Biochemistry of Urea Cycle Disorders

Protein Metabolism - Digestion

• Protein digestion is necessary for absorption, resynthesis of necessary proteins, and immune processes.
• Mouth: No protein digestion occurs.
• Stomach:
  • Hydrochloric acid (HCl) converts native protein to acid-metaprotein, leading to denaturation of secondary, tertiary, and quaternary protein structures.
  • Pepsin, an enzyme secreted by chief cells in the gastric mucosa (pH 1-2), is secreted as pepsinogen (inactive form).
  • Pepsinogen is activated by HCl or pepsin to form pepsin.
  • Pepsin is an endopeptidase that hydrolyzes peptide bonds between phenylalanine, tyrosine, and tryptophan.
  • End products: a mixture of protein, proteoses, peptones, and polypeptides.
• Duodenum:
  • Trypsin and chymotrypsin (secreted as trypsinogen and chymotrypsinogen by pancreatic acini, pH 8).
  • Trypsinogen and chymotrypsinogen are activated by enterokinase to become trypsin and chymotrypsin.
  • Trypsin is an endopeptidase that hydrolyzes peptide bonds between basic amino acids (arginine and lysine).
  • Chymotrypsin is also an endopeptidase but acts on peptide bonds between uncharged aromatic amino acids.
  • End products: proteoses, peptones, and polypeptides.
  • Carboxypeptidase (source: pancreatic acini, pH 8) is an exopeptidase, and activates by trypsin). Cleaves the C-terminal amino acids in peptides. End product: single amino acids.
  • Elastase(s) (source: pancreatic acini, pH 8), also activated by trypsin. An endopeptidase that acts on non-polar amino acids (Val, Leu, Ser & Ala) to produce peptides.
• Small Intestine:
  • Aminopeptidase (source: glands of Bruner and Lieberkuhn, pH 5-7). An exopeptidase acting on the peptide bond at the free NH2 of polypeptides. End product: free amino acids.
  • Dipeptidases and tripeptidases (source: glands of Bruner and Lieberkuhn, pH 5-7). Exopeptidases acting on dipeptides and tripeptides respectively. End product: free amino acids.

Protein Metabolism - Absorption

• Dietary proteins are almost completely digested into amino acids.
• Absorption site: jejunum and ileum.
• Absorption is an active process requiring energy (ATP hydrolysis).
• Mechanism of absorption:
  • Endocytosis (a small amount of intact protein is absorbed and degraded in lysosomes).
  • Active transport: L-amino acids (naturally occurring) are absorbed actively using specific carrier proteins present in small intestines, similar to glucose absorption. Carrier proteins have sites for amino acids and sodium.
  • Competition during absorption: amino acids of the same group compete with each other. Vitamin B6 and manganese play a role in amino acid absorption.
  • Simple diffusion (D-amino acids are absorbed by simple diffusion).
• Absorption of proteins without digestion occurs in infants (absorption of immunoglobulins from colostrum). In adults, some intact proteins may be absorbed (antigen-antibody reaction).

Protein Metabolism - Amino Acid Absorption Mechanisms

• Two mechanisms:
  • Carrier proteins transport system: main system for amino acid absorption. An active process requiring ATP to transport amino acids and sodium, one carrier protein for each group of amino acids
  • Glutathione transport system (r-Glutamyl cycle): glutathione transports amino acids from the intestinal lumen into the cytosol of intestinal mucosa cells. The process is energy-dependent (requiring 3 ATP molecules per amino acid absorbed).

Protein Metabolism - Body Protein Dynamic

• Body proteins (except collagen) are in a constant state of degradation and resynthesis.
• Synthesis is greater than degradation.
• Protein required for: growth, replacement of cells, milk production during lactation.
• Adult protein requirement: 30-60 g/day (0.8 g/kg body weight/day). Daily requirement depends on factors like age, sex, and lactation.

Protein Metabolism - Nitrogen Utilization

• Nitrogen intake: Proteins and nucleoproteins are the primary sources. Protein contains 16g nitrogen per 100g.
• Nitrogen output:
  • Urine: major route of excretion, includes non-protein nitrogenous compounds (e.g., urea, uric acid, ammonia).
  • Stools: digestive juices, shed epithelial cells, and undigested fats.
  • Sweat: Urea
  • Other: Milk and menstrual fluids, hairs, and nails

Protein Metabolism - Nitrogen Balance

• Definition: The quantitative difference between nitrogen intake and output daily in grams.
• Three states of nitrogen balance:
  • Equilibrium: intake equals output (healthy adults on an adequate diet).
  • Positive: intake exceeds output (pregnancy, lactation, recovery from illness, and growth periods).
  • Negative: output exceeds intake (wasting diseases, inadequate diet, excessive protein catabolism).

Protein Metabolism - Plasma Amino Acids

• Plasma amino acid levels vary throughout the day (circadian changes).
• Level depends on nutritional state (fed or post-absorption).
• Normal range: 4-8 mg/dL.

Protein Metabolism - Amino Acid Pool Sources

• Exogenous sources: Absorbed amino acids from dietary proteins.
• Endogenous sources: Synthesized non-essential amino acids.
• Tissue catabolism: From breakdown of tissue proteins.

Protein Metabolism - Amino Acid Fate

• Protein synthesis: Amino acids are incorporated into proteins (plasma proteins, tissue proteins, enzymes, some hormones).
• Synthesis of nitrogenous compounds: Glutathione, purine, and pyrimidine bases.
• Ketogenic or glucogenic amino acid metabolism pathways for fuel and energy
• Synthesis of other specialized products: certain amino acids produce specific substances (e.g., phenylalanine → adrenaline, tryptophan → serotonin).
• Catabolism of amino acids: Produces a-keto acids and urea

Protein Metabolism - Deamination

• Definition: Removal of the amino group (NH2) from amino acids in the form of ammonia (NH3).
• Site: Liver and kidney.
• Types:
  • Transamination: Transfer of an amino group from one amino acid to a keto acid, forming a new amino acid and a new keto acid.
  • Oxidative deamination: Removal of the amino group from an amino acid while oxidizing it to form a-keto acid and NH3.
  • Trans-deamination: Combination of transamination and oxidative deamination.

Protein Metabolism - Enzymes involved in deamination

• Transaminases: Enzymes that catalyze transamination reactions.
• Pyridoxal phosphate (vitamin B6): Coenzyme of transaminases.
• L-Amino acid dehydrogenase: Enzyme acting on L-amino acids (except glutamate), low activity but present in liver and kidney; requiring FMN as coenzyme.
• D-Amino acid dehydrogenase (FAD is the coenzyme): Enzyme acts on D amino acids and glycine; present in liver and kidneys

Protein Metabolism - Ammonia Metabolism

• Sources: Deamination of amino acids, intestinal bacteria acting on dietary proteins or urea, renal tubular cell's action in cases of acidosis.
• Fate: Ammonia is highly toxic, rapidly removed from circulation by the liver.
• Pathways:
  • Anabolic pathway: Formation of glutamate and other non-essential amino acids, and synthesis of purines and pyrimidines.
  • Catabolic pathway: Formation and excretion of glutamine, mainly in the kidneys (by glutaminase).
• Urine excretion: The kidney excretes ammonia that accounts of up to 40 % of urinary ammonia.
• Urea formation: Ammonia is converted to urea in the urea cycle in the liver.
• Urea Cycle: The main process of catabolizing amino acids in the body resulting in urea formation. A 5 step pathway in the liver's mitochondria. Liver is the only site for urea production. 5 enzymes are essential for Urea cycle function.

Protein Metabolism - Factors affecting urea levels

• Protein Diet: Increased protein intake leads to increased urea formation.
• Liver Disease: Liver's inability to синтезировать urea leads to decreased urea and increased blood ammonia.
• Kidney Disease: Inability of the kidney to excrete urea leads to a buildup (increased levels) of urea in the blood.

Protein Metabolism - Urea Cycle Disorders

• Defects in the 5 enzymes of the urea cycle can cause hyperammonemia (high blood ammonia levels).
• Types include hyperammonemia type I (carbamoyl phosphate synthetase I deficiency), hyperammonemia type II (ornithine transcarbamoylase deficiency), citrullinemia (argininosuccinate synthetase deficiency), argininosuccinic aciduria (argininosuccinase deficiency), and hyperargininemia (arginase deficiency).

Protein Metabolism - Additional Points

• Circadian changes in plasma amino acid levels occur throughout the day and are dependent on the nutritional status.

This quiz tests your knowledge on the urea cycle, including the functions of key enzymes, the activation of carbamoyl phosphate synthetase I, and the consequences of liver disease on urea levels. Ideal for students studying biochemistry and metabolic disorders.