Digestion of  proteins.

General and specific pathways of amino acids transformation.


PROTEIN CATABOLISM – hydrolysis breaks peptide bonds yielding amino acids




PROTEIN CATABOLISMattaches an amino group of an amino acid to a keto acid converting a keto acid

into an amino acid. The original amino acid becomes a keto acid.

1. New amino acid can be used for synthesis

2. Keto acid can be broken down in the TCA cycle

DEAMINATION – uses deaminase, water & NAD

1. breaks down an amino acid into a keto acid

and an ammonia.

2. liver cells convert ammonia to urea via the

PROTEIN ANABOLISM – dehydration synthesis

A. Amination – attaches amino group to a keto


B. Ten essential amino acids

C. Deficiency diseases

1. marasmus

2. kwashiorkor

D. Genetic metabolic disorder - PKU



Breakdown of Food and Fat

Breakdown of Food

Breakdown of Food


  The digestive process breaks down food by chemical and mechanical action into substances that can pass into the bloodstream and be processed by body cells.



  Certain nutrients, such as salts and minerals, can be absorbed directly into the circulation. Fat, complex carbohydrates, and proteins are broken down into smaller molecules before being absorbed.

  Fat is split into glycerol and fatty acids; carbohydrates are split into monosaccharide sugars; and proteins are split into linked amino acids called peptides, and then into individual amino acids.





1: Mouth and oesophagus

  Food is chewed with the teeth and mixed with saliva. The enzyme amylase, present in saliva, begins the breakdown of starch into sugar. Each lump of soft food, called a bolus, is swallowed and propelled by contractions down the oesophagus into the stomach.


2: Stomach

  Pepsin is an enzyme produced when pepsinogen, a substance secreted by the stomach lining, is modified by hydrochloric acid (also produced by the stomach lining).


  Pepsin breaks proteins down into smaller units, called polypeptides and peptides. Lipase is a stomach enzyme that breaks down fat into glycerol and fatty acids. The acid produced by the stomach also kills bacteria.



3: Duodenum

  Lipase, a pancreatic enzyme, breaks down fat into glycerol and fatty acids. Amylase, another enzyme produced by the pancreas, breaks down starch into maltose, a disaccharide sugar. Trypsin and chymotrypsin are powerful pancreatic enzymes that split proteins into polypeptides and peptides.

4: Small Intestine

  Maltase, sucrase, and lactase are enzymes produced by the lining of the small intestine. They convert disaccharide sugars into monosaccharide sugars. Peptidase, another enzyme produced in the intestine, splits large peptides into smaller peptides and then into amino acids.


5: Large Intestine

  Undigested food enters the large intestine, where water and salt are absorbed by the intestinal lining. The residue, together with waste pigments, dead cells , and bacteria, is pressed into faeces and stored for excretion.



Urea Cycle




Humans are totally dependent on other organisms for converting atmospheric nitrogen into forms available to the body. Nitrogen fixation is carried out by bacterial nitrogensases forming reduced nitrogen, NH4+ which can then be used by all organisms to form amino acids.


Overview of the flow of nitrogen in the biosphere. Nitrogen, nitrites and nitrates are acted upon by bacteria (nitrogen fixation) and plants and we assimilate these compounds as protein in our diets. Ammonia incorporation in animals occurs through the actions of glutamate dehydrogenase and glutamine synthase. Glutamate plays the central role in mammalian nitrogen flow, serving as both a nitrogen donor and nitrogen acceptor.

Reduced nitrogen enters the human body as dietary free amino acids, protein, and the ammonia produced by intestinal tract bacteria. A pair of principal enzymes, glutamate dehydrogenase and glutamine synthatase, are found in all organisms and effect the conversion of ammonia into the amino acids glutamate and glutamine, respectively. Amino and amide groups from these 2 substances are freely transferred to other carbon skeletons by transamination and transamidation reactions.


Representative aminotransferase catalyzed reaction.

Aminotransferases exist for all amino acids except threonine and lysine. The most common compounds involved as a donor/acceptor pair in transamination reactions are glutamate and -ketoglutarate (-KG), which participate in reactions with many different aminotransferases. Serum aminotransferases such as serum glutamate-oxaloacetate-aminotransferase (SGOT) (also called aspartate aminotransferase, AST) and serum glutamate-pyruvate aminotransferase (SGPT) (also called alanine transaminase, ALT) have been used as clinical markers of tissue damage, with increasing serum levels indicating an increased extent of damage. Alanine transaminase has an important function in the delivery of skeletal muscle carbon and nitrogen (in the form of alanine) to the liver. In skeletal muscle, pyruvate is transaminated to alanine, thus affording an additional route of nitrogen transport from muscle to liver. In the liver alanine transaminase tranfers the ammonia to -KG and regenerates pyruvate. The pyruvate can then be diverted into gluconeogenesis. This process is refered to as the glucose-alanine cycle.

The Glutamate Dehydrogenase Reaction

The reaction catalyzed by glutamate dehydrogenase is:




Glutamate dehydrogenase can utilize either NAD orNADP as cofactor. In the forward reaction as shown above glutamate dehydrogenase is important in converting free ammonia and -ketoglutarate (-KG) to glutamate, forming one of the 20 amino acids required for protein synthesis. However, it should be recognized that the reverse reaction is a key anapleurotic process linking amino acid metabolism with TCA cycle activity.In the reverse reaction, glutamate dehydrogenase provides an oxidizable carbon source used for the production of energy as well as a reduced electron carrier, NADH. As expected for a branch point enzyme with an important link to energy metabolism, glutamate dehydrogenase is regulated by the cell energy charge. ATP and GTP are positive allosteric effectors of the formation of glutamate, whereas ADP and GDP are positive allosteric effectors of the reverse reaction. Thus, when the level of ATP is high, conversion of glutamate to -KG and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is also a principal amino donor to other amino acids in subsequent transamination reactions. The multiple roles of glutamate in nitrogen balance make it a gateway between free ammonia and the amino groups of most amino acids.


The Glutamine Synthase Reaction

The reaction catalyzed by glutamine synthase is:

glutamate + NH4+ + ATP -------> glutamine + ADP + Pi + H+


The glutamine synthatase reaction is also important in several respects. First it produces glutamine, one of the 20 major amino acids. Second, in animals, glutamine is the major amino acid found in the circulatory system. Its role there is to carry ammonia to and from various tissues but principally from peripheral tissues to the kidney, where the amide nitrogen is hydrolyzed by the enzyme glutaminase (reaction below); this process regenerates glutamate and free ammonium ion, which is excreted in the urine.  

glutamine + H2O -------> glutamate + NH3

Note that, in this function, ammonia arising in peripheral tissue is carried in a nonionizable form which has none of the neurotoxic or alkalosis-generating properties of free ammonia.

Liver contains both glutamine synthetase and glutaminase but the enzymes are localized in different cellular segments. This ensures that the liver is neither a net producer nor consumer of glutamine. The differences in cellular location of these two enzymes allows the liver to scavange ammonia that has not been incorporated into urea. The enzymes of the urea cycle are located in the same cells as those that contain glutaminase. The result of the differential distribution of these two hepatic enzymes makes it possible to control ammonia incorporation into either urea or glutamine, the latter leads to excretion of ammonia by the kidney.
When acidosis occurs the body will divert more glutamine from the liver to the kidney. This allows for the conservation of bicarbonate ion since the incorporation of ammonia into urea requires bicarbonate (see below). When glutamine enters the kidney, glutaminase releases one mole of ammonia generating glutamate and then glutamate dehydrogenase releases another mole of ammonia generating a-ketoglutarate. The ammonia will ionizes to ammonium ion ( NH4+) which is excreted. The net effect is a reduction in the pH (see also
Kidneys and Acid-Base Balance).

Digestive Tract Nitrogen

While glutamine, glutamate, and the remaining nonessential amino acids can be made by animals, the majority of the amino acids found in human tissues necessarily come from dietary sources (about 400g of protein per day). Protein digestion begins in the stomach, where a proenzyme called pepsinogen is secreted, autocatalytically converted to Pepsin A, and used for the first step of proteolysis. However, most proteolysis takes place in the duodenum as a consequence of enzyme activities secreted by the pancreas. All of the serine proteases and the zinc peptidases of pancreatic secretions are produced in the form of their respective proenzymes. These proteases are both endopeptidase and exopeptidase, and their combined action in the intestine leads to the production of amino acids, dipeptides, and tripeptides, all of which are taken up by enterocytes of the mucosal wall.
A circuitous regulatory pathway leading to the secretion of proenzymes into the intestine is triggered by the appearance of food in the intestinal lumen. Special mucosal endocrine cells secret the peptide hormones cholecystokinin (CCK) and secretin into the circulatory system. Together, CCK and secretin cause contraction of the gall bladder and the exocrine secretion of a bicarbonate-rich, alkaline fluid, containing protease proenzymes from the pancreas into the intestine. A second, paracrine role of CCK is to stimulate adjacent intestinal cells to secrete enteropeptidase, a protease that cleaves trypsinogen to produce trypsin. Trypsin also activates trypsinogen as well as all the other proenzymes in the pancreatic secretion, producing the active proteases and peptidases that hydrolyze dietary polypeptides.
Subsequent to luminal hydrolysis, small peptides and amino acids are transferred through enterocytes to the portal circulation by diffusion, facilitated diffusion, or active transport. A number of Na+-dependent amino acid transport systems with overlapping amino acid specificity have been described. In these transport systems, Na+ and amino acids at high luminal concentrations are co-transported down their concentration gradient to the interior of the cell. The ATP-dependent Na+/K+ pump exchanges the accumulated Na+ for extracellular K+, reducing intracellular Na+ levels and maintaining the high extracellular Na+ concentration (high in the intestinal lumen, low in enterocytes) required to drive this transport process.
Transport mechanisms of this nature are ubiquitous in the body. Small peptides are accumulated by a proton (H+) driven transport process and hydrolyzed by intracellular peptidases. Amino acids in the circulatory system and in extracellular fluids are transported into cells of the body by at least 7 different ATP-requiring active transport systems with overlapping amino acid specificities.

Hartnup disorder is an autosomal recessive impairment of neutral amino acid transport affecting the kidney tubules and small intestine. It is believed that the defect lies in a specific system responsible for neutral amino acid transport across the brush-border membrane of renal and intestinal epithelium. The exact defect has not yet been characterized. The characteristic diagnostic feature of Hartnup disorder is a dramatic neutral hyperaminoaciduria. Additionally, individuals excrete indolic compounds that originate from the bacterial degradation of unabsorbed tryptophan. The reduced intestinal absorption and increased renal loss of tryptophan lead to a reduced availability of tryptophan for niacin and nicotinamide nucleotide biosynthesis. As a consequence affected individuals frequently exhibit pellegra-like rashes. .

Many other nitrogenous compounds are found in the intestine. Most are bacterial products of protein degradation. Some have powerful pharmacological (vasopressor) effects.

Products of Intestinal Bacterial Activity




Vasopressor Amines



















Indole and skatole

All amino acids



Prokaryotes such as E. coli can make the carbon skeletons of all 20 amino acids and transaminate those carbon skeletons with nitrogen from glutamine or glutamate to complete the amino acid structures. Humans cannot synthesize the branched carbon chains found in branched chain amino acids or the ring systems found in phenylalanine and the aromatic amino acids; nor can we incorporate sulfur into covalently bonded structures. Therefore, the 10 so-called essential amino acids must be supplied from the diet. Nevertheless, it should be recognized that,depending on the composition of the diet and physiological state of an individual,one or another of the non-essential amino acids may also become a required dietary component. For example, arginine is not usually considered to be essential, because enough for adult needs is made by the urea cycle.

However, the urea cycle generally does not provide sufficient arginine for the needs of a growing child.

To take a different type of example, cysteine and tyrosine are considered non-essential but are formed from the essential amino acids methionine and phenylalanine, respectively. If sufficient cysteine and tyrosine are present in the diet, the requirements for methionine and phenylalanine are markedly reduced; conversely, if methionine and phenylalanine are present in only limited quantities, cysteine and tyrosine can become essential dietary components. Finally, it should be recognized that if the -keto acids corresponding to the carbon skeleton of the essential amino acids are supplied in the diet, aminotransferases in the body will convert the keto acids to their respective amino acids, largely supplying the basic needs.
Unlike fats and carbohydrates, nitrogen has no designated storage depots in the body. Since the half-life of many proteins is short (on the order of hours), insufficient dietary quantities of even one amino acid can quickly limit the synthesis and lower the body levels of many essential proteins. The result of limited synthesis and normal rates of protein degradation is that the balance of nitrogen intake and nitrogen excretion is rapidly and significantly altered. Normal, healthy adults are generally in nitrogen balance, with intake and excretion being very well matched. Young growing children, adults recovering from major illness, and pregnant women are often in positive nitrogen balance. Their intake of nitrogen exceeds their loss as net protein synthesis proceeds. When more nitrogen is excreted than is incorporated into the body, an individual is in negative nitrogen balance. Insufficient quantities of even one essential amino acid is adequate to turn an otherwise normal individual into one with a negative nitrogen balance. The biological value of dietary proteins is related to the extent to which they provide all the necessary amino acids. Proteins of animal origin generally have a high biological value; plant proteins have a wide range of values from almost none to quite high. In general, plant proteins are deficient in lysine, methionine, and tryptophan and are much less concentrated and less digestible than animal proteins. The absence of lysine in low-grade cereal proteins, used as a dietary mainstay in many underdeveloped countries, leads to an inability to synthesize protein (because of missing essential amino acids) and ultimately to a syndrome known as kwashiorkor, common among children in these countries.

Essential vs. Nonessential Amino Acids























The amino acids arginine, methionine and phenylalanine are considered essential for reasons not directly related to lack of synthesis. Arginine is synthesized by mammalian cells but at a rate that is insufficient to meet the growth needs of the body and the majority that is synthesized is cleaved to form urea. Methionine is required in large amounts to produce cysteine if the latter amino acid is not adequately supplied in the diet. Similarly, phenyalanine is needed in large amounts to form tyrosine if the latter is not adequately supplied in the diet.


Removal of Nitrogen from Amino Acids



Nitrogen elimination begins intracellularly with protein degradation. There are two main routes for converting intracellular proteins to free amino acids: a lysosomal pathway, by which extracellular and some intracellular proteins are degraded, and cytosolic pathways that are important in degrading proteins of intracellular origin. In one cytosolic pathway a protein known as ubiquitin is activated by conversion to an AMP derivative, and cytosolic proteins that are damaged or otherwise destined for degradation are enzymically tagged with the activated ubiquitin. Ubiquitin-tagged proteins are then attacked by cytosolic ATP-dependent proteases that hydrolyze the targeted protein, releasing the ubiquitin for further rounds of protein targeting.

More on The Ubiquitin System for Protein Modification and Degradation

The dominant reactions involved in removing amino acid nitrogen from the body are known as transaminations. This class of reactions funnels nitrogen from all free amino acids into a small number of compounds; then, either they are oxidatively deaminated, producing ammonia, or their amine groups are converted to urea by the urea cycle. Transaminations involve moving an -amino group from a donor a-amino acid to the keto carbon of an acceptor -keto acid. These reversible reactions are catalyzed by a group of intracellular enzymes known as aminotransferases  (transaminases), which employ covalently bound pyridoxal phosphate as a cofactor (see reaction mechanism)

Aminotransferases exist for all amino acids except threonine and lysine. The most common compounds involved as a donor/acceptor pair in transamination reactions are glutamic acid and -ketoglutaric acid, which participate in reactions with many different aminotransferases. Serum aminotransferases such as serum glutamate - oxaloacetate - aminotransferase (SGOT) have been used as clinical markers of tissue damage, with increasing serum levels indicating an increased extent of damage.

A small but clinically important amount of creatinine is excreted in the urine daily, and the creatinine clearance rate is often used as an indicator of kidney function. The first reaction in creatinine formation is the transfer of the amido (or amidine) group of arginine to glycine, forming guanidinoacetate. Subsequently, a methyl group is transferred from the ubiquitous 1-carbon-donor S-adenosylmethionine to guanidinoacetate to produce creatine (from which phosphocreatine is formed), some of which spontaneously cyclizes to creatinine, and is eliminated in the urine. The quantity of urine creatinine is generally constant for an individual and approximately proportional to muscle mass. In individuals with damaged muscle cells, creatine leaks out of the damaged tissue and is rapidly cyclized, greatly increasing the quantity of circulating and urinary creatinine.

Because of the participation of -ketoglutarate in numerous transaminations, glutamate is a prominent intermediate in nitrogen elimination as well as in anabolic pathways. Glutamate formed in the course of nitrogen elimination is either oxidatively deaminated by liver glutamate dehydrogenase, forming ammonia, or converted to glutamine by glutamine synthase and transported to kidney tubule cells. There the glutamine is sequentially deamidated by glutaminase and deaminated by kidney glutamate dehydrogenase.

The ammonia produced in the latter two reactions is excreted as NH4+ in the urine, where it helps maintain urine pH in the normal range of pH 4 to pH 8. The extensive production of ammonia by peripheral or liver glutamate dehydrogenase is not feasible because of the highly toxic effects of circulating ammonia. Normal serum ammonium concentrations are in the range of 20-40 mmol, and an increase in circulating ammonia to about 400 mmol causes alkalosis and neurotoxicity.
A final, therapeutically useful amino acid-related reaction is the amidation of aspartic acid to produce asparagine. The enzyme asparagine synthase catalyzes the ATP, requiring the transamidation reaction shown below:


      Most cells perform this reaction well enough to produce all the asparagine they need. However, some leukemia cells require exogenous asparagine, which they obtain from the plasma. Chemotherapy using the enzyme asparaginase takes advantage of this property of leukemic cells by hydrolyzing serum asparagine to ammonia and aspartic acid, thus depriving the neoplastic cells of the asparagine that is essential for their characteristic rapid growth.
In the peroxisomes of mammalian tissues, especially liver, there are 2 stereospecific amino acid oxidases involved in elimination of amino acid nitrogen. D-amino acid oxidase is an FAD-linked enzyme, and while there are few D-amino acids that enter the human body the activity of this enzyme in liver is quite high. L-amino acid oxidase is FMN-linked and has broad specificity for the L amino acids.A number of substances, including oxygen, can act as electron acceptors from the flavoproteins. If oxygen is the acceptor the product is hydrogen peroxide, which is then rapidly degraded by the catalases found in liver and other tissues.
Missing or defective biogenesis of peroxisomes or L-amino acid oxidase causes generalized hyper-aminoacidemia and hyper-aminoaciduria, generally leading to neurotoxicity and early death.

Amino Acid Biosynthesis 



Glutamate and Aspartate

Glutamate and aspartate are synthesized from their widely distributed -keto acid precursors by simple 1-step transamination reactions. The former catalyzed by glutamate dehydrogenase and the latter by aspartate aminotransferase, AST.Aspartate is also derived from asparagine through the action of asparaginase. The importance of glutamate as a common intracellular amino donor for transamination reactions and of aspartate as a precursor of ornithine for the urea cycle is described in the Nitrogen Metabolism page.

Alanine and the Glucose-Alanine Cycle

Aside from its role in protein synthesis, alanine is second only to glutamine in prominence as a circulating amino acid. In this capacity it serves a unique role in the transfer of nitrogen from peripheral tissue to the liver. Alanine is transferred to the circulation by many tissues, but mainly by muscle, in which alanine is formed from pyruvate at a rate proportional to intracellular pyruvate levels. Liver accumulates plasma alanine, reverses the transamination that occurs in muscle, and proportionately increases urea production. The pyruvate is either oxidized or converted to glucose via gluconeogenesis. When alanine transfer from muscle to liver is coupled with glucose transport from liver back to muscle, the process is known as the glucose-alanine cycle. The key feature of the cycle is that in 1 molecule, alanine, peripheral tissue exports pyruvate and ammonia (which are potentially rate-limiting for metabolism) to the liver, where the carbon skeleton is recycled and most nitrogen eliminated.There are 2 main pathways to production of muscle alanine: directly from protein degradation, and via the transamination of pyruvate by glutamate-pyruvate aminotransferase (also called alanine transaminase, ALT).

glutamate + pyruvate <-------> -KG + alanine

Cysteine Biosynthesis

 The sulfur for cysteine synthesis comes from the essential amino acid methionine. A condensation of ATP and methionine catalyzed by methionine adenosyltransferase yields S-adenosylmethionine (SAM or AdoMet).


Biosynthesis of S-adenosylmethionine, SAM

SAM serves as a precurosor for numerous methyl transfer reactions (e.g. the conversion of norepinephrine to epinenephrine, see Specialized Products of Amino Acids). The result of methyl transfer is the conversion of SAM to S-adenosylhomocysteine. S-adenosylhomocysteine is then cleaved by adenosylhomocyteinase to yield homocysteine and adenosine. Homocysteine can be converted back to methionine by methionine synthase, a reaction that occurs under methionine-sparing conditions and requires N5-methyl-tetrahydrofolate as methyl donor. This reaction was discussed in the context of vitamin B12-requiring enzymes in the Vitamins page. Transmethylation reactions employing SAM are extremely important, but in this case the role of S-adenosylmethionine in transmethylation is secondary to the production of homocysteine (essentially a by-product of transmethylase activity). In the production of SAM all phosphates of an ATP are lost: one as Pi and two as PPi. It is adenosine which is transferred to methionine and not AMP. In cysteine synthesis, homocysteine condenses with serine to produce cystathionine, which is subsequently cleaved by cystathionase to produce cysteine and -ketobutyrate. The sum of the latter two reactions is known as trans-sulfuration. Cysteine is used for protein synthesis and other body needs, while the ketobutyrate is decarboxylated and converted to propionyl-CoA. While cysteine readily oxidizes in air to form the disulfide cystine, cells contain little if any free cystine because the ubiquitous reducing agent, glutathione effectively reverses the formation of cystine by a non-enzymatic reduction reaction.


Utilization of methionine in the synthesis of cysteine

The 2 key enzymes of this pathway, cystathionine synthase and cystathionase (cystathionine lyase), both use pyridoxal phosphate as a cofactor, and both are under regulatory control. Cystathionase is under negative allosteric control by cysteine, as well, cysteine inhibits the expression of the cystathionine synthase gene. Genetic defects are known for both the synthase and the lyase. Missing or impaired cystathionine synthase leads to homocystinuria and is often associated with mental retardation, although the complete syndrome is multifaceted and many individuals with this disease are mentally normal. Some instances of genetic homocystinuria respond favorably to pyridoxine therapy, suggesting that in these cases the defect in cystathionine synthase is a decreased affinity for the cofactor. Missing or impaired cystathionase leads to excretion of cystathionine in the urine but does not have any other untoward effects. Rare cases are known in which cystathionase is defective and operates at a low level. This genetic disease leads to methioninuria with no other consequences.

Tyrosine Biosynthesis

Tyrosine is produced in cells by hydroxylating the essential amino acid phenylalanine. This relationship is much like that between cysteine and methionine. Half of the phenylalanine required goes into the production of tyrosine; if the diet is rich in tyrosine itself, the requirements for phenylalanine are reduced by about 50%. Phenylalanine hydroxylase is a mixed-function oxygenase: one atom of oxygen is incorporated into water and the other into the hydroxyl of tyrosine. The reductant is the tetrahydrofolate-related cofactor tetrahydrobiopterin, which is maintained in the reduced state by the NADH-dependent enzyme dihydropteridine reductase.


Biosynthesis of tyrosine from phenylalanine

Missing or deficient phenylalanine hydroxylase leads to the genetic disease known as phenlyketonuria (PKU), which if untreated leads to severe mental retardation. The mental retardation is caused by the accumulation of phenylalanine, which becomes a major donor of amino groups in aminotransferase activity and depletes neural tissue of -ketoglutarate. This absence of -ketoglutarate in the brain shuts down the TCA cycle and the associated production of aerobic energy, which is essential to normal brain development.

The product of phenylalanine transamination, phenylpyruvic acid, is reduced to phenylacetate and phenyllactate, and all 3 compounds appear in the urine. The presence of phenylacetate in the urine imparts a "mousy" odor. If the problem is diagnosed early, the addition of tyrosine and restriction of phenylalanine from the diet can minimize the extent of mental retardation.

In other pathways, tetrahydrobiopterin is a cofactor. The effects of missing or defective dihydropteridine reductase cause even more severe neurological difficulties than those usually associated with PKU caused by deficient hydroxylase activity.

Ornithine and Proline Biosynthesis

Glutamate is the precursor of both proline and ornithine, with glutamate semialdehyde being a branch point intermediate leading to one or the other of these 2 products. While ornithine is not one of the 20 amino acids used in protein synthesis, it plays a significant role as the acceptor of carbamoyl phosphate in the urea cycle. Ornithine serves an additional important role as the precursor for the synthesis of the polyamines. The production of ornithine from glutamate is important when dietary arginine, the other principal source of ornithine, is limited. The fate of glutamate semialdehyde depends on prevailing cellular conditions. Ornithine production occurs from the semialdehyde via a simple glutamate-dependent transamination, producing ornithine.


Ornithine synthesis from glutamate

When arginine concentrations become elevated, the ornithine contributed from the urea cycle plus that from glutamate semialdehyde inhibit the aminotransferase reaction, with accumulation of the semialdehyde as a result. The semialdehyde cyclizes spontaneously to 1pyrroline-5-carboxylate which is then reduced to proline by an NADPH-dependent reductase.

Serine Biosynthesis

The main pathway to serine starts with the glycolytic intermediate 3-phosphoglycerate.


An NADH-linked dehydrogenase converts 3-phosphoglycerate into a keto acid, 3-phosphopyruvate, suitable for subsequent transamination. Aminotransferase activity with glutamate as a donor produces 3-phosphoserine, which is converted to serine by phosphoserine phosphatase.

Glycine Biosynthesis

The main pathway to glycine is a 1-step reaction catalyzed by serine hydroxymethyltransferase.


This reaction involves the transfer of the hydroxymethyl group from serine to the cofactor tetrahydrofolate (THF), producing glycine and N5,N10-methylene-THF. Glycine produced from serine or from the diet can also be oxidized by glycine cleavage complex, GCC, to yield a second equivalent of N5,N10-methylene-tetrahydrofolate as well as ammonia and CO2.


Glycine is involved in many anabolic reactions other than protein synthesis including the synthesis of purine nucleotides, heme, glutathione, creatine and serine.


Aspartate/Asparagine and Glutamate/Glutamine Biosynthesis

Glutamate is synthesized by the reductive amination of -ketoglutarate catalyzed by glutamate dehydrogenase; it is thus a nitrogen-fixing reaction. In addition, glutamate arises by aminotransferase reactions, with the amino nitrogen being donated by a number of different amino acids. Thus, glutamate is a general collector of amino nitrogen. Aspartate is formed in a transamintion reaction catalyzed by aspartate transaminase, AST. This reaction uses the aspartate -keto acid analog, oxaloacetate, and glutamate as the amino donor. Aspartate can also be formed by deamination of asparagine catalyzed by asparaginase. Asparagine synthetase and glutamine synthetase, catalyze the production of asparagine and glutamine from their respective amino acids. Glutamine is produced from glutamate by the direct incorporation of ammonia; and this can be considered another nitrogen fixing reaction. Asparagine, however, is formed by an amidotransferase reaction. Aminotransferase reactions are readily reversible. The direction of any individual transamination depends principally on the concentration ratio of reactants and products. By contrast, transamidation reactions, which are dependent on ATP, are considered irreversible. As a consequence, the degradation of asparagine and glutamine take place by a hydrolytic pathway rather than by a reversal of the pathway by which they were formed. As indicated above, asparagine can be degraded to aspartate.


Amino Acid Catabolism

Glutamine/Glutamate and Asparagine/Aspartate Catabolism

Glutaminase is an important kidney tubule enzyme involved in converting glutamine (from liver and from other tissue) to glutamate and NH3+, with the NH3+ being excreted in the urine. Glutaminase activity is present in many other tissues as well, although its activity is not nearly as prominent as in the kidney. The glutamate produced from glutamine is converted to -ketoglutarate, making glutamine a glucogenic amino acid. Asparaginase is also widely distributed within the body, where it converts asparagine into ammonia and aspartate. Aspartate transaminates to oxaloacetate, which follows the gluconeogenic pathway to glucose. Glutamate and aspartate are important in collecting and eliminating amino nitrogen via glutamine synthetase and the urea cycle, respectively. The catabolic path of the carbon skeletons involves simple 1-step aminotransferase reactions that directly produce net quantities of a TCA cycle intermediate. The glutamate dehydrogenase reaction operating in the direction of -ketoglutarate production provides a second avenue leading from glutamate to gluconeogenesis.

Alanine Catabolism

Alanine is also important in intertissue nitrogen transport as part of the glucose-alanine cycle. Alanine's catabolic pathway involves a simple aminotransferase reaction that directly produces pyruvate. Generally pyruvate produced by this pathway will result in the formation of oxaloacetate, although when the energy charge of a cell is low the pyruvate will be oxidized to CO2 and H2O via the PDH complex and the TCA cycle. This makes alanine a glucogenic amino acid.

Arginine, Ornithine and Proline Catabolism

The catabolism of arginine begins within the context of the urea cycle. It is hydrolyzed to urea and ornithine by arginase. Ornithine, in excess of urea cycle needs, is transaminated to form glutamate semialdehyde. Glutamate semialdehyde can serve as the precursor for proline biosynthesis as described above or it can be converted to glutamate. Proline catabolism is a reversal of its synthesis process. The glutamate semialdehyde generated from ornithine and proline catabolism is oxidized to glutamate by an ATP-independent glutamate semialdehyde dehydrogenase. The glutamate can then be converted to ketoglutarate in a transamination reaction. Thus arginine, ornithine and proline, are glucogenic.

Serine Catabolism

The conversion of serine to glycine and then glycine oxidation to CO2 and NH3, with the production of two equivalents of N5,N10-methyleneTHF, was described above. Serine can be catabolized back to the glycolytic intermediate, 3-phosphoglycerate, by a pathway that is essentially a reversal of serine biosynthesis. However, the enzymes are different. Serine can also be converted to pyruvate through a deamination reaction catalyzed by serine/threonine dehydratase.

Threonine Catabolism

There are at least 3 pathways for threonine catabolism. One involves a pathway initiated by threonine dehydrogenase yielding a-amino-b-ketobutyrate. The a-amino-b-ketobutyrate is either converted to acetyl-CoA and glycine or spontaneously degrades to aminoacetone which is converted to pyruvate. The second pathway involves serine/threonine dehydratase yielding a-ketobutyrate which is further catabolized to propionyl-CoA and finally the TCA cycle intermediate, succinyl-CoA. The third pathway utilizes threonine aldolase. The products of this reaction are both ketogenic (acetyl-CoA) and glucogenic (pyruvate).

Glycine Catabolism

Glycine is classified as a glucogenic amino acid, since it can be converted to serine by serine hydroxymethyltransferase, and serine can be converted back to the glycolytic intermediate, 3-phosphoglycerate or to pyruvate by serine/threonine dehydratase. Nevertheless, the main glycine catabolic pathway leads to the production of CO2, ammonia, and one equivalent of N5,N10-methyleneTHF by the mitochondrial glycine cleavage complex.

Cysteine Catabolism

There are several pathways for cysteine catabolism. The simplest, but least important pathway is catalyzed by a liver desulfurase and produces hydrogen sulfide, (H2S) and pyruvate. The more important catabolic pathway is via a cytochrome-P450-coupled enzyme, cysteine dioxygenase that oxidizes the cysteine sulfhydryl to sulfinate, producing the intermediate cysteinesulfinate. Cysteinesulfinate can serve as a biosynthetic intermediate undergoing decarboxylation and oxidation to produce taurine. Catabolism of cysteinesulfinate proceeds through transamination to b-sulfinylpyruvate which is in undergoes desulfuration yielding bisulfite, (HSO3-) and the glucogenic product, pyruvate. The enzyme sulfite oxidase uses O2 and H2O to convert HSO3- to sulfate, (SO4-) and H2O2. The resultant sulfate is used as a precursor for the formation of 3'-phosphoadenosine-5'-phosphosulfate,PAPS.


PAPS is used for the transfer of sulfate to biological molecules such as the sugars of the glycosphingolipids.Other than protein, the most important product of cysteine metabolism is the bile salt precursor taurine, which is used to form the bile acid conjugates taurocholate and taurochenodeoxycholate.The enzyme cystathionase can also transfer the sulfur from one cysteine to another generating thiocysteine and pyruvate. Transamination of cysteine yields -mercaptopyruvate which then reacts with sulfite, (SO32-), to produce thiosulfate, (S2O32-) and pyruvate. Both thiocysteine and thiosulfate can be used by the enzyme rhodanese to incorporate sulfur into cyanide, (CN-), thereby detoxifying the cyanide to thiocyanate.

Methionine Catabolism

The principal fates of the essential amino acid methionine are incorporation into polypeptide chains, and use in the production of -ketobutyrate and cysteine via SAM as described above. The transulfuration reactions that produce cysteine from homocysteine and serine also produce -ketobutyrate, the latter being converted to succinyl-CoA. Regulation of the methionine metabolic pathway is based on the availability of methionine and cysteine. If both amino acids are present in adequate quantities, SAM accumulates and is a positive effector on cystathionine synthase, encouraging the production of cysteine and ketobutyrate (both of which are glucogenic). However, if methionine is scarce, SAM will form only in small quantities, thus limiting cystathionine synthase activity. Under these conditions accumulated homocysteine is remethylated to methionine, using N5-methylTHF and other compounds as methyl donors.

Valine, Leucine and Isoleucine Catabolism

This group of essential amino acids are identified as the branched-chain amino acids, BCAAs. Because this arrangement of carbon atoms cannot be made by humans, these amino acids are an essential element in the diet. The catabolism of all three compounds initiates in muscle and yields NADH and FADH2 which can be utilized for ATP generation. The catabolism of all three of these amino acids uses the same enzymes in the first two steps. The first step in each case is a transamination using a single BCAA aminotransferase, with -ketoglutarate as amine acceptor. As a result, three different -keto acids are produced and are oxidized using a common branched-chain -keto acid dehydrogenase, yielding the three different CoA derivatives. Subsequently the metabolic pathways diverge, producing many intermediates. The principal product from valine is propionylCoA, the glucogenic precursor of succinyl-CoA. Isoleucine catabolism terminates with production of acetylCoA and propionylCoA; thus isoleucine is both glucogenic and ketogenic. Leucine gives rise to acetylCoA and acetoacetylCoA, and is thus classified as strictly ketogenic. There are a number of genetic diseases associated with faulty catabolism of the BCAAs. The most common defect is in the branched-chain -keto acid dehydrogenase. Since there is only one dehydrogenase enzyme for all three amino acids, all three keto acids accumulate and are excreted in the urine. The disease is known as Maple syrup urine disease because of the characteristic odor of the urine in afflicted individuals. Mental retardation in these cases is extensive. Unfortunately, since these are essential amino acids, they cannot be heavily restricted in the diet; ultimately, the life of afflicted individuals is short and development is abnormal The main neurological problems are due to poor formation of myelin in the CNS.

Phenylalanine and Tyrosine Catabolism

Phenylalanine normally has only two fates: incorporation into polypeptide chains, and production of tyrosine via the tetrahydrobiopterin-requiring phenylalanine hydroxylase. Thus, phenylalanine catabolism always follows the pathway of tyrosine catabolism. The main pathway for tyrosine degradation involves conversion to fumarate and acetoacetate, allowing phenylalanine and tyrosine to be classified as both glucogenic and ketogenic. Tyrosine is equally important for protein biosynthesis as well as an intermediate in the biosynthesis of several physiologically important metabolites e.g. dopamine, norepinephrine and epinephrine (see Specialized Products of Amino Acids). As in phenylketonuria (deficiency of phenylalanine hydroxylase), deficiency of tyrosine transaminase leads to urinary excretion of tyrosine and the intermediates between phenylalanine and tyrosine. The adverse neurological symptoms are the same for the two diseases. Genetic diseases (such as various tyrosinemias and alkaptonuria) are also associated with other defective enzymes of the tyrosine catabolic pathway. The first genetic disease ever recognized, alcaptonuria, is caused by defective homogentisic acid oxidase. Homogentisic acid accumulation is relatively innocuous, causing urine to darken on exposure to air, but no life-threatening effects accompany the disease. The other genetic deficiencies lead to more severe symptoms, most of which are associated with abnormal neural development, mental retardation, and shortened life span.

Lysine Catabolism

Lysine catabolism is unusual in the way that the -amino group is transferred to -ketoglutarate and into the general nitrogen pool. The reaction is a transamination in which the -amino group is transferred to the -keto carbon of -ketoglutarate forming the metabolite, saccharopine. Unlike the majority of transamination reactions, this one does not employ pyridoxal phosphate as a cofactor. Saccharopine is immediately hydrolyzed by the enzyme -aminoadipic semialdehyde synthase in such a way that the amino nitrogen remains with the -carbon of -ketoglutarate, producing glutamate and -aminoadipic semialdehyde. Because this transamination reaction is not reversible, lysine is an essential amino acid. The ultimate end-product of lysine catabolism is acetoacetyl-CoA Genetic deficiencies in the enzyme -aminoadipic semialdehyde synthase have been observed in individuals who excrete large quantities of urinary lysine and some saccharopine. The lysinemia and associated lysinuria are benign. Other serious disorders associated with lysine metabolism are due to failure of the transport system for lysine and the other dibasic amino acids across the intestinal wall. Lysine is essential for protein synthesis; a deficiencies of its transport into the body can cause seriously diminished levels of protein synthesis. Probably more significant however, is the fact that arginine is transported on the same dibasic amino acid carrier, and resulting arginine deficiencies limit the quantity of ornithine available for the urea cycle. The result is severe hyperammonemia after a meal rich in protein. The addition of citrulline to the diet prevents the hyperammonemia. Lysine is also important as a precursor for the synthesis of carnitine, required for the transport of fatty acids into the mitochondria for oxidation. Free lysine does not serve as the precursor for this reaction, rather the modified lysine found in certain proteins. Some proteins modify lysine to trimethyllysine using SAM as the methyl donor to transfer methyl groups to the -amino of the lysine side chain. Hydrolysis of proteins containing trimethyllysine provide the substrate for the subsequent conversion to carnitine.

Histidine Catabolism

Histidine catabolism begins with release of the amino group catalyzed by histidase, introducing a double bond into the molecule. As a result, the deaminated product, urocanate, is not the usual -keto acid associated with loss of -amino nitrogens. The end product of histidine catabolism is glutamate, making histidine one of the glucogenic amino acids. Another key feature of histidine catabolism is that it serves as a source of ring nitrogen to combine with tetrahydrofolate (THF), producing the 1-carbon THF intermediate known as N5-formiminoTHF. The latter reaction is one of two routes to N5-formiminoTHF. The principal genetic deficiency associated with histidine metabolism is absence or deficiency of the first enzyme of the pathway, histidase. The resultant histidinemia is relatively benign. The disease, which is of relatively high incidence (1 in 10,000), is most easily detected by the absence of urocanate from skin and sweat, where it is normally found in relative abundance. Decarboxylation of histidine in the intestine by bacteria gives rise to histamine. Similarly, histamine arises in many tissues by the decarboxylation of histidine, which in excess causes constriction or dilation of various blood vessels. The general symptoms are those of asthma and various allergic reactions.

Tryptophan Catabolism

A number of important side reactions occur during the catabolism of tryptophan on the pathway to acetoacetate. The first enzyme of the catabolic pathway is an iron porphyrin oxygenase that opens the indole ring. The latter enzyme is highly inducible, its concentration rising almost 10-fold on a diet high in tryptophan. Kynurenine is the first key branch point intermediate in the pathway. Kynurenine undergoes deamniation in a standard transamination reaction yielding kynurenic acid. Kynurenic acid and metabolites have been shown to act as antiexcitotoxics and anticonvulsives. A second side branch reaction produces anthranilic acid plus alanine. Another equivalent of alanine is produced further along the main catabolic pathway, and it is the production of these alanine residues that allows tryptophan to be classified among the glucogenic and ketogenic amino acids. The second important branch point converts kynurenine into 2-amino-3-carboxymuconic semialdehyde, which has two fates. The main flow of carbon elements from this intermediate is to glutarate. An important side reaction in liver is a transamination and several rearrangements to produce limited amounts of nicotinic acid, which leads to production of a small amount of NAD+ and NADP+ Aside form its role as an amino acid in protein biosynthesis, tryptophan also serves as a precursor for the synthesis of serotonin and melatonin. These products are discussed in Specialized Products of Amino Acids