CH.15: Nitrogen Metabolism II

Nitrogen metabolism

• Animals have mechanisms for disposing of excess and toxic nitrogen-containing molecules

• Digestion of protein produce large amounts of 20 different amino acids

• Body has no dedicated storage form for amino acids

• Only reserves are the functional proteins—the biggest mass is in the muscle proteins

• Muscle proteins are part of the contractile machinery, if broken down to provide amino acids for gluconegogenesis in liver, then muscle wasting occurs

Protein turnover

• Proteins are continually synthesized and degraded

• Serves 3 purposes:

  • Protects cells from the accumulation of abnormal proteins

  • Responds to environmental changes by degrading enzymes, peptides, and hormones

  • Degrade developmental proteins—longevity of proteins differs significantly (ranging from minutes to years)

• Ubiquination

• Target mechanisms

Ubiquination

• Ubiquitin, a small eukaryotic protein, is covalently attached to a protein to be degraded

• Target protein is then degraded by proteolytic complex called a protesome

Target mechanisms

• N-terminal residues—proteins with certain N-terminal amino acids, such as met or alanine have long half-lives

• PEST sequence—proteins with sequence of proline, glutamine, serine and threonine have short half-lives

• Oxidized residues—oxidized amino acids promote protein degradation

Catabolism of amino acids

• First stage—Deamination

  • Transamination

  • Oxidative deamination

• Second stage—Degradation of the C-skeleton

Deamination

• Removal of the amino group from amino acids

• Involved 2 reactions:

  • Transamination

  • Oxidative deamination

Degradation of the C-skeleton

C-skeleton converted to a variety of compounds of the glycolytic and citric acid intermediates (pyruvate, acetyl CoA and a-ketoglutarate)

Transport of ammonia

• Ammonia is toxic

• High levels can impair brain function and cause coma

• Level in blood is kept very low

• Transport of NH₄⁺ from peripheral tissues to the liver

  • Most tissue

  • Muscle

  • At the liver

Transport of NH₄⁺ from peripheral tissues to liver

• Most tissue

  • NH₄⁺ is first incorporated into glutamate → glutamine by glutamine synthetase

• Muscle

  • NH₄⁺ is transferred to a-ketoglutarate → glutamate and the amino group is then transported by the alanine cycle

• At the liver:

  • Glutamine → (glutaminase) → glutamate and NH₄⁺

  • Additional NH₄⁺ is generated as:

    • Glutamate → (glutamate dehydrogenase) → a-ketoglutarate

Urea cycle

• Occurs in the liver

• Net reaction

  • CO₂ + NH₄⁺ + aspartate + 3 ATP + 2 H₂O → urea + fumarate + 2 ADP + 2 Pi + AMP + PPi + 5 H⁺

• Urea cycle begins in the mitochondria

• After the second step citrulline is transported to the cytosol, consist of 5 enzyme catalyzed reactions and 2 transport mechanisms

• First step (committed step)

  • Hydrolysis of 1 ATP is used to drive the production of carbamate and the second ATP is used to phosphorylate the carbamate

Control of urea cycle

• Long term—changes in dietary protein consumption alter the levels of enzymes of the urea cycle

• Short term—enzymes are controlled by the concentration of their substrates

• N-acetylglutamate (allosteric activator of carbamoyl phosphate synthetase I)

• (glutamate + acetyl CoA → (N-acetylglutamate synthase) → N-acetylglutamate)

Catabolism of amino acids c-skeletons

• Amino acids degradation form TCA intermediates or their precursors, which are then metabolized to CO₂ and H₂O or used in gluconeogenesis

• Breakdown of carbon follows 2 general pathways:

  • Glucogenic amino acids

  • Ketogenic amino acids

  • Glucogenic and ketogenic

Glucogenic amino acids

• Ones the yield pyruvate, oxaloacetate, fumarate, succinyl CoA or a-ketoglutarate upon degraadation

• The rest of the 20 amino acids that are not mentioned below

Ketogenic amino acids

• Ones that yield acetyl CoA or acetoacetyl CoA upon degradation

• Leucine and lysine

Glucogenic and ketogenic

Isoleucine, phenylalanine, tryptophan, tyrosine, threonine

Nucleotide degradation

• Degradation occurs as normal turnover of nucleic acids, nucleotides and as digestion of dietary nucleic acids

• Dietary nuclei acids are degraded by enzymes of the pancreas and intestine

• Nucleic acids → (nucleases) → oligonucleotides

• DNA → (deoxyribonucleases (DNases)) → oligonucleotides

• RNA → (ribonucleases (RNases)) → oligonucleotides

• Oligonucleotides → (phosphodiesterases) → mononucleotides

• Mononucleotides → (nucleotidases) → nucleosides

• Nucleosides → (nucleosidases) → base + ribose

• Nucleosides + Pi → (nucleoside phosphorylase) → base + ribose-a-1-phosphate

• Dietary purine and pyrimidines are not use in nucleic acids synthesis they are degraded

Purine catabolism

• Ultimate fate of uric acid depends on the organism

• Uric acids may be converted to allantoin, allantoic acid, urea or ammonia

Pyrimidine catabolism

• Unlike purines, pyrimidine rings are degraded

• Nucleotides → (nucleotidase) → nucleosides

• Nucleoside → (pyrimidine nucleoside phsphorylase) → base and ribose-1-phosphate

• Cytidine must be converted to uridine (deoxycytidine to deoxyuridine) before they can be degraded

• Cytosine and uracil are degraded to b-alanine

• Thymine is converted to b-aminoisobutyrate

• Because of their high solubility in water, the production of large amount of b-alanine or b-aminoisobutyrate does not cause problems like the overproduction of uric acid does