Amino Acid Metabolism

• The chemical transformation of amino acids are distinct from those of carbohydrates or lipids in that they involve the elemental nitrogen
• Mammals synthesize certain amino acids and obtain the rest from their diets

  • Excess dietary amino acids are not simply excreted but are converted to common metabolites serving as metabolic fuels
• Protein Degradation

  • Extracellular and intracellular proteins may be digested by lysosomal proteases
  • Other proteins to be degraded are first conjugated to the protein ubiquitin
  • The proteasome, a barrel shaped complex, unfolds ubiquitinated proteins in an ATP-dependent process and proteolytically degrades them
• Cells continuously synthesize proteins from and degrade them to amino acids

  • To store nutrients in the form of proteins and to break them down in times of metabolic need
  • To eliminate abnormal proteins whose accumulation would be harmful to the cell
  • To permit the regulation of cellular metabolism by eliminating superfluous enzymes and regulatory proteins
• In the half lives of different enzymes, the short lived enzymes is if they perform their functions, they are rapidly degraded, whereas the relatively stable enzymes have nearly constant catalytic activities under physiological conditions
• Lysosomes Degrade many proteins

  • contain ∼50 hydrolytic enzymes including a variety of proteases called cathepsins
  • maintains an internal pH of ∼5, and its enzymes have acidic pH optima
  • protects the cell against accidental lysosomal leakage since lysosomal enzymes are largely inactive at cytosolic pH's
• Lysosomes

  • Degrade substances that the cell takes up via endocytosis
  • They also recycle intracellular constituents that are enclosed within vesicles that fuse with lysosomes, a process called autophagy
  • In starving cell, a selective pathway of lysosomes is activated by importing and degrading cytosolic proteins containing specifically KFERQ sequence
• Glutamate is the precursor of proline, ornithine, and arginine
• Conversion of glutamate to proline involves the following reactions

  • Reduction of gamma carboxyl group to an aldehyde by the following steps
  • Phosphorylation of carboxyl group by y-glutamyl kinase
  • reduction of the Glutamate 5 phosphate by G5P dehydrogenase
  • Formation of an internal schiff base with further reduction to proline by the ff
  • Glutamate-5-semialdehyde cyclizes spontaneously forming pyrroline 5 carboxylate
  • Final reduction to proline by pyrroline 5 carboxylate reductase
• In humans, a three step pathway is utilized

  • Glutamate-5-semialdehyde is transaminated to yield ornithine by ornithine delta transaminase
  • Ornithine is converted to arginine by reactions in the urea cycle
• Serine, cysteine, and glycine are derived from 3-phosphoglycerate
• Serine is formed from 3 phosphoglycerate in a three reaction pathway

  • Conversion of 3 phosphoglycerate to 3 phosphohydroxypyruvate by 3 phosphoglycerate dehydrogenase, serine's phosphorylated keto acid analog
  • Transamination of 3 phosphohydroxypyruvate to phosphoserine by PLP aminotransferase
  • Hydrolysis of phosphoserine to serine by phosphoserine phosphatase
• Serine participates in glycine in two ways

  • Direct conversion of serine to glycine by serine hydroxymethyltransferase in a reaction that also yields N^5,N^10-methylene-THF
  • Condensation of the N^5,N^10 methylene THF with CO2 and NH4+ by glycine synthase
• In animals, cysteine is synthesized from serine and homocysteine, a breakdown product of methionine

  • Homoserine combines with serine through the enzyme cystathionine synthase to yield cystathionine, which subsequently forms cysteine and a-ketobutyrate by cystathione y-lyase
  • Cysteine's sulfhydryl group is derived from the essential amino acid methionine
• Plants and microorganisms synthesize the essential amino acids
• Lysine, methionine, and threonine are synthesized from aspartate
• The synthesis of the lysine, methionine, and threonine biosynthesis begin with aspartokinase to yield aspartyl-B-Phosphate
• Lysine, methionine, and threonine are synthesized from aspartate

  • Aspartokinase yields phosphorylation of aspartate to yield aspartyl-B-phosphate
  • Each of the pathways involved are independently controlled
  • E coli has three isozymes of aspartokinase that respond differently to the three amino acids in terms feedback inhibition of enzyme activity and repression of enzyme synthesis
• Methionine synthase or homocysteine methyltransferase catalyzes the methylation of homocysteine to form methionine using N^5-methyl-THF as its methyl group donor

  • It is the only coenzyme B12- associated enzyme in mammals besides methylmalonyl-CoA mutase, but the coenzyme B12's cobalt ion in methionine synthase is axially liganded by a methyl group to form methylcobalamin rather than a 5'-adenosyl group as in methylmalonly-CoA mutase
• In animals, the primary function of methionine synthase is not de novo methionine synthesis, as Met is an essential amino acid, but it functions in the cyclic synthesis of SAM for use in biological methylations
• Leucine, Isoleucine, and Valine are derived from pyruvate

  • Pyruvate forms an adduct with TPP that is decarboxylated to hydroxyethyl TPP
  • Adds either to the keto group of a second pyruvate to form acetolactate or to the keto group of alpha-ketobutyrate to form a-aceto-a-hydroxybutyrate to form isoleucine
• Leucine biosynthetic pathway branches off from the valine pathway

  • The final reactions in each pathway which begin with pyruvate rather than an amino acid, is the PLP Dependent transfer of an amino group from glutamate t form the amino acid
• Cells continuously synthesize proteins and degrade them to amino acids

  • Stores nutrients in the form of proteins and break them down in times of metabolic need, processes that are most important in muscle tissue
  • Eliminate abnormal proteins whose accumulation would be harmful to the cell
  • Permit the regulation of cellular metabolism by eliminating superfluous enzymes and regulatory proteins
• Proteins are marked for degradation by covalently linking them to ubiquitin

  • Ubiquitin activating enzyme (E1) - requires ATP to form a thioester bond with the with ubiquitin
  • Ubiquitin conjugating enzyme (E2s) - attaches ubiquitin to cellular proteins
  • Ubiquitin protein ligase (E3) - transfers the activated ubiquitin from E2 to a Lys ε-amino group of a previously bound protein, forming an isopeptide bond
• • In order for a protein to be degraded, it must be linked to a chain of at least four tandemly linked ubiquitin molecules
  • Ubiquitin are removed by ubiquitin ISOPEPTIDASES
• Other signals which identifies protein for destruction

  • Cyclin destruction boxes, which are amino acid sequences that mark cell-cycle proteins for destruction
  • Protein rich in PEST sequences
• The proteasome unfolds and hydrolyzes ubiquinated polypeptides

  • A 26 S large protease complex digests the ubiquinated proteins
  • An ATP driven multisubunit proteases spares ubiquitin, which is then recycled.
  • Has two components: 20S (catalytic unit), and 19S (regulatory unit)
• 20S Proteasome

  • Has 2 copies each of 14 homologous proteins
  • Arranged in 4 rings of 7 subunits that stack to form a barrel
  • The outer rings are made up alpha subunits and the inner ring are made up of beta subunits
  • A sealed barrel
• The proteasome and other proteases generate free amino acids
• • Transamination interconverts an amino acid and an α-keto acid.
  • Oxidative deamination of glutamate releases ammonia for disposal.
• Free amino acids originate from the degradation of cellular proteins and from the digestion of dietary proteins
• The gastric protease pepsin, the pancreatic enzymes trypsin, chymotrypsin, and elastase, and a host of other endo- and exopeptidases degrade polypeptides to oligopeptides and amino acids. These substances are absorbed by the intestinal mucosa and transported via the bloodstream to be absorbed by other tissues.
• • The predominant amino group acceptor is alpha-ketoglutarate, producing glutamate and new alpha-ketoacid
  • Glutamate’s amino group, in turn, can be transferred to oxaloacetate, yielding aspartate and re-forming alpha-ketoglutarate
• The enzymes that catalyze transamination, called aminotransferases or

  transaminases, require the coenzyme pyridoxal-5′-phosphate

  • PLP is a derivative of pyridoxine
  • The coenzyme is covalently attached to the enzyme via a Schiff base (imine) linkage formed by the condensation of its aldehyde group with the ε-amino group of an enzyme Lys residue
  • The Schiff base, which is conjugated to the pyridinium ring, is the center of the coenzyme’s activity.
• SGOT and SGPT are the two most common types of liver enzymes
• Glutamate Can Be Oxidatively Deaminated

  • Glutamate dehydrogenase, a mitochondrial enzyme, is the only known
  • enzyme that can accept either NAD+ or NADP+ as its redox coenzyme.