Catabolism of Amino Acids

CATABOLISM OF AMINO ACIDS

SOURCES AND FATES OF AMINO ACIDS IN THE BODY

  • Sources of Amino Acids:

    • Dietary Proteins: Proteins consumed through diet are a primary source.

    • Synthesis: Non-essential amino acids can be synthesized by the body.

    • Breakdown of Tissue Proteins: Degradation of tissue proteins also contributes (approximately 2/3 of amino acids).

  • Pathways for Amino Acids:

    • Digestion Overview: Approximately 1/3 of ingested proteins are digested into free amino acids which can enter the bloodstream.

    • Transport Locations: Amino acids are transported amongst various sites:

    • Gut, Liver, Kidneys, and all body tissues

    • Excess amino acids are stored in the amino acid pool for further biosynthesis of tissue proteins or oxidative degradation.

  • End Products of Amino Acid Metabolism:

    • Amino acids can be converted into:

    • Acetyl CoA

    • TCA intermediates

    • Glucose

    • Ketone bodies

    • Fats

  • Biosynthesis of Small Biomolecules: Besides protein synthesis, amino acids contribute to the biosynthesis of biomolecules such as purines, pyrimidines, biogenic amines, and bile acids.

PROTEIN CATABOLISM

  • Process Overview: Proteolysis of dietary proteins occurs in the stomach and lumen of the small intestine, releasing free amino acids into the bloodstream.

    • Intracellular Proteolysis: Proteins that are taken up via the endocytic pathway are degraded in lysosomes.

    • Controlled Proteolysis: Ubiquitin-tagged intracellular proteins are broken down in the proteasomes of all cells.

  • Digestive Enzymes and Their Roles:

    • Endopeptidases: Hydrolyze peptide bonds within a polypeptide chain. Examples include:

    • Pepsin: Active in the stomach, operates at pH 1.5-2.5, cleaves before Tyr, Phe, and between Leu and Glu.

    • Trypsin: Active in the small intestine (pH 7.5-8.5), cleaves after Lys and Arg.

    • Chymotrypsin: Also active at pH 7.5-8.5, cleaves after Trp, Phe, Tyr, Met, and Leu.

    • Exopeptidases: Split peptide bonds at the ends of proteins, including aminopeptidases and carboxypeptidases.

  • Hydrolysis Process: Proteins are hydrolyzed into polypeptides, oligopeptides, and finally into amino acids which are transported to target tissues.

ABSORPTION OF AMINO ACIDS

  • Transport Mechanism: Amino acids are absorbed via a semi-specific Na+-dependent transport system:

    • Sodium-dependent carriers transport Na+ along with an amino acid.

  • Types of Amino Acid Carriers: At least six different carriers transport various categories of amino acids:

    • Neutral AA

    • Proline and hydroxyproline

    • Acidic AA

    • Basic AA (Lys, Arg)

    • Cysteine

DISORDERS OF AMINO ACID TRANSPORT

Cystinuria

  • Description: Autosomal recessive disorder caused by mutations in transporter genes in the kidney, impairing reabsorption of basic amino acids and cysteine.

  • Implication: Cysteine is oxidized to insoluble cystine, leading to kidney stone formation.

Hartnup Disease

  • Description: A rare autosomal recessive disorder characterized by a defect in the transport of neutral amino acids, including essential amino acids (Ile, Leu, Val, Phe, Thr, Trp).

  • Clinical Impact: Limitation on the availability of essential amino acids can result in various clinical disorders.

LYSOSOMAL DEGRADATION

  • Mechanism: Lysosomes break down proteins taken up by endocytosis or that traffic within the endocytic pathway.

  • Enzymatic Environment:

    • Contain approximately 50 hydrolytic enzymes (proteases) with an optimal acidic pH (~5).

    • Degradation in well-nourished cells is non-selective; in starving cells, selective degradation of cytosolic proteins with pentapeptide KFERQ occurs.

CONTROLLED PROTEOLYSIS

  • Mechanism: Ubiquitin tags proteins for destruction; the proteasome digests these proteins, contributing to the regulation of biological functions.

  • Key Enzymes in Ubiquitin Conjugation:

    • E1: Ubiquitin-Activating Enzyme

    • E2: Ubiquitin-Conjugating Enzyme

    • E3: Ubiquitin-Protein Ligase

DETERMINANTS FOR UBIQUITINATION

  1. N-terminal Rule: The identity of the amino-terminal amino acid influences the protein's half-life.

    • For example, Methionine (N-terminus) yields a half-life of around 20 hours, whereas Arginine results in a half-life of just 2 minutes.

  2. Cyclin Destruction Boxes: Specific amino acid sequences marking cell cycle proteins for destruction.

  3. PEST Sequences: Sequences rich in proline, glutamic acid, serine, and threonine also mark proteins for degradation.

Processes Regulated by Protein Degradation

  • Gene transcription

  • Cell cycle progression

  • Organ formation

  • Circadian rhythms

  • Inflammatory responses

  • Tumor suppression

  • Cholesterol metabolism

  • Antigen processing

NITROGEN BALANCE

  • Definitions:

    • Normal/Nitrogen Equilibrium: Occurs when dietary nitrogen intake equals nitrogen loss through excretion.

    • Positive Nitrogen Balance: When dietary nitrogen intake exceeds nitrogen loss.

    • Negative Nitrogen Balance: When dietary nitrogen intake is less than nitrogen loss.

  • Application: Daily protein recommendations:

    • General: Approximately 0.8 g/kg/day.

    • Strength athletes: 1.4 - 1.7 g/kg/day to maintain muscle mass.

Effects of Excess Intake

  • Intakes over 3 g/kg/day can have negative health impacts.

METABOLIC CIRCUMSTANCES OF AMINO ACID OXIDATION

  • Sources of Amino Acids:

    • Leftover from normal protein turnover.

    • Excess dietary amino acids exceeding synthesis needs.

    • Proteins can be degraded for energy during states of scarcity, such as starvation or uncontrolled diabetes.

  • Amino Acid Degradation: Unutilized amino acids from catabolism are broken down into carbon skeletons, mainly in the liver.

  • First Step: Involves the removal of nitrogen (deamination).

Processes of Deamination

  1. Transamination: Catalyzed by transaminases.

  2. Oxidative Deamination: Performed mainly by glutamate dehydrogenase and L-amino acid oxidase.

  3. Dehydratase Action: Enzymatically removes water, subsequently followed by deamination (e.g., serine dehydratase and threonine dehydratase).

α-AMINO ACIDS AND α-KETO ACIDS

  • Diagram Representation: Showing the conversion of various amino acids into respective α-keto acids including Pyruvate, Oxaloacetate, and α-Ketoglutarate as part of transamination processes morphed visually (not shown here).

TRANSAMINATION

  • Key Aspects:

    • Dominant reactions involve the transfer of amino acid nitrogen.

    • Facilitates a funneling of nitrogen from free amino acids to a limited number of compounds for further oxidative deamination or entry into urea cycle.

  • Key Enzymes: Transaminases (aminotransferases) which are vital for these reactions facilitating amino group transfers from one substrate to another (usually from α-amino acid to α-keto acid).

MECHANISM OF AMINOTRANSFERASES

  • Cofactor Required: All aminotransferases need pyridoxal-5-phosphate (PLP), a derivative of Vitamin B6.

  • Process:

    • PLP attaches to the enzyme via a Schiff base linkage, aiding in amino group transfer to and from α-keto acids.

  • Overall Reaction: Converting amino acids into respective keto acids, primarily glycine, alanine, and aspartate, via transamination, yielding their distinct keto forms.

COMMON AMINOTRANSFERASES

  1. Alanine Transaminase (ALT): Primarily in the liver, important for liver function diagnostics.

  2. Aspartate Transaminase (AST): Found in multiple tissues, indicating tissue damage when elevated (heart, liver, skeletal muscles).

  3. Transaminase Enzyme Naming: Enzymes are named based on the specific amino acid donor.

OXIDATIVE DEAMINATION

  • Process:

    • During oxidative deamination, an amino acid is converted into a keto acid, releasing ammonia, which enters the urea cycle.

    • Notable enzyme: Glutamate dehydrogenase, which regulates ammonia production and is influenced by metabolites (GTP, NADH).

    • Main product: α-ketoglutarate is recycled within the TCA cycle or utilized for gluconeogenesis.

DEHYDRATASE MECHANISM

  • Specificity: Direct deamination of serine and threonine via dehydratases such as threonine dehydratase, leading to ammonium ions.

NITROGEN TRANSPORT TO THE LIVER

  • Transport Mechanisms:

    • Amino acid decomposition occurs in tissues outside the liver, with muscles predominating during prolonged exercise and fasting.

    • Alanine Cycle: Excess amino groups from skeletal muscle are transferred to pyruvate forming alanine which travels to the liver. Here, transamination occurs to replenish glucose through gluconeogenesis.

Glutamine Transport

  • Transport of nitrogen occurs as glutamine via glutamine synthetase which involves glutamate, ATP, and ammonium to carry nitrogen to the liver for processing.

SUMMARY OF NITROGEN DELIVERED TO LIVER CELLS

  • Mechanisms:

    • Ingested amino acids from dietary proteins are processed resulting in various nitrogen carriers (urea, uric acid) and intermediary compounds (e.g., α-ketoglutarate, glutamate).

  • Clinical Importance: Monitoring nitrogen levels is crucial for metabolic health, with concentrations shifting based on dietary intake and liver metabolism.

UREA CYCLE

Importance of the Urea Cycle

  • In the liver, NH4+ generated from amino acid degradation feeds into the Urea Cycle, necessary for converting excess ammonia to urea for excretion.

  • Normal Blood Levels: [NH4+] should be below 70µM, excess ammonia is toxic and must be transformed to urea to prevent toxicity.

Sources of Urea Atoms

  • Combining NH4+ from amino acid breakdown with carbon from CO2 leads to urea formation within the cycle:

    • 1 nitrogen from Asp

    • 1 nitrogen directly from NH4+

    • 1 carbon from CO2

    • Ornithine acts as a carrier, facilitating the entire process.

COMPARTMENTALIZATION OF UREA CYCLE

  • Locations: Relies on two sites within the liver:

    • Mitochondrial Matrix: Site for carbamoyl phosphate formation and citrulline synthesis.

    • Cytosol: Cleavage of argininosuccinate, hydrolysis of arginine.

Enzymes in the Urea Cycle

  1. Carbamoyl Phosphate Synthetase: Essential for step one; requires N-acetylglutamate to activate.

    • Utilizes ATP and combines CO2 and NH3 to produce carbamoyl phosphate.

    • The reaction is critical and irreversible.

  2. Ornithine Transcarbamoylase (OTC): Forms citrulline from ornithine and carbamoyl phosphate.

  3. Argininosuccinate Synthetase: Introduces another nitrogen from aspartate to form argininosuccinate.

  4. Argininosuccinase: Cleavage of argininosuccinate into arginine and fumarate.

  5. Arginase: Hydrolyzes arginine to generate urea and recycle ornithine.

OVERALL REACTION AND ENERGETICS

  • Energy Considerations: Four high-energy phosphate bonds are broken per molecule of urea created, showcasing the energy requirement for nitrogen removal from the body through the urea cycle.

FATES OF OXALOACETATE

  • Connection with TCA Cycle: Fumarate production links urea cycle and TCA cycle.

  • Metabolic Pathways from Oxaloacetate:

    • Notably, links to gluconeogenesis, pyruvate formation, and citrate synthesis.

  • Regulation: Urea cycle rate is controlled by enzyme concentrations based on dietary intake, determining nitrogen metabolism efficiency.

FINE CONTROL OF UREA CYCLE

  • N-acetylglutamate serves as an allosteric activator, synthesizing in the liver from acetyl-CoA, regulating urea cycle activity based on available substrates (acetyl-CoA and glutamate).

DEFECTIVE UREA CYCLE ENZYMES AND INHERITED DISEASES

  • Deficiencies in urea cycle enzymes lead to elevated NH4+, with some causing life-threatening symptoms. Management involves dietary adjustments to decrease ammonia load.

Specific Disorders

  1. Hyperammonemia Type I: Carbamoyl phosphate synthetase deficiency causes glycine and glutamine accumulation, linked to ammonia toxicity.

  2. Hyperammonemia Type II (Ornithinemia): Caused by OTC deficiency, leading to elevated blood level of ammonia and characteristic symptoms of glycine accumulation.

  3. Citrullinemia: Argininosuccinate synthetase deficiency leads to the buildup of ammonia and citrulline in the bloodstream; management includes special diets to enhance citrulline clearance.

  4. Argininosuccinic Aciduria: Involves a deficiency of argininosuccinase causing hyperammonemia, requiring a low protein diet.

  5. Hyperargininemia: Resulting from arginase deficiency manifesting as elevated arginine levels.

FATE OF UREA IN THE BODY

  • Urea diffuses from the liver into the blood for filtration by the kidneys and excretion through urine, emphasizing the importance of effective renal function.

  • In cases of kidney failure, urea levels rise in plasma leading to increased intestinal reabsorption, highlighting the systemic impacts of renal function on nitrogen metabolism.

FATES OF CARBON SKELETONS FROM AMINO ACIDs

  • Energy Contributions: Account for 10-15% of human total energy production; converges into six major metabolic products:

    • Pathway Breakdown:

    • 7 amino acids to acetyl-CoA

    • 5 to α-ketoglutarate

    • 4 to succinyl-CoA

    • 2 each to fumarate and oxaloacetate.

    • Some amino acids are ketogenic and glucogenic.

Key Distinctions Between Amino Acids

  • Ketogenic Amino Acids: Include Leucine and Lysine, converting into ketone bodies via acetoacetyl CoA.

  • Glucogenic Amino Acids: Convert into glucose precursors via pyruvate, α-ketoglutarate and others.

ENZYME COFACTORS FOR ONE-CARBON TRANSFER REACTIONS

  • Biotin: Involved in carboxylations.

  • S-Adenosylmethionine: Transfers methyl groups.

  • Tetrahydrofolate: Versatile for various carbon transfers due to its structure.

ENTRY POINT METABOLISM OF PYRUVATE:

  • Amino Acids Entering via Pyruvate: Examples include alanine, serine, and cysteine.

  • Conversion Examples:

    • Alanine transfers its amino group to yield pyruvate.

    • Serine interconverts with glycine and can contribute to pyruvate production.

ACETYL CoA AS AN ENTRY POINT

  • ** This section can cover various amino acids leading to acetyl-CoA, maintaining specificity towards their pathways.**

OTHER USES OF TRYPTOPHAN

  • Metabolic Utilization: Tryptophan's indole ring can be converted into other important metabolites like serotonin (neurotransmitter) and Nicotinate (precursor for NAD).

ACETOACETYL CoA AS AN ENTRY POINT

  • Includes discussion on degradation pathways for phenylalanine leading to various metabolic conditions such as alkaptonuria and tyrosinemia, discussing implications and treatment protocols for the disorders.

PHENYLKETONURIA

  • Disease Mechanism: Caused by a deficiency in phenylalanine hydroxylase which leads to the accumulation of phenylalanine and toxic metabolites leading to mental retardation.

  • Treatment Approaches: Aimed towards dietary management, particularly low-phenylalanine dietary interventions during growth periods.