BCH 333 Chapter 23: Protein Turnover and Amino Acid Catabolism

2 sources of amino acids

• intracellular protein turnover (proteins constantly being made and degraded

• Dietary protein intake

• (Also, branched chain amino acids in muscle—severe starvation; last ditch effort before death)

Essential amino acids in mammals

• Histidine

• Isoleucine

• Lysine

• Leucine

• Methionine

• Phenylalanine

• Threonine

• Tryptophan

• Valine

• Includes most of the complicated R groups; must be obtained from the diet/can’t be synthesized

Dietary protein breakdown

• broken down to amino acids and oligopeptides

• In the stomach:

  • Nonenzymatically—acid denatures proteins by catalyzing acid hydrolysis of peptide bonds

  • Enzymatically—proteolysis by pepsin (from pancreas → dumped into the stomach)

• Further broken down by intestinal epithelial peptidases in the lumen of the gut

• Ultimately, amino acids are released into the blood

Excess amino acids

• cannot be stored OR excreted

• Some are left intact for biosynthesis (cells take up for polypeptide synthesis, etc.)

• Some are broken down

  • Amino groups are removed and discarded as urea (nitrogen disposal by the urea cycle)

  • Carbon skeletons get used as fuel (glucose/glycogen synthesis, cellular respiration, or fatty acid synthesis)

Amino acid degradation

• main site in mammals is the liver

• 1st step—removal of nitrogen

• 2nd step—ammonium ion is converted to urea in most terrestrial vertebrates via the urea cycle

Nitrogen removal

• Amino acid + α-ketoglutarate → α-keto acid + glutamate

  • Transamination (aminotransferase)

  • Can think of glutamate as a nitrogen carrier in the breakdown of amino acids

  • amino group is transferred from the amino acid to an alpha keto acid

  • Serine (→ pyruvate) and threonine (→ α-ketybutyrate) can be directly deaminated via dehydratases, which catalyze dehydration and deamination of the amino acids

• Glutamate + NAD⁺ + H2O → NADH + NH₄⁺ + α-ketoglutarate

  • Oxidative deamination

  • Catalyzed by glutamate dehydrogenase in mitochondria

• NH4+ → urea cycle

Branched chain amino acid degradation in muscle

• breakdown of skeletal muscle

• Nitrogen must be transported to liver via the glucose-alanine cycle for the above step to occur

Glucose alanine cycle

• skeletal muscle: protein —> amino acids —> alanine

  • 2 pyruvate + 2 amino acids <=> 2 alanine + 2 alpha keto acids (transamination)

  • Transfers amino group from AA onto pyruvate

• Liver: alanine —> pyruvate —> glucose (gluconeogenesis)

  • Alanine —> 2 pyruvate + NH2 (deamination; + 4 ATP —> urea) —> glucose

• Function: muscle protein is degraded to generate additional ATP for muscle contraction (must keep blood glucose levels up bc some tissues can only use glucose for fuel)

• Can think of alanine as the blood transport form of pyruvate (there are no pyruvate transporters in the PM, which helps with regulation (don’t want it to escape willy nilly)

Urea cycle

• amino acids

  • Nitrogen → urea

  • Carbon skeletons → CAC/glycolytic intermediates (which one depends on which amino acid is being broken down)

• Don’t need to know enzyme names

• Need to be able to identify structures (but don’t need to be able to draw)

• CO2 + H2O <=> H2CO3 <=> H+ + HCO₃^-

• HCO₃^- + ATP → ADP + carboxyphosphate (good LG)

• Carboxyphosphate + NH3 → Pi + carbamic acid

• Carbamic acid + ATP → ADP + carbamoyl phosphate (good LG; high transfer potential)

• Ornithine + carbamoyl phosphate → citrulline + Pi

  • Ornithine = lysine but 1C shorter

  • Occurs in mitochondrial matrix (along with all previous steps)

• Citrulline → transported to cytoplasm

• Citrulline (cytoplasm) + aspartate + ATP → AMP + PPi + argininosuccinate

  • Argininosuccinate = arginine + succinate (guanidinium group and a succinate group, almost)

  • Occurs in cytoplasm, along with all following steps

• Argininosuccinate → arginine + fumarate (carbon skeleton from aspartate, oxidized version of succinate → to CAC)

  • This step links urea cycle to CAC and gluconeogenesis; fumarate → malate → oxaloacetate → PEP → glucose

• Arginine + H2O → ornithine (regenerated) + urea (excreted)

Nitrogen in life cycle

• average human excretes ~22 lbs of urea per year, most of which goes to waste instead of being used as fertilizer for plants (one of plants’ key nutrients that they need)

• Haber Process—industrial nitrogen fixation process; insanely energy intensive due to the extreme stability of N2 (the most energy intensive process we have)

Urea cycle defects

• there are no alternative pathways, so all defects lead to hyperammonemia

• Brain damage/severe CNS damage effects occur soon after birth

• Treatments aim to circumvent the metabolic block

  • Ex: when there is an argininosuccinaase deficiency, can supply excess arginine to force the excretion of argininosuccinate (which has two N’s; basically substitutes for urea)

Fate of amino acid carbon skeletons

• major metabolic intermediates for CAC or gluconeogenesis

• 2 groups of breakdown sources—ketogenic amino acids and glucogenic amino acids (can be both; it’s just classified by what the carbon skeleton becomes)

  • Don’t need to know the classifications of each or their pathways of catabolism; just be able to tell whether an amino acid is ketogenic, glucogenic, or both based on the end product

Ketogenic amino acid products

• acetyl CoA

• Acetoacetyl CoA

• Can use these for CAC and to make ketone bodies; can NOT be used for gluconeogenesis

Glucogenic amino acid porducts

• pyruvate

• α-ketoglutarate

• Succinyl CoA

• Fumarate

• Oxaloacetate

• These are things that could be used for the CAC OR gluconeogenesis

Alcaptonuria

• results from a defect of homogentisate oxidase

• Results in the accumulation of homogentisate in the urine and tissues such as the eyes, which results in a dark highly colored polymer when exposed to air

• The condition isn’t really deadly, just a pain in the ass to live with (higher risk of arthritis, etc.)

Maple syrup urine disease

• defect in the oxidative decarboxylation of branched amino acids (leucine, valine, isoleucine)

• Elevated levels of these amino acids in the blood and urine

• Results in mental and physical retardation unless diet is controlled early in life

Phenylketonuria (PKU)

• Defect in phenylalanine hydroxylase

• Phe accumulates in all body fluids, resulting in severe mental retardation

• Therapy: low [Phe] diet; must start verrryyyyy shortly after birth (can be detected pretty much right after birth)

• Autosomal recessive mutation; ~1.5% of the population is heterozygotes

• One of the most common metabolic disorders