General pathways of amino acids transformation



Deamination of amino acids, it kinds. The role of vitamins in deamination of amino acids.

Removal of an amino group from a molecule.

the elimination of an amino group (NH2) from organic compounds. Deamination is accompanied by the substitution of some other group, such as H, OH, OR, or Hal, for the amino group or by the formation of a double bond. In particular, deamination is brought about by the action of nitrous acid on primary amines. In this reaction, acyclic amines yield alcohols (I) and olefins (II), for example:


The deamination of alicyclic amines is accompanied by ring expansion or contraction. In the presence of strong inorganic acids, aromatic amines and nitrous acid yield diazonium salts. Such reactions as hydrolysis, hydrogenolysis, decomposition of quaternary ammonium salts, and pyrolytic reactions also result in deamination.

Deamination plays an important part in the life processes of animals, plants, and microorganisms. Oxidative deamination, with the formation of ammonia and α-keto acids, is characteristic of d-amino acids. Amines also undergo oxidative deamination. Except for glutamate dehydrogenase, which deaminates L-glutamic acid, oxidases of natural amino acids are not very active in animal tissues. Therefore, most L-amino acids undergo indirect deamination by means of prior transamination, with the formation of glutamic acid, which then undergoes oxidative deamination or other transformations. Other types of deamination are reductive, hydrolytic (deamination of amino derivatives of purines, pyrimidines, and sugars), and intramolecular (histidine deamination), which occur mainly in microorganisms.


Oxidative Deamination Reaction


Deamination is also an oxidative reaction that occurs under aerobic conditions in all tissues but especially the liver. Duringoxidative deamination, an amino acid is converted into the corresponding keto acid by the removal of the amine functional group as ammonia and the amine functional group is replaced by the ketone group. The ammonia eventually goes into the urea cycle.

Oxidative deamination occurs primarily on glutamic acid because glutamic acid was the end product of many transamination reactions.

The glutamate dehydrogenase is allosterically controlled by ATP and ADP. ATP acts as an inhibitor whereas ADP is an activator.

 Central Role for Glutamic Acid:

Apparently most amino acids may be deaminated but this is a significant reaction only for glutamic acid. If this is true, then how are the other amino acids deaminated? The answer is that a combination of transamination and deamination of glutamic acid occurs which is a recycling type of reaction for glutamic acid. The original amino acid loses its amine group in the process. The general reaction sequence is shown on the left.


Deamination of adenine results in the formation of hypoxanthine. Hypoxanthine, in a manner analogous to the imine tautomer of adenine, selectively base pairs with cytosine instead of thymine. This results in a post-replicative transition mutation, where the original A-T base pair transforms into a G-C base pair.

Transamination of amino acids, mechanism, role of enzymes and coenzymes.

In the degradation of most standard amino acids, an early step in degradation consists in transamination, which is the transfer of the α-amino group from the amino acid to an α-keto acid. There are several different aminotransferases, each of which is specific for an individual amino acid or for a group of chemically similar ones, such as the branched amino acids leucine, isoleucine, and valine. The α-keto acid that accepts the amino group is always α-ketoglutarate (Figure). Transamination is freely reversible; therefore, both glutamate and α-ketoglutarate are substrates of every single transaminase. If amino groups are to be transferred between two amino acids other than glutamate, this will still occur by transient formation of glutamate (Figure).

Transamination reactions. a: Glutamate pyruvate transaminase (also called alanine amino transferase) transfers the α-amino group from alanine to α-ketoglutarate, which yields glutamate and pyruvate. b: All transaminases have α-ketoglutarate as one of their substrates. Transfer of amino groups between arbitrary amino and α-keto acids (here: alanine and oxaloacetate) occurs by transient transfer to α-ketoglutarate.


The mechanism of transamination is depicted in Figure  for alanine, yet is the same with all transaminases. The reaction occurs in two stages:

1.             Transfer of the amino group from alanine to the enzyme, which releases pyruvate, and

2.             Transfer of the amino group from the enzyme to α-ketoglutarate, which releases glutamate.

In Figure, only the first half-reaction is shown, since the second half-reaction is the exact reversal of the first one; this also implies that the entire reaction is reversible. Overall, the mechanism consists in the first substrate arriving and leaving before the second substrate enters and leaves; this is dubbed a Ping Pong Bi Bi reaction (Figure).1 While two different substrates must be used for the the reaction to have a net effect, it is of course possible for amino acid 1 and amino acid 2 to be identical—the reaction will work just fine but achieve no net turnover.

The reaction mechanism revolves around the coenzyme pyridoxal phosphate (PLP):

1.             At the outset of the reaction, PLP is bound as a Schiff base to the ε-amino group of a lysine residue in the active site (Figure).

2.             The bond between PLP and the enzyme is separated, and PLP forms a Schiff base with the amino acid substrate instead (Figure, steps 1 and 2).

3.             The liberated lysine residue abstracts the α hydrogen as a proton (step 3), and the electron left behind travels all the way down the PLP ring. PLP is often said to act as an 'electron sink'. This has the effect of turning the bond between the α carbon and the α nitrogen into a Schiff base.

4.             The Schiff base is hydrolyzed to yield the α-keto acid and the amino derivative of the PLP (called pyridoxamine phosphate; steps 4 and 5).

The PLP in its various forms stays within the the active site throughout, even when not bound to the enzyme covalently. As stated above, the second half reaction is the exact reversal of the first, and you might want to draw the individual steps for yourself.


Decarboxylisation of amino acids, role of enzymes and co-enzymes.


 Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. The reverse process, which is the first chemical step in photosynthesis, is called carboxylation, the addition of CO2 to a compound. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases.

The term "decarboxylation" literally means removal of the COOH (carboxyl group) and its replacement with a proton. The term simply relates the state of the reactant and product. Decarboxylation is one of the oldest organic reactions, since it often entails simple pyrolysis, and volatile products distill from the reactor. Heating is required because the reaction is less favorable at low temperatures. Yields are highly sensitive to conditions. In retrosynthesis, decarboxylation reactions can be considered the opposite of homologation reactions, in that the chain length becomes one carbon shorter. Metals, especially copper compounds, are usually required. Such reactions proceed via the intermediacy of metal carboxylate complexes.

Decarboxylation of aryl carboxylates can generate the equivalent of the corresponding aryl anion, which in turn can undergocross coupling reactions


Alkylcarboxylic acids and their salts do not always undergo decarboxylation readily. Exceptions are the decarboxylation of beta-keto acids, α-unsaturated acids, and α-phenyl, α-nitro, and α-cyanoacids. Such reactions are accelerated due to the formation of a zwitterionic tautomer in which the carbonyl is protonated and the carboxyl group is deprotonated. Typically fatty acids do not decarboxylate readily. Reactivity of an acid towards decarboxylation depends upon stability of carbanion intermediate formed in above mechanism. Many reactions have been named after early workers in organic chemistry. The Barton decarboxylation, Kolbe electrolysis, Kochi reaction and Hunsdiecker reaction are radical reactions. The Krapcho decarboxylation is a related decarboxylation of an ester. In ketonic decarboxylation a carboxylic acid is converted to a ketone.

PROTEIN CATABOLISM – hydrolysis breaks peptide bonds yielding amino acids


PROTEIN CATABOLISM – attaches 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





























































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 a-ketoglutarate (a-KG), which participate in reactions with many different aminotransferases. Serum aminotransferases such as serum glutamate-oxaloacetate-aminotransferase (SGOT) (also calledaspartate 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. Alaninetransaminase 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 a-KG and regenerates pyruvate. The pyruvate can then be diverted intogluconeogenesis. 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 glutamatedehydrogenase is important in converting free ammonia and a-ketoglutarate (a-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 positiveallosteric 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 a-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 enzymeglutaminase (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 theneurotoxic 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 ofHartnup 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.

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,oneor 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 formethionine 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 a-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

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 cytosolicpathways 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 areenzymically 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 a-amino group from a donor a-amino acid to the keto carbon of an acceptor a-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 a-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 arginineto 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 spontaneouslycyclizes 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 a-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 enzymeasparagine 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 theasparagine 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 aminoacids.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.

Oddsei - What are the odds of anything.