form aspartate (using glutamate as the nitrogen donor)
This aspartate re-enters the urea cycle as the second nitrogen donor
The NADH generated by malate dehydrogenase can feed the electron transport chain

This means the urea cycle is not just a detox loop - it is physically coupled to the TCA cycle, and the liver can run both simultaneously to process amino acids.

Why Compartmentalisation Matters

The physical co-location of GDH and CPS-I in the mitochondrial matrix is not accidental:

NH₃ is membrane-permeable and toxic - if it were released into the cytosol or blood, it would cause damage
By capturing it instantly with CPS-I in the same compartment, the liver keeps free ammonia concentrations extremely low (normal blood NH₃: 30-60 μM)
If CPS-I fails (e.g. CPS-I deficiency or OTC deficiency), carbamoyl phosphate overflows into the cytosol and drives excess pyrimidine synthesis, producing orotic aciduria - a diagnostic clue

Clinical Consequence: When This Fails

When liver cells are destroyed (hepatic failure), GDH continues producing NH₃ from amino acids but CPS-I activity collapses. NH₃ enters the circulation and crosses the blood-brain barrier. In the brain:

NH₃ + α-ketoglutarate → glutamate (via GDH) - depleting TCA intermediates
Glutamate + NH₃ → glutamine - further draining α-ketoglutarate
Result: impaired TCA cycle, reduced ATP, and hepatic encephalopathy (asterixis, disorientation, coma)

Sources:

Basic Medical Biochemistry: A Clinical Approach, 6e, pp. 1321-1326
Lippincott's Illustrated Reviews: Biochemistry, 8e, pp. 712-715

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