Amino Acid Metabolism and the Urea Cycle — Transamination, Deamination, Gluconeogenesis, and Nitrogen Excretion

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Amino Acid Metabolism covers how amino acids are processed — their nitrogen removal (transamination, oxidative deamination), fate of their carbon skeletons, and the urea cycle for ammonia detoxification. INI CET frequently tests the urea cycle enzymes, glucogenic vs ketogenic amino acids, and inborn errors.

High-Yield Facts for INI CET:

• Transamination: Amino group transferred from amino acid → α-ketoglutarate → glutamate (ALT/AST); vitamin B6 (PLP) is cofactor
• Oxidative deamination: Glutamate → α-ketoglutarate + NH₃ (glutamate dehydrogenase; uses NAD⁺ or NADP⁺); this is the primary source of free ammonia
• Urea cycle location: Mitochondrial matrix + cytosol (liver); converts toxic NH₃ + CO₂ → urea (non-toxic, water-soluble, excreted in urine)
• Urea cycle enzymes: Carbamoyl phosphate synthetase I (CPS-I), Ornithine transcarbamylase (OTC — most common urea cycle disorder), Argininosuccinate synthetase, Argininosuccinate lyase, Arginase
• Glucogenic amino acids: Can be converted to glucose (pyruvate or TCA intermediates); Ketogenic: Can be converted to acetyl-CoA/acetoacetate (leucine, lysine only); Both: Isoleucine, tryptophan, phenylalanine, tyrosine, threonine

⚡ Exam tip: In liver failure, ammonia accumulates → hepatic encephalopathy (asterixis, confusion, coma). Ornithine transcarbamylase (OTC) deficiency is the most common urea cycle disorder — X-linked, presents in newborn males with hyperammonemia.

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Amino Acid Metabolism and the Urea Cycle — INI CET (AIIMS PG) Study Guide

Protein Digestion and Amino Acid Absorption

Digestion:

• Stomach: Pepsin (from pepsinogen) begins protein digestion; HCl denatures proteins
• Pancreas: Trypsin, chymotrypsin, carboxypeptidases (from inactive zymogens) continue hydrolysis
• Small intestine: Aminopeptidases and dipeptidases complete hydrolysis to free amino acids

Absorption:

• Occurs in jejunum via Na⁺-dependent transporters (different for neutral, acidic, basic amino acids)
• Disorders: Hartnup disease (neutral amino acid transporter defect → pellagra-like symptoms)

Transamination and Deamination

Transamination:

• Transfer of amino group from amino acid to α-ketoglutarate → α-keto acid + glutamate
• Catalyzed by transaminases/deaminases (ALT, AST)
• Vitamin B6 (pyridoxal phosphate/PLP) is the cofactor — binds to enzyme’s active site
• Most amino acids undergo transamination to glutamate before further processing

Key Transaminases:

Enzyme	Reaction	Clinical Use
ALT (SGPT)	Alanine + α-KG ↔ Pyruvate + Glutamate	Liver injury marker
AST (SGOT)	Aspartate + α-KG ↔ OAA + Glutamate	Liver/cardiac injury marker
Branched-chain amino acid transaminase	BCAA + α-KG ↔ corresponding α-ketoacid + Glutamate	Catabolizes leucine, isoleucine, valine

Oxidative Deamination:

• Glutamate dehydrogenase (GDH): Glutamate + NAD(P)⁺ + H₂O → α-ketoglutarate + NH₃ + NAD(P)H
• This is the primary reaction that generates free ammonia for the urea cycle
• GDH is allosterically regulated: ATP and GTP inhibit; ADP and GDP activate
• This links amino acid metabolism to energy status — when energy is low, amino acids are deaminated and used for gluconeogenesis

The Glutamine Shuttle:

• Glutamine synthesized from glutamate + NH₃ (glutamine synthetase, requires ATP)
• Glutamine carries ammonia to kidney and intestine
• In kidney: glutamine → NH₃ (excreted as NH₄⁺) → helps with acid excretion (compensates for metabolic acidosis)
• In intestine: glutamine → glutamate + NH₃ → portal circulation → liver

The Urea Cycle

Purpose: Convert toxic ammonia (NH₃) to non-toxic urea for excretion

Overall Reaction: 2 NH₃ + CO₂ + 3 ATP + aspartate → Urea + fumarate + 2 ADP + AMP + PPi + 2 Pi

Steps (alternating between mitochondria and cytosol):

Step 1: Formation of Carbamoyl Phosphate (Mitochondria)

• CPS-I (Carbamoyl phosphate synthetase I): NH₃ + CO₂ + 2 ATP → Carbamoyl phosphate
• Requires: 2 ATP (1 for activation, 1 for phosphorylation), Mg²⁺, N-acetylglutamate (NAG) as essential activator
• NAG is synthesized from acetyl-CoA + glutamate (arginine activates NAG synthetase)
• CPS-I is the rate-limiting enzyme of the urea cycle

Step 2: Ornithine Transcarbamylase (OTC) — Mitochondrial

• Carbamoyl phosphate + Ornithine → Citrulline (released into cytosol)
• Most commonly deficient urea cycle enzyme (X-linked recessive)
• OTC deficiency → hyperammonemia, orotic aciduria (orotic acid in urine)

Step 3: Argininosuccinate Synthetase (ASS) — Cytosol

• Citrulline + Aspartate + ATP → Argininosuccinate + AMP + PPi
• Uses ATP (high energy)

Step 4: Argininosuccinate Lyase (ASL) — Cytosol

• Argininosuccinate → Arginine + Fumarate
• Fumarate enters TCA cycle (links urea cycle to energy metabolism)

Step 5: Arginase — Cytosol

• Arginine → Ornithine + Urea
• Ornithine returns to mitochondria (via ornithine transporter)
• Arginine is also the source of NO synthesis (via nitric oxide synthase)

Energy Cost: 3 ATP → 4 high-energy phosphate bonds (ATP → AMP + PPi is equivalent to 2 ATP)

NAG (N-acetylglutamate) as Regulator:

• NAG is an obligatory activator of CPS-I
• Synthesized by N-acetylglutamate synthase (NAGS) — activated by arginine
• If NAG is absent, CPS-I is inactive → urea cycle does not function
• Carglumic acid (N-carbamylglutamate) is a drug for NAGS deficiency — mimics NAG

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Fate of Amino Acid Carbon Skeletons

After transamination/deamination, amino acids become α-ketoacids (carbon skeletons):

Glucogenic Amino Acids (→ Pyruvate or TCA intermediates → Glucose):

• Alanine → Pyruvate
• Cysteine → Pyruvate, SO₄²⁻
• Glycine → Serine → Pyruvate
• Histidine → Glutamate → α-KG
• Serine → Pyruvate
• Threonine → Pyruvate
• Valine → Succinyl-CoA
• Glutamate → α-KG
• Glutamine → α-KG
• Arginine → α-KG
• Proline → α-KG

Ketogenic Amino Acids (→ Acetyl-CoA or Acetoacetate):

• Leucine → Acetyl-CoA + Acetoacetate (purely ketogenic — only 2 amino acids are purely ketogenic)
• Lysine → Acetoacetate

Both Glucogenic and Ketogenic:

• Isoleucine → Acetyl-CoA + Succinyl-CoA
• Tryptophan → Acetyl-CoA + Alanine (indole ring → acetoacetate)
• Phenylalanine → Fumarate + Acetoacetate (tyrosine transamination → fumarate)
• Tyrosine → Fumarate + Acetoacetate
• Threonine → Pyruvate + Acetyl-CoA

Leucine Catabolism:

• Only purely ketogenic amino acid
• Deaminated → α-ketoisocaproate → HMG-CoA → acetoacetate + acetyl-CoA
• HMG-CoA also produced from leucine → cholesterol synthesis (may explain why leucine-rich diets affect cholesterol)

One-Carbon Metabolism and Methylation

Folate Cycle:

• THF (tetrahydrofolate) accepts and transfers one-carbon units
• Sources of one-carbon units: Serine (most important), glycine, choline, histidine
• One-carbon units carried at 3 oxidation levels: Formyl (-CHO), methylene (-CH₂-), methyl (-CH₃)
• Functions: Purine synthesis (formyl-THF donates C2 and C8 of purine ring), Pyrimidine synthesis (thymidylate synthase uses methyl-THF for dTMP synthesis), Amino acid metabolism (histidine → formiminoglutamate), Methylation reactions

S-Adenosylmethionine (SAM) Cycle:

• Methionine + ATP → SAM (active methyl donor)
• SAM donates methyl → homocysteine (becomes SAH → homocysteine)
• Homocysteine → Methionine (via methionine synthase, requires B12) OR → Cysteine (via transsulfuration, requires B6)
• Elevated homocysteine = risk factor for thrombosis, atherosclerosis, neural tube defects

Methylation Reactions:

• DNA methylation (CpG islands → gene silencing)
• RNA methylation (m6A in mRNA)
• Phosphatidylcholine synthesis (phosphatidylethanolamine → phosphatidylcholine)
• Myelin formation, neurotransmitters (dopamine → epinephrine via phenylethanolamine-N-methyltransferase)

Metabolic Disorders of Amino Acid Metabolism

Phenylketonuria (PKU):

• Deficiency of phenylalanine hydroxylase (PAH) OR BH4 cofactor deficiency
• Phenylalanine accumulates → converted to phenylpyruvate → excreted as phenylacetate (musty odor)
• Results: Intellectual disability, seizures, fair hair/skin (tyrosine deficiency → melanin reduced), eczema
• Treatment: Low phenylalanine diet (special medical foods); BH4 supplementation for BH4-responsive PKU
• Variant: Tyrosinemia (fumarylacetoacetate hydrolase deficiency) → severe liver disease,得名 from fumarylacetoacetate

Maple Syrup Urine Disease (MSUD):

• Deficiency of branched-chain α-ketoacid dehydrogenase (BCKDH) complex
• Cannot metabolize leucine, isoleucine, valine → their α-ketoacids accumulate
• Presents: Sweet/maple syrup odor of urine, neurological dysfunction, feeding difficulty in newborn
• Treatment: Low BCAA diet; thiamine supplementation (some forms are thiamine-responsive)

Homocystinuria:

• Deficiency of cystathionine β-synthase (CBS) — most common cause
• Homocysteine accumulates → urinary excretion; elevated blood homocysteine
• Features: Marfanoid habitus, lens dislocation (downward — infra), intellectual disability, thromboembolism, osteoporosis
• Treatment: B6 supplementation (pyridoxine-responsive in some), methionine-restricted diet, betaine supplementation
• Other causes: Defects in homocysteine remethylation (MTHFR deficiency, cobalamin metabolism)

Alkaptonuria:

• Deficiency of homogentisate oxidase
• Homogentisic acid accumulates → oxidized to benzoquinone acetic acid → dark pigment in connective tissue (ochronosis), urine turns black on standing
• Clinical: Dark urine, arthritis (ochronotic), dark connective tissue

Hartnup Disease:

• Defect in neutral amino acid transporter (SLC6A19) in intestine and kidney
• Tryptophan malabsorption → reduced niacin synthesis → pellagra-like symptoms (photosensitive rash, diarrhea, neurological symptoms)
• Treatment: Niacin (nicotinamide) supplementation, high-protein diet

Cystinuria:

• Defect in dibasic amino acid transporter (SLC3A1, SLC7A9) — cystine, lysine, ornithine, arginine
• Cystine stones in urinary tract (cystine is poorly soluble)
• Treatment: Hydration, alkalinize urine, penicillamine (binds cystine → more soluble)

Urea Cycle Disorders:

• Most common: OTC deficiency (X-linked); CPS-I deficiency (autosomal recessive)
• Presents: Hyperammonemia, lethargy, vomiting, cerebral edema, respiratory alkalosis (from hyperventilation)
• Lab: Elevated ammonia, orotic acid in OTC deficiency (since carbamoyl phosphate accumulates → shunts to pyrimidine synthesis → orotic acid)
• TX: Protein restriction, nitrogen scavengers (sodium benzoate + phenylacetate/phenylbutyrate), carglumic acid (if NAGS deficiency), dialysis if severe, liver transplant (definitive)

⚡ INI CET High-Yield: Urea cycle alternates between mitochondria and cytosol — CPS-I and OTC are mitochondrial; the rest are cytosolic. Fumarate from argininosuccinate lyase links to TCA cycle. Elevated ammonia = encephalopathy. Orotic aciduria in OTC deficiency distinguishes it from CPS-I deficiency. Glucagon stimulates ketogenesis from amino acids during fasting. SAM is the universal methyl donor. Remember the distinction between transamination (no ammonia release, PLP cofactor) and oxidative deamination (produces ammonia via glutamate dehydrogenase).

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