BB ch 18

Oxidative Degradation of Amino Acids

• Three physiological contexts in humans when amino acids are oxidized

  • Continuous turnover of cellular proteins (normal synthesis ⇌ degradation)

  • Excess amino acids from a protein-rich diet

  • Starvation or uncontrolled diabetes (muscle proteins mobilized for energy)

First Step: Removal of the $\alpha$-Amino Group (Transamination)

• Catalyzed by aminotransferases (aka transaminases)

• General reaction

  • $\text{Amino acid}<em>1 + \alpha\text{-ketoglutarate} \rightleftharpoons \alpha\text{-keto acid}</em>1 + \text{glutamate}$

• Key participants

  • Amino donor: any amino acid

  • Amino acceptor: $\alpha$-ketoglutarate

  • Coenzyme: pyridoxal phosphate (PLP, active form of vitamin B$_6$)

• Reversibility: reaction readily reversible → central for amino-group trafficking

Fate of Carbon Skeletons: Glucogenic vs Ketogenic

• Glucogenic amino acids → carbon skeletons yielding glucose precursors (pyruvate or oxaloacetate)

• Ketogenic amino acids → carbon skeletons yielding acetyl-CoA or acetoacetyl-CoA → ketone bodies

• Visualization (Fig. 18-xx): glucogenic (pink) vs ketogenic (blue) pathways converging on TCA intermediates

Classification List (Table 23.2)

• Purely ketogenic: Leucine, Lysine

• Purely glucogenic (representative): Asp, Asn, Ala, Gly, Ser, Cys, Glu, Gln, Arg, Pro, His, Val, Met, etc.

• Both glucogenic & ketogenic: Ile, Phe, Tyr, Trp, Thr (dual entry points)

Protein Digestion & Amino-Acid Absorption

• Stomach (low pH ~1–2)

  • Parietal cells → HCl

  • Chief cells → pepsinogen → pepsin (active protease)

• Pancreas

  • Secretes zymogens (trypsinogen, chymotrypsinogen, proelastase, procarboxypeptidases) via pancreatic duct (pH ≈ 7)

  • Zymogens activated in small intestine

• Small-intestinal mucosa absorbs free amino acids → portal vein → liver

Intracellular Paths of Amino Groups vs Carbon Skeletons (Liver)

• Amino groups → urea cycle (NH$_4^+$ + aspartate → urea)

• Carbon skeletons → TCA cycle, gluconeogenesis, ketogenesis, etc.

• “Aspartate-argininosuccinate shunt” links urea cycle with TCA (fumarate ↔ oxaloacetate)

• DO TRANSAMINATION RXNS AT HOME

Excretory Forms of Nitrogen

• NH$<em>3$/NH$</em>4^+$ (ammonotelic; aquatic vertebrates)

• Urea $\big(\mathrm{NH<em>2CONH</em>2}\big)$ (ureotelic; mammals, sharks)

• Uric acid (uricotelic; birds, reptiles)

Pyridoxal Phosphate (PLP) Chemistry

• Covalently bound to aminotransferases via Schiff-base (internal aldimine) with active-site Lys

• Key PLP-facilitated reactions at the $\alpha$-carbon

  • Transamination (major) KNOW STEPS

  • Racemization (L⇌D interchange)

  • Decarboxylation (neurotransmitter formation, etc.)

• Catalytic cycle (simplified)

  1. External aldimine with substrate amino acid

  2. Quinonoid/carbanion stabilization via PLP electron sink

  3. Rearrangements → release of $\alpha$-keto acid + pyridoxamine phosphate

  4. Second $\alpha$-keto acid enters → reverse process regenerates PLP + new amino acid

Oxidative Deamination of Glutamate

• Location: liver mitochondria

• Enzyme: glutamate dehydrogenase (only mammalian enzyme that uses both $\mathrm{NAD^+}$ and $\mathrm{NADP^+}$)

• Reaction
  $\text{Glutamate} + \mathrm{NAD(P)^+} + H<em>2O \rightarrow \alpha\text{-ketoglutarate} + NH</em>4^+ + \mathrm{NAD(P)H}$

• Links transamination (cytosol) with ammonia disposal (mitochondria)

Ammonia Transport: Non-Toxic Carriers

• Glutamine (all tissues → liver/kidney)

  • Enzyme: glutamine synthetase
    $\text{Glutamate} + NH<em>4^+ + ATP \rightarrow \text{Glutamine} + ADP + P</em>i$

  • In liver mitochondria, glutaminase reconverts glutamine → glutamate + NH$_4^+$

• Alanine (muscle → liver; glucose-alanine cycle)

  • Muscle: pyruvate + NH$_4^+$ → alanine (via alanine aminotransferase)

  • Liver: alanine → pyruvate + NH$_4^+$; pyruvate → glucose (gluconeogenesis) → back to muscle

The Urea Cycle (Ornithine Cycle)

• Overall: $NH<em>4^+ + HCO</em>3^- + Asp + 3\,ATP \rightarrow \text{Urea} + 2\,ADP + AMP + 4\,P_i + Fumarate$

• Compartmentation

  • Step 1 in mitochondrial matrix; Steps 2-4 in cytosol

• Reactions

  • Carbamoyl phosphate synthase I (CPS I)

    • $NH<em>4^+ + HCO</em>3^- + 2\,ATP \rightarrow \text{Carbamoyl-P} + 2\,ADP + P_i$

    • Allosterically activated by $N\text{-acetylglutamate}$ (short-term regulation)

      1. Ornithine transcarbamoylase

    • Ornithine + carbamoyl-P → citrulline (exported to cytosol)

      2. Argininosuccinate synthetase

    • Citrulline + Asp + ATP → argininosuccinate + AMP + PP_i (adenylate intermediate)

      3. Argininosuccinase

    • Argininosuccinate → arginine + fumarate (fumarate ↔ malate ↔ oxaloacetate)

      4. Arginase

    • Arginine + H$_2$O → ornithine + urea (ornithine re-enters mitochondrion)

• Energetic considerations

  • Direct cost: 3 ATP (~3 × 4 ~P)

  • Fumarate → malate → oxaloacetate → NADH (≈2.5 ATP) offsets cost

Regulation of Urea Production

• Short-term: CPS I activated by $N\text{-acetylglutamate}$ (increased when glutamate + acetyl-CoA high)

• Long-term: enzyme synthesis up-regulated by high protein intake or starvation

Essential vs Non-Essential Amino Acids NOT IMPORTANT FOR EXAM

• Humans cannot synthesize 9 standard amino acids in adequate amounts (His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val)

• Conditionally essential (Arg, Cys, Gln, Gly, Pro, Tyr) required in growth, illness

• PKU disease: A genetic disorder that leads to the accumulation of phenylalanine, as individuals with PKU lack the enzyme necessary to convert phenylalanine to tyrosine, making dietary management critical.

Entry of Amino-Acid Carbon Skeletons into Central Metabolism

• 20 catabolic pathways converge to 6 major products feeding the TCA cycle DONT MEMORIZE

  • To pyruvate ⇒ Ala, Cys, Gly, Ser, Thr, Trp

  • To $\alpha$-ketoglutarate ⇒ Arg, Glu, Gln, His, Pro

  • To succinyl-CoA ⇒ Ile, Met, Thr, Val

  • To fumarate ⇒ Phe, Tyr

  • To oxaloacetate ⇒ Asp, Asn

  • To acetyl-CoA or acetoacetyl-CoA ⇒ Leu, Ile, Lys, Phe, Thr, Trp, Tyr

Representative Specific Pathways

Asn & Asp ➝ Oxaloacetate

• Asparaginase: asparagine + H$<em>2$O → aspartate + NH$</em>4^+$

• Aspartate aminotransferase (PLP): aspartate + $\alpha$-ketoglutarate ⇌ oxaloacetate + glutamate

Phenylalanine / Tyrosine Catabolism & Genetic Disorders

• Initial step: phenylalanine hydroxylase converts Phe → Tyr (cofactor tetrahydrobiopterin BH$_4$)

• Inborn errors

  • Phenylketonuria (PKU): defect in Phe hydroxylase → Phe accumulation, mental retardation; treated with low-Phe diet & BH$_4$

  • Alkaptonuria: homogentisate 1,2-dioxygenase deficiency → dark urine

  • Tyrosinemias I–III: various downstream enzyme defects (fumarylacetoacetase, etc.)

Trp, Lys, Phe, Tyr, Leu, Ile, Thr ➝ Acetyl-CoA/Acetoacetate

• Examples: Leu → acetoacetate + acetyl-CoA via HMG-CoA intermediate (ketogenic)

• Trp degradation also yields nicotinate (vitamin B$_3$ precursor), serotonin & indoleacetate

Met, Ile, Thr, Val ➝ Succinyl-CoA

• Common intermediate: propionyl-CoA → $\mathrm{D\text{-}methylmalonyl\text{-}CoA}$ (propionyl-CoA carboxylase, biotin) → $\mathrm{L}$-methylmalonyl-CoA → succinyl-CoA (methylmalonyl-CoA mutase, coenzyme B$_{12}$)

• Clinical note: vitamin B$_{12}$ deficiency → methylmalonic acidemia

Clinical & Metabolic Connections

• Starvation/diabetes mellitus: increased protein catabolism → increased urea production & potential ketoacidosis (from ketogenic AAs)

• Ammonia neurotoxicity: brain converts NH$_3$ → glutamine; hyperammonemia causes cerebral edema

• Therapeutic enzyme: asparaginase exploits leukemia cells’ need for external Asn

Energetics & Integration (“Krebs Bicycle”)

• Urea cycle + TCA cycle interlock via fumarate/oxaloacetate shuttle

• Net result: efficient removal of nitrogen with minimal ATP expense via NADH recovery

Summary Equations

• Net urea cycle
  $NH<em>4^+ + HCO</em>3^- + Asp + 3\,ATP + 2\,H<em>2O \rightarrow \text{Urea} + 2\,ADP + AMP + 4\,P</em>i + Fumarate$

• ATP gain offset
  $\text{Fumarate} \rightarrow \text{Malate} \rightarrow \text{Oxaloacetate} + NADH \;(\approx 2.5\,ATP)$