Protein Metabolism and Urea Cycle

Ketogenic and Glucogenic Amino Acids

  • Purely Ketogenic Amino Acids:
    • Leucine and lysine cannot be used for gluconeogenesis. They directly enter into ketone body formation.
  • Both Glucogenic and Ketogenic Amino Acids:
    • Tyrosine, isoleucine, phenylalanine, and tryptophan can enter both the glucogenic and ketogenic pathways.

Protein Turnover and Degradation

  • Proteins in the body have varying lifespans:
    • Short-lived proteins (seconds, minutes, hours) are often regulatory or misfolded proteins and need to be rapidly degraded.
    • Long-lived proteins (e.g., collagen in tendons, lens crystallins in eyes) can last decades.
  • Protein Degradation Mechanisms:
    • Lysosomal Degradation:
    • Acid hydrolases in lysosomes degrade proteins without the use of ATP.
    • Targeted protein degradation through the ubiquitin-proteasome system (requires ATP).
  • Ubiquitination:
    • Proteins tagged with ubiquitin signal for degradation. Ubiquitin attaches to proteins via enzymes using ATP.
    • Degradation results in peptide fragments for further breakdown by non-specific proteases in the cytosol.
  • Regulation of Protein Lifespan:
    • Proteins subject to regulatory mechanisms can be protected from ubiquitination if longer action is needed.
    • Ubiquitination and subsequent degradation require ATP and are fundamental cellular mechanisms.

Proteomic Analysis

  • Proteomics:
    • The study of protein sequences across healthy and diseased tissues. Essential for identifying disease markers and treatment strategies.
  • Digestion of proteins using enzymes (e.g., trypsin, chymotrypsin) provides sequence-specific information.

Digestion of Proteins

  • Peptide Bond Hydrolysis:
    • Hydrolysis is the process of breaking peptide bonds in proteins, adding water molecules to break these bonds.
  • Key Enzymes:
    • Trypsin: Recognizes arginine or lysine.
    • Chymotrypsin: Recognizes several amino acids.
    • Elastase and carboxypeptidases A and B also have specificities for different amino acids.
  • Activation of Digestive Enzymes:
    • Enzymes like pepsin are activated in acidic conditions (pH ~1) via gastrin stimulation.
    • Trypsin and others are activated in the intestines with the help of secretin.

Urea Cycle

  • Key Points of Urea Cycle:
    • Location: Urea cycle only occurs in the liver.
    • Purpose: Removal of excess nitrogen via urea formation.
    • Key substrates: Aspartate, ammonia, bicarbonate, three ATPs, and water produce urea, fumarate, ADPs, AMP, inorganic phosphate, and pyrophosphate.
  • First Steps in Mitochondria:
    • Carbamoyl Phosphate Synthetase (CPS1): Rate-limiting enzyme for the cycle, uses 2 ATP to produce carbamoyl phosphate. Activated by N-acetylglutamate (NAG).
    • Ornithine Transcarbamylase: Combines carbamoyl phosphate with ornithine to form citrulline.
  • Steps in Cytosol:
    • Argininosuccinate Synthetase: Joins citrulline and aspartate into argininosuccinate using ATP.
    • Argininosuccinate Lyase: Converts argininosuccinate into fumarate and arginine.
    • Arginase: Hydrolyzes arginine to form urea and ornithine.

Health Implications

  • Any defect within urea cycle enzymes can lead to hyperammonemia, which is potentially lethal.
  • Genetic disorders affecting these enzymes are usually screened in newborns to prevent severe health outcomes.

Shortages and Deficiencies

  • Deficiency in NAG synthase or urea cycle enzymes results in hyperammonemia and associated neurological damage.

Nitrogen Metabolism and Transport

  • Transamination and Oxidative Deamination:
    • Transamination transfers an amino group from amino acids to α-ketoglutarate forming glutamate and α-keto acids.
    • Oxidative deamination removes an amino group from glutamate producing free ammonia.
  • Key Enzymes Involved: - Aminotransferases (e.g., alanine aminotransferase (ALT)) link amino acids to α-keto acids and produce glutamate.
  • Transport Mechanism:
    • Major carriers of ammonia include alanine and glutamine, with the liver ultimately processing these molecules in the urea cycle.

Metabolic Regulation

  • Cellular conditions (energy levels, nutrient availability) influence processes (e.g., the direction of transamination reactions may change based on cellular demands).

Summary of Nitrogen Flow

  • Nitrogen flow is regulated in glutamine and glutamate cycles, focusing on enzymes such as glutamate dehydrogenase and transaminases. Each reaction must be reversible to maintain balance in nitrogen metabolism and support various cellular functions.