Digestion of dietary proteins
Digestion of dietary proteins starts in the stomach. Secretion of HCl activates formation of pepsin from pepsinogen which hydrolyses peptide bonds of dietary proteins to release aromatic amino acids. Similarly, in the small intestine digestion continues. Zymogens are activated for the breakdown of peptide bonds to release amino acids which are absorbed into the small intestine.

Amino acid deamination
Transamination is a process by which amino group is transferred to the keto acid to yield the keto acid of the original amino acid and a new amino acid, catalyzed by amino transferases. Glutamate is oxidatively deaminated in the mitochondrion and release ammonia.
 
The Urea Cycle
This cyclic pathway takes place in the liver, partly in the mitochondria and partly in cytosol. There is interrelation between urea cycle and citric acid cycle. Fumarate of the urea cycle is taken up by citric acid cycle. Carbamoyl phosphate synthetase I is the regulatory enzyme.

Metabolic breakdown of individual amino acids
Catabolism of amino acids gives rise to the intermediate compounds of citric acid cycle. Alanine, serine, cysteine and asparagine are converted to oxaloacetate. Glutamine, proline, arginine and histidine are converted to α-ketoglutarate through glutamate. Succinyl CoA is a point of entry for non polar amino acids like methionine, valine and isoleucine. Leucine is degraded to acetyl CoA and acetoacetate. Tryptophan, lysine, leucine, phenylalanine, tyrosine and isoleucine donate their carbons to acetyl CoA. Various disorders of amino acid catabolism are observed due to the defective enzymes. Tryptophan, tyrosine, glycine and glutamate are the precursors of some of the biologically important compounds. Biotin, Tetrahydrofolate or S-Adenosyl methionine is the enzyme cofactors in catabolism which transfer carbon compounds.

Amino acid biosynthesis
Nonessential amino acids are formed from intermediates of carbohydrate metabolism. Alanine is formed from pyruvate and aspartate from oxaloacetate. Asparagine is formed from aspartate. Glutamate is formed from α ketoglutarate and glutamine from glutamate. Glutamate is the precursor of proline and arginine. Cysteine is synthesized from 3 – phosphoglycerate. During the process, serine is the intermediate compound which gives rise to glycine.
Threonine is an essential amino acid. It is formed from β-aspartate. Methionine and lysine also have a common precursor. Valine, Leucine and isoleucine are formed from pyruvate. Phenyl alanine, tyrosine and Tryptophan are formed from phosphoenol pyruvate and erythrose – 4 – phosphate through the intermediate compound called chorismate. Histidine originates from PRPP and ATP.

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Dietary proteins are digested in the stomach and small intestine to yield amino acids which are absorbed in the latter. The amino acids undergo transamination and oxidative deamination. The ammonia released by the above process is transported in the form of glutamine or alanine. The urea cycle is the cyclic pathway wherein the ammonia gets detoxified to urea in the liver. Amino acids are degraded into various compounds which are intermediates of the ultimate oxidative common pathway to release energy. Amino acids are synthesized from different intermediates of citric acid cycle.

• Concept is explained with two well laid out concept maps.
• Digestion is explained with animation, as also are reactions.
• Urea cycle and citric acid cycle are described with structures and animations.
• Tabulation of amino acids to make it easy to recollect.
• Degradation pathways of major amino acids are shown.
• Syntheses of pathways of all 20 amino acids are depicted.

Digestion of dietary proteins

• Introduction
• Digestion in the stomach
• Digestion in the small intestine

Amino acid deamination

• Transamination
• Oxidative deamination
• Transport of ammonia

The urea cycle

• Cyclic pathway
• Reactions of the urea cycle
• Inter-relation between the urea cycle and the citric acid cycle
• Regulation and energetics
• Disorders of the urea cycle

Metabolic breakdown of individual amino acids

• Overview
• Degradation of amino acids to pyruvate
• Degradation of oxaloacetate and α-ketoglutarate
• Degradation to succinyl CoA
• Degradation to acetyl CoA
• Degradation to ketogenic amino acids
• Amino acids as biosynthetic precursors
• Enzyme cofactors in catabolism

Amino acid biosynthesis

• Biosynthesis of nonessential amino acids
• Biosynthesis of essential amino acids