BIOC 4331 Lecture 45-46 (AA Catabolism and Urea Cycle)

What are nitrate assimilation and nitrogen fixation?

• Nitrate assimilation = NO₃⁻ → NH₄⁺ in plants/fungi/bacteria

• Nitrogen fixation = N₂ → NH₄⁺ by prokaryotes only

• Animals cannot do either and depend on plants/microbes for organic nitrogen

Why must mammals detoxify NH4+?

• NH₄⁺ is toxic → cerebral edema, coma, death

• Mammals convert excess amino nitrogen mainly into urea for urine excretion

What are the two fates of amino acid catabolism?

• Amino group → NH₄⁺ → urea

• Carbon skeleton → α-keto acids → TCA cycle → for energy, glucose, or fat/ketones

How does protein digestion work?

1. Protein causes release gastrin → parietal cells secrete HCl + chief cells secrete pepsinogen

2. Acid activates pepsin

3. Secretin released into blood → Triggers pancrease to release HCO₃⁻ into intestine (neutralize pH)

4. Pancreatic protease zymogens digest proteins

5. AAs absorbed by transporters

Why are digestive proteases secreted as zymogens, and what causes acute pancreatitis?

• Zymogens prevent autodigestion

• Acute pancreatitis = blocked pancreatic duct → zymogens activate into active enzymes → proteases digest/degrade pancreas

Where are amino groups mainly metabolized, and which AAs are key?

• Liver

• Glutamate (E), glutamine (Q), alanine (A), and aspartate (D)

What is transamination?

• Reversible aminotransferase reaction transferring amino groups to α-ketoglutarate → glutamate + α-keto acid

• Enzymes named by donor

What cofactor do aminotransferases use?

• Pyridoxal phosphate (PLP), the vitamin B6/pyrido-xine coenzyme

  • Prosthetic group of aminotransferases

• PLP binds enzyme Lys by Schiff base linkage and becomes PMP after accepting an amino group

Why is glutamate central in nitrogen metabolism?

Glutamate collects amino groups and acts as a universal amino donor

What does glutamate dehydrogenase do?

• In liver mitochondria, oxidative deamination: glutamate → α-ketoglutarate + NH₄⁺

• Can use either NAD+ or NADP+ as the cofactor

How is ammonia safely transported from most tissues?

• Excess NH₄⁺ + glutamate → glutamine by glutamine synthetase

• Glutamine travels to liver

• Liver mitochondrial glutaminase releases NH₄⁺

What is the glucose-alanine cycle?

• Muscle pyruvate accepts amino groups → alanine

• Alanine carries nitrogen + pyruvate carbon from skeletal muscle → to liver

• Liver makes urea + glucose, returning glucose to muscle

How is the glucose-alanine cycle related to the Cori cycle?

• Both send muscle carbon to liver for gluconeogenesis

• Alanine also carries nitrogen

How does aspartate feed the urea cycle?

• Oxaloacetate + glutamate → aspartate + α-ketoglutarate

• Aspartate donates the second nitrogen to urea

What are the major nitrogen excretion forms?

• Ammonia = aquatic animals

• Urea = terrestrial vertebrates/sharks

• Uric acid = birds/reptiles

• Urea/uric acid safely package excess nitrogen

What is the purpose and location of the urea cycle?

• Converts toxic NH₄⁺ + CO₂ → arginine → urea

• Occurs in liver, partly mitochondrial matrix and partly cytosol

What are the two direct nitrogen sources in urea?

• Free NH₄⁺ enters as carbamoyl phosphate

• Aspartate donates the second nitrogen

What indirect carriers feed nitrogen into the urea cycle?

• Glutamine (blood)

• Glutamate

• Alanine (muscle)

• All feed NH₄⁺ or aspartate formation

How much energy does the urea cycle use?

3 ATP total, but 4 high-energy phosphate bonds per urea

What is the aspartate-argininosuccinate shunt?

Link between urea cycle and TCA cycle using fumarate, malate, OAA, and aspartate

How does the malate-aspartate shuttle connect to urea/gluconeogenesis?

Moves OAA equivalents; aspartate feeds urea cycle, and cytosolic OAA supports gluconeogenesis

Which amino acids are essential for humans? Draw them.

• Histidine — His/H

• Isoleucine — Ile/I

• Leucine — Leu/L

• Lysine — Lys/K

• Methionine — Met/M

• Phenylalanine — Phe/F

• Threonine — Thr/T

• Tryptophan — Trp/W

• Valine — Val/V

Which amino acids are glucogenic, ketogenic or both?

Glucogenic: Histidine, Methionine, Valine

Ketogenic: Leucine, Lysine

Both: Isoleucine, Threonine, Tryptophan, Tryosine, Phenylalanine

What makes an amino acid glucogenic vs ketogenic?

• Glucogenic → pyruvate/TCA intermediates → glucose

• Ketogenic → acetyl-CoA/acetoacetate → ketone bodies

Why is acetyl-CoA converted to ketones during starvation/diabetes?

1. OAA is limiting b/c gluconeogenesis

2. High mito NADH (from β oxidation) inhibits TCA cycle, so acetyl-CoA accumulates → ketones

Which enzymes are inhibited by high mitochondrial NADH from β-oxidation?

• PDH

• Isocitrate dehydrogenase

• α-ketoglutarate dehydrogenase

What ketone bodies are made/exported during starvation?

• Acetoacetate

• β-hydroxybutyrate

• Exported as fuel for heart, muscle, kidney, and brain

• Acetone is also formed (breathed out)

What is the main OAA carbon flow during starvation/diabetes?

OAA_[mito] → aspartate (via malate-aspartate shuttle) → OAA_[cyto] → gluconeogenesis

What is the citrate shuttle normally used for?

Exports acetyl-CoA equivalents to cytosol for fatty acid synthesis and helps generate NADPH

Why is the citrate shuttle NOT a major OAA source for gluconeogenesis in starvation?

• Acetyl-CoA goes to ketone bodies during starvation

• Little citrate forms in the liver because high NADH (from β-oxidation) downregulates the TCA cycle

How are citric acid cycle enzymes regulated by energy?

• High ATP/NADH inhibit

• Low ATP/AMP activate

• Products cause product inhibition