Amino Acid Metabolism Notes

Amino Acid Metabolism

Learning Objectives

  • Transamination mechanism
  • Glucose-alanine cycle
  • Urea cycle
  • Aspartate argininosuccinate shunt
  • Degradation of ketogenic and glucogenic amino acids
  • Conversion of amino acids to metabolic precursors
  • Nitrogen fixation
  • Metabolic precursors of amino acids
  • Essential and non-essential amino acids
  • Synthesis of amino acids
  • Tetrahydrofolate
  • S-adenosylmethionine
  • The activated methyl cycle
  • Feed back regulation amino acid synthesis

Overview of Amino Acid Metabolism

  • No protein stores exist, so essential amino acids must come from the diet.
  • Proteins constantly undergo synthesis and breakdown.
  • Amino acids are also used to synthesize some non-protein metabolites.
  • Amino acids are either used as building blocks or burned for energy (approximately 10% of our energy needs).
  • Catabolism of amino acids increases during times of starvation.

Divergent Pathways of NH3 Groups and Carbon Skeletons

  • Intracellular and dietary protein sources contribute to the amino acid pool.
  • Amino acids can be used for:
    • Biosynthesis of amino acids, nucleotides, and biological amines.
    • Catabolism, leading to carbon skeletons (α-keto acids) and NH3.
  • NH3 is converted to carbamoyl phosphate and enters the urea cycle for nitrogen excretion as urea.
  • Carbon skeletons are converted to α-keto acids, which can enter the citric acid cycle.
  • The aspartate-argininosuccinate shunt of the citric acid cycle connects the urea cycle and citric acid cycle.
  • Oxaloacetate from the citric acid cycle can be used for glucose synthesis via gluconeogenesis.

Removal of Amino Group via Transamination

  • Amino groups can be removed by transamination.
  • In liver cytosol, amino groups are transferred to α-ketoglutarate (α-KG), forming glutamate.
  • Transaminases (aka aminotransferases) require pyridoxal phosphate cofactor.
  • The amino group must be processed for excretion (urea cycle).

Pyridoxal Phosphate and Transamination

  • Pyridoxal phosphate (PLP) is a required cofactor for transaminases.
  • PLP participates in the transfer of amino groups.
  • The aldehyde group of pyridoxal phosphate is converted to pyridoxamine phosphate during transamination.

Transport of Amino Groups as Glutamine or Alanine

  • Other tissues may send their amino groups as glutamine through the bloodstream to the liver for processing.
  • In concert with the Cori cycle, skeletal muscle may send pyruvate through the bloodstream as alanine (the glucose-alanine cycle).
  • This operates when muscle proteins are undergoing catabolism.

Summary of Paths of Amino Groups

  • Amino acids from ingested protein are converted to α-keto acids and glutamate. Also cellular protein is converted into these.
  • Glutamine from muscle and other tissues, and alanine from muscle contribute to glutamate formation.
  • Glutamate can be converted to NH4+, urea, or uric acid through several reactions. Also glutamine can be converted into Glutamate through glutaminase. The reaction produces NH3.
  • Glutamate can be converted to aspartate and α-ketoglutarate via aspartate aminotransferase. The reaction produces NH3, and oxaloacetate.
  • Alanine is converted to pyruvate. The reaction produces NH3 and α-ketoglutarate.

Urea Cycle

  • The urea cycle occurs in the liver and spans two compartments: the mitochondrial matrix and the cytosol.
  • The overall process involves several steps:
    • Glutamine from extrahepatic tissues contributes NH3.
    • Alanine from muscle contributes to NH3.
    • Glutamate is formed from α-ketoglutarate.
    • Glutamine is converted to glutamate via glutaminase, releasing NH3.
    • Glutamate is converted to α-ketoglutarate via glutamate dehydrogenase, releasing NH3.
    • Aspartate aminotransferase converts oxaloacetate to aspartate, utilizing NH3.
    • Carbamoyl phosphate synthetase I combines HCO3- and NH3 with 2 ATP to form carbamoyl phosphate.
    • Carbamoyl phosphate reacts with ornithine to form citrulline.
    • Citrulline reacts with aspartate and ATP to form argininosuccinate (via a citrullyl-AMP intermediate).
    • Argininosuccinate is cleaved to form fumarate and arginine.
    • Arginine is cleaved to form urea and ornithine. Ornithine is regenerated, and urea is released.

Preparatory Step: Carbamoyl Phosphate Synthetase I

  • Occurs in the mitochondrial matrix.
  • The first step in the urea cycle involves the coupling of ammonia (NH3) with bicarbonate (HCO3-) to form carbamoyl phosphate.
  • The synthesis is complex, requiring four steps.

Step 1: Ornithine Transcarbamoylase

  • Also occurs in the matrix, but citrulline is transported to the cytosol.
  • The first nitrogen in the form of carbamoyl phosphate enters the cycle.

Step 2: Argininosuccinate Synthetase

  • Citrulline reacts with aspartate to form argininosuccinate.
  • The second nitrogen, in the form of aspartate, enters the cycle.
  • An ATP molecule is used and converted to AMP and PPi, going through a citrullyl-AMP intermediate.

Step 3: Argininosuccinase

  • Argininosuccinate is cleaved into arginine and fumarate by argininosuccinase.
  • The carbon skeleton of aspartate is preserved in the form of fumarate.

Step 4: Arginase

  • Arginine is cleaved by arginase into urea and ornithine.
  • Ornithine is transported into the mitochondria to begin another cycle.
  • Urea is excreted.

Krebs' Bicycle

  • Links the urea cycle and citric acid cycle.
  • Fumarate produced in the urea cycle is an intermediate in the citric acid cycle. Aspartate-argininosuccinate shunt of citric acid cycle

Fates of Carbon Skeletons

  • Glucogenic amino acids are degraded to pyruvate or TCA intermediates.
  • Ketogenic amino acids are degraded to acetoacetyl-CoA or acetyl-CoA.
  • Some amino acids are both glucogenic and ketogenic.

Pyruvate as a Point of Entry into Metabolism

  • Several amino acids are degraded to pyruvate.
  • Examples include alanine, serine, cysteine, glycine, threonine, and tryptophan.

Asparagine and Aspartate Degradation

  • Asparagine and aspartate are degraded to oxaloacetate.
  • L-asparaginase is an effective chemotherapeutic agent in the treatment of cancers that must obtain asparagine from the blood (acute lymphoblastic leukemia).

Alpha-Ketoglutarate as Entry Point

  • The carbon skeletons of several five-carbon amino acids enter the citric acid cycle as α-ketoglutarate.
  • These amino acids are first converted into glutamate.
  • Glutamate is oxidatively deaminated by glutamate dehydrogenase to yield α-ketoglutarate.

Succinyl CoA as Entry Point

  • Succinyl CoA is a point of entry for the three nonpolar amino acids methionine, valine, and isoleucine.
  • Propionyl CoA and methylmalonyl CoA are intermediates in the breakdown of these amino acids.
  • The same pathway is used in β-oxidation of fatty acids with an odd number of carbon atoms.

Overview of Amino Acid Anabolism

  • Biologically useful nitrogen compounds are generally scarce in nature.
  • Most organisms maintain strict economy in their use of ammonia, amino acids, and nucleotides, often salvaging and reusing them.
  • The nitrogen cycle maintains a pool of biologically available nitrogen.

Assimilation of NH3 into Amino Acids

  • Once ammonia has been formed via nitrogen fixation, the nitrogen can be incorporated into either glutamate or glutamine for further use:
    • Glutamate (Glu) is the source of amino groups for the synthesis of most amino acids.
    • Glutamine (Gln) is the source of amino groups for the synthesis of most other nitrogen-containing molecules (e.g., nucleotides).

Essential vs. Non-Essential Amino Acids

  • Amino acids that can be synthesized by humans are called nonessential amino acids and are usually synthesized by simple reactions.
  • Amino acids that are required in the diet are called essential amino acids. These amino acids usually have complex synthetic pathways and cannot be synthesized by humans.

Amino Acids Synthesis

  • The carbon skeletons for amino acid synthesis are provided by intermediates of the glycolytic pathway, the citric acid cycle, and the pentose phosphate pathway.

Tetrahydrofolate (THF)

  • Tetrahydrofolate carries activated one-carbon units.
  • Sources: serine, glycine, histidine, tryptophan. These are converted into THF-C1
  • Biosynthetic destinations: purine bases, thymine, S-adenosylmethionine → choline, phospholipids, creatine, epinephrine, DNA methylation
  • THF+C<em>n→THF−C1→C</em>n+1productsTHF + C<em>n \rightarrow THF-C1 \rightarrow C</em>{n+1} products

S-Adenosylmethionine (SAM)

  • S-Adenosylmethionine (SAM) is the activated methyl donor in most biochemical reactions.
  • The methyl group in SAM is more reactive than in THF.
  • Donation of a methyl group by S-adenosylmethionine results in S-adenosylhomocysteine.
  • S-adenosylhomocysteine is cleaved to yield adenosine and homocysteine.
  • SAM is the major donor of methyl groups to many different acceptors, such as phospholipids and DNA bases.

Feedback Inhibition

  • The rate of synthesis of amino acids depends mainly on the amount of the biosynthetic enzymes and on their activities.
  • The final product in biosynthetic pathways often inhibits the enzyme that catalyses the committed step.