Why urea cycle is important

Hydroxylation of phenylalanine by aromatic amino acid hydroxylase phenylalanine hydroxylase yields tyrosine. Because tyrosine is made from phenylalanine and the latter is an essential amino acid in humans, it is not clear whether to classify tyrosine as essential or non-essential.

Some define it as a conditionally essential amino acid. Others simply categorize it as non-essential. As noted above, tyrosine can arise as a result of hydroxylation of phenylalanine. In addition, plants can synthesize tyrosine by oxidation of prephenate followed by transamination of the resulting 4-hydroxyphenylpyruvate Figure 6.

The hydroxyl group on tyrosine is a target for phosphorylation by protein kinase enzymes involved in signal transduction pathways Figure 6.

In photosystem II of chloroplasts, tyrosine, at the heart of the system, acts as an electron donor to reduce oxidized chlorophyll. The hydrogen from the hydroxyl group of tyrosine is lost in the process, requiring re-reduction by four core manganese clusters. Tyrosine is also important in the small subunit of class I ribonucleotide reductases where it forms a stable radical in the catalytic action of the enzyme see HERE.

Tyrosine is a precursor of catecholamines, such as L-dopa, dopamine, norepinephrine, and epinephrine Figure 6. The thyroid hormones triiodothyronine T3 and thyroxine T4 are also synthesized from tyrosine. As shown in Figure 6. Combinations of iodinated tyrosines give rise to thyroxine and triiodothyronine. These are subsequently cleaved from the protein and released into the bloodstream.

Oxidation and polymerization of tyrosine is involved in synthesis of the family of melanin pigments. Tyrosine is involved in the synthesis of at least two types - eumelanin and pheomelanin Figure 6. Another molecule derived from tyrosine is the benzoquinone portion of Coenzyme Q CoQ.

This pathway requires the enzyme HMG-CoA Reductase and since this enzyme is inhibited by cholesterol-lowering statin drugs, CoQ can be limited in people being treated for high cholesterol levels. Dopamine plays several important roles in the brain and body. A member of the catecholamine and phenethylamine families, its name comes from the fact that it is an amine made by removing a carboxyl group from L-DOPA.

Dopamine is synthesized in the brain and kidneys. It is also made in plants, though its function in plants is not clear. Conversion of dopamine to norepinephrine Figure 6. Dopamine is a neurotransmitter, being released by one nerve cell and then traveling across a synapse to signal an adjacent nerve cell.

Rewards, such as food or social interaction, increase dopamine levels in the brain, as do addictive drugs. Other brain dopamine pathways are involved in motor control and in managing the release of various hormones. Outside the nervous system, dopamine is a local chemical messenger. In blood vessels, it inhibits norepinephrine release and causes vasodilation.

In the kidneys, it increases sodium excretion and urine output. It reduces gastrointestinal motility and protects intestinal mucosa in the digestive system and in the immune system, it reduces lymphocyte activity. The effect dopamine has on the pancreas is to reduce insulin production. With the exception of the blood vessels, dopamine is synthesized locally and exerts its effects near the cells that release it.

Epinephrine also called adrenalin is a catecholamine chemically related to norepinephrine that is a hormone with medical applications. It is used to treat anaphylaxis, cardiac arrest, croup, and, in some cases, asthma, when other treatments are not working, due to its ability to favor bronchodilation. Epinephrine is the drug of choice for treating anaphylaxis. In the body, it is produced and released by adrenal glands and some neurons. Physiological effects of epinephrine may include rapid heart beat, increased blood pressure, heart output, pupil dilation, blood sugar concentration and increased sweating.

Other physical effects may include shakiness, increased anxiety, and an abnormal heart rhythm. Norepinephrine also called noradrenalin is a catecholamine molecule that acts as a hormone and neurotransmitter. It is chemically similar to epinephrine, differing only in the absence of a methyl group on its amine. Norepinephrine is made and released by the central nervous system locus coeruleus of the brain and the sympathetic nervous system. Norepinephrine is at its lowest levels during sleep and at its highest levels during stress fight or flight response.

The primary function of norepinephrine is to prepare the body for action. It increases alertness, enhances memory functions, and helps to focus attention.

Norepinephrine increases heart rate and blood pressure, increases blood glucose and blood flow to skeletal muscle and decreases flow of blood to the gastrointestinal system. Norepinephrine may be injected to overcome critically low blood pressure and drugs countering its effects are used to treat heart conditions. The family of amino acids derived from pyruvate has four members, each with a simple aliphatic side chain no longer than four carbons.

The simplest of these is alanine. Alanine is the amino acid that is most easily produced from pyruvate. The simple transamination catalyzed by alanine transaminase produces alanine from pyruvate. Alternative pathways for synthesis of alanine include catabolism of valine, leucine, and isoleucine. The glucose-alanine cycle is an important nitrogen cycle related to the Cori cycle that occurs between muscle and liver cells in the body see HERE.

In it, breakdown of glucose in muscles leads to pyruvate. When nitrogen levels are high, pyruvate is transaminated to alanine, which is exported to hepatocytes. In the liver cells, the last transamination of the glucose-alanine cycle occurs. Glucose can then be made by gluconeogenesis from pyruvate. This pathway may be particularly important in the brain. Another way of removing excess ammonium from a tissue is by attaching it to glutamate to make glutamine. Glutamate is a neurotransmitter, so having an alternative way of removing amines glucose-alanine cycle is important, especially in the brain.

Like valine and isoleucine, leucine is an essential amino acid in humans. In adipose tissue and muscle, leucine is used in sterol synthesis. It is the only amino acid to stimulate muscle protein synthesis, and as a dietary supplement in aged rats, it slows muscle degradation. Leucine is an activator of mTOR, a protein which, when inhibited, has been shown to increase life span in Saccharomyces cerevisiae, C.

Metabolism of leucine, valine, and isoleucine also called Branched Chain Amino Acids - BCAAs starts with decarboxylation of pyruvate and attachment of the two-carbon hydroxyethyl fragment to thiamine pyrophosphate Figure 6. This molecule is a branch point for synthesis of leucine and valine. Transamination of it catalyzed by leucine aminotransferase and using glutamate gives the final product of leucine top of next column. An essential amino acid in humans, valine is derived in plants from pyruvate and shares part of its metabolic synthesis pathway with leucine and a small slice of it with isoleucine.

Metabolism of all three amino acids starts with decarboxylation of pyruvate and attachment of the two-carbon hydroxyethyl fragment to thiamine pyrophosphate Figure 6. The reaction is catalyzed by acetolactate synthase. Shown on next page. Interestingly, several of the enzymes of valine metabolism catalyze reactions in the isoleucine pathway.

Though the substrates are slightly different, they are enough like the valine intermediates that they are recognized as substrates. Isoleucine has a second asymmetric center within it, but only one isomeric form of the four possible ones from the two centers is found biologically. Regulation of synthesis of the branched chain amino acids BCAAs - valine, leucine, and isoleucine is complex. The enzyme catalyzing its synthesis is threonine deaminase Figure 6.

The enzyme is inhibited by its own product isoleucine and activated by valine, a product of a parallel pathway. Thus, when valine concentration is high, the balances shifts in favor of production of isoleucine and since isoleucine competes with valine and leucine for hydroxyethyl-TPP, synthesis of these two amino acids goes down. When isoleucine concentration increases, threonine deaminase is inhibited, shifting the balance back to production of valine and leucine.

Another control mechanism for regulation of leucine synthesis occurs in bacteria and is known as attenuation. In this method, accumulation of leucine speeds the process of translation of a portion of the mRNA copy of the leucine operon coding sequences for enzymes necessary to make leucine.

This, in turn, causes transcription of the genes of the leucine operon to terminate prematurely, thus stopping production of the enzymes necessary to make leucine. When leucine levels fall, translation slows, preventing transcription from terminating prematurely and allowing leucine metabolic enzymes to be made. Thus, leucine levels in the cell control the synthesis of enzymes necessary to make it.

Synthesis of histidine literally occurs in a class by itself - there are no other amino acids in its synthesis family.

The amino acid is made in plants Arabidopsis, in this case by a pathway that begins with ribosephosphate. The overall pathway is show in the green text boxes on the next two pages. Abbreviations used in the boxes are shown below.

Histidine is a feedback inhibitor of ATP-phosphoribosyltransferase and thus helps to regulate its own synthesis. Histidine is the only amino acid to contain an imidazole ring.

It is ionizable and has a pKa of about 6. A cysteine analog commonly referred to as the 21st amino acid, selenocysteine Figure 6. Although it is rare, selenocysteine has been found in proteins in bacteria, archaea and eukaryotes. In contrast to amino acids such as phosphoserine, hydroxyproline, or acetyl-lysine, which arise as a result of post-translational modifications, selenocysteine is actually built into growing peptide chains in ribosomes during the process of translation.

This alternative reading of the UGA is dependent on formation of a special hairpin loop structure in the mRNA encoding selenoproteins. Selenium is rather toxic, so cellular and dietary concentrations are typically exceedingly low. About 25 human proteins are known to contain the amino acid. These include five glutathione peroxidases, and three thioredoxin reductases.

Iodothyronine deiodinase, a key enzyme that converts thyroxine to the active T3 form, also contains selenocysteine in its active site. All of these proteins contain a single selenocysteine.

Besides selenocysteine, at least two other biological forms of a seleno-amino acid are known. These include 1 selenomethionine Figure 6. The specifics of the process of translation will be described elsewhere in the book, but to get selenocysteine into a protein, the tRNA carrying selenocysteine pairs with a stop codon UGA in the mRNA in the ribosome.

Thus, instead of stopping translation, selenocysteine can incorporated into a growing protein and translation continues instead of stopping. Four genes are involved in preparation of selenocysteine for incorporation into proteins. They are known as sel A, sel B, sel C, and sel D. Sel C codes for the special tRNA that carries selenocysteine. The amino acid initially put onto the selenocysteine tRNA is not selenocysteine, but rather serine.

Action of sel A and sel D are necessary to convert the serine to a selenocysteine. An intermediate in the process is selenophosphate, which is the selenium donor. It is derived from H2Se, the form in which selenium is found in the cell. The tRNA carrying selenocysteine has a slightly different structure than other tRNAs, so it requires assistance in translation. The sel B gene encodes for an EF-Tu-like protein that helps incorporate the selenocysteine into the protein during translation.

Using UGA codons to incorporate selenocysteine into proteins could wreak havoc if done routinely, as UGA, in fact, almost always functions as a stop codon and is only rarely used to code for selenocysteine. Fortunately, there is a mechanism to ensure that the reading of a UGA codon as selenocysteine occurs only when the mRNA encodes a selenoprotein.

Like selenocysteine, pyrrolysine is a rare, unusual, genetically encoded amino acid found in some cells. Proteins containing it are enzymes involved in methane metabolism and so far have been found only methanogenic archaeans and one species of bacterium.

The amino acid is found in the active site of the enzymes containing it. It is sometimes referred to as the 22nd amino acid. Synthesis of the amino acid biologically begins with two lysines. One is converted to 3R Methyl-D-ornithine, which is attached to the second lysine. After elimination of an amine group, cyclization, and dehydration, L-pyrrolysine is produced.

This unusual tRNA can pair with the UAG stop codon during translation and allow for incorporation of pyrrolysine into the growing polypeptide chain during translation in a manner similar to incorporation of selenocysteine. The urea cycle holds the distinction of being the first metabolic cycle discovered - in , five years before the citric acid cycle. It is an important metabolic pathway for balancing nitrogen in the bodies of animals and it takes place primarily in the liver and kidney.

Organisms, like humans, that excrete urea are called ureotelic. Those that excrete uric acid birds, for example are called uricotelic and those that excrete ammonia fish are ammonotelic. Ammonia, of course, is generated by metabolism of amines and is toxic, so managing levels of it is critical for any organism. Excretion of ammonia by fish is one reason that an aquarium periodically requires cleaning and replacement of water.

Liver failure can lead to accumulation of nitrogenous waste and exacerbates the problem. As shown in Figure 1. Of the five reactions, three occur in the cytoplasm and two take place in the mitochondrion. The reaction making carbamoyl phosphate, catalyzed by carbamoyl phosphate synthetase is not shown in the figure.

As discussed elsewhere in this book, ornithine intersects the metabolic pathways of arginine and proline. Ornithine is found in the cytoplasm and is transported into the mitochondrion by the ornithine-citrulline antiport of the inner mitochonrial membrane. In the matrix of the mitochondrion, two reactions occur relevant to the cycle.

The first is formation of carbamoyl phosphate from bicarbonate, ammonia, and ATP catalyzed by carbamoyl phosphate synthetase I. Carbamoyl phosphate then combines with ornithine in a reaction catalyzed by ornithine transcarbamoylase to make citrulline.

The citrulline is transported out to the cytoplasm by the ornithine-citrulline antiport mentioned above. In the cytoplasm, citrulline combines with L-aspartate using energy of ATP to make citrullyl-AMP an intermediate followed by argininosuccinate.

The reaction is catalyzed by argininosuccinate synthase. Urea is less toxic than ammonia and is released in the urine. Some organisms make uric acid for the same reason.

It is worth noting that aspartic acid, ammonia, and bicarbonate enter the cycle and fumarate and urea are produced by it. Points to take away include 1 ammonia is converted to urea using bicarbonate and the amine from aspartate; 2 aspartate is converted to fumarate which releases more energy than if aspartate were converted to oxaloacetate, since conversion of fumarate to malate to oxaloacetate in the citric acid cycle generates an NADH, but direct conversion of aspartate to oxaloacetate does not; and 3 glutamate and aspartate are acting as shuttles to funnel ammonia into the cycle.

Glutamate, as will be seen below, is a scavenger of ammonia. The urea cycle is controlled both allosterically and by substrate concentration. The cycle requires N-acetylglutamate NAG for allosteric activation of carbamoyl phosphate synthetase I. Thus, an indicator of high amine levels, arginine, and an important shuttler of amine groups, glutamate, stimulates the enzyme that activates the cycle. At the substrate level, all of the other enzymes of the urea cycle are controlled by the concentrations of substrates they act upon.

Only at high concentrations are the enzymes fully utilized. Complete deficiency of any urea cycle enzyme is fatal at birth, but mutations resulting in reduced expression of enzymes can have mixed effects. Since the enzymes are usually not limiting for these reactions, increasing substrate can often overcome reduced enzyme amounts to a point by simply fully activating enzymes present in reduced quantities.

However, if the deficiencies are sufficient, ammonium can accumulate and this can be quite problematic, especially in the brain, where mental deficiencies or lethargy can result. Reduction of ammonium concentration relies on the glutamate dehydrogenase reaction named for the reverse reaction. From an energy perspective, the urea cycle can be said to break even or generate a small amount of energy, if one includes the energy produced in releasing ammonia from glutamate one NADH.

There are two NADHs produced including the one for converting fumarate to oxaloacetate , which give ATPs, depending on how efficiently the cell performs electron transport and oxidative phosphorylation. Thus, the cycle either breaks even in the worst case or generates 2 ATPs in the best case. Amino acids are divided according to the pathways involved in their degradation. There are three general categories. Ones that yield intermediates in the glycolysis pathway are called glucogenic and those that yield intermediates of acetyl-CoA or acetoacetate are called ketogenic.

Those that involve both are called glucogenic and ketogenic. These are shown in Figures 6. Some amino acids, like tryptophan, phenylalanine, and tyrosine yield hormones or neurotransmitters on further metabolism as noted earlier.

Others like cysteine and methionine must dispose of their sulfur and all of the amino acids must rid themselves of nitrogen, which can happen via the urea cycle, transamination, or both. Breakdown of tyrosine Figure 6. Enzymes involved include 1 tyrosine transaminase; 2 p-hydroxylphenylpyruvate dioxygenase; 3 homogentisate dioxygenase; 4 maleylacetoacetate cis-trans-isomerase; and 5 4-fumaryl acetoacetate hydrolase.

Breakdown of leucine is a multi-step process ultimately yielding the ketone body acetoacetate and acetyl-CoA. Breakdown of isoleucine yields intermediates that are both ketogenic and glucogenic. These include acetyl-CoA and propionyl-CoA. Transamination Before beginning discussion of the pathways, it is worthwhile to discuss a reaction common to the metabolism of most of the amino acids and other nitrogen-containing compounds and that is transamination.

A specific reaction of this type is shown in Figure 6. Synthesis varies It is also important to recognize that organisms differ considerably in the amino acids that they can synthesize. Glutamine Synthesis of glutamine proceeds from glutamate via catalysis of the enzyme glutamine synthetase, one of the most important regulatory enzymes in all of amino acid metabolism Figure 6. Proline Synthesis of proline starts with several reactions acting on glutamate.

This, in turn, is reduced to form proline by pyrrolinecarboxylate reductase. Arginine Arginine is a molecule synthesized in the urea cycle and, thus, all urea cycle molecules can be considered as precursors. It catalyzes an unusual five electron reduction reaction that proceeds in the following manner Yet another way to synthesize arginine biologically is by reversal of the arginase reaction of the urea cycle Arginine can also be made starting with glutamate. Serine family Serine is a non-essential amino acid synthesized from several sources.

Covalent modification target Serine in proteins can be the target of glycosylation or phosphorylation. Vertebrates can also synthesize glycine in their livers using the enzyme glycine synthase. Cysteine Cysteine can be synthesized from several sources.

Another route to making cysteine is a two-step process that begins with serine, catalyzed first by serine-O-acetyltransferase and then by cysteine synthase Cysteine can be also released from cystine by cystine reductase Finally, cysteine can be made from cysteic acid by action of cysteine lyase. Aspartate family Metabolism of aspartic acid is similar to that of glutamate. Aspartate can also be generated from asparagine by the enzyme asparaginase.

Further, aspartate can be produced by reversal of a reaction in the urea cycle see HERE Aspartate is also a precursor to four amino acids that are essential in humans. Asparagine Asparagine, too, is an amino acid produced in a simple transamination reaction. Methionine Metabolism of methionine overlaps with metabolism of the other sulfur-containing amino acid, cysteine.

Threonine Though threonine is chemically similar to serine, the metabolic pathway leading to threonine does not overlap with that of serine. Enzymes in Figure 6. Lysine To get from aspartate to lysine, nine reactions and two non-enzymatic steps are involved, as seen in Figure 6. Aromatic amino acids The aromatic amino acids, tryptophan, phenylalanine, and tyrosine can all be made starting with two simple molecules - PEP and erythrosephosphate Figure 6.

Tryptophan synthesis The proteogenic amino acid with the largest R-group, tryptophan is an essential amino acid distinguished structurally by its indole group. Regulation Regulation of tryptophan synthesis in bacteria occurs partly via a process called attenuation that operates through the trp operon. Melatonin Melatonin is a compound made from tryptophan that is found in a wide spectrum of biological systems, including plants, animals, fungi, and bacteria.

The remaining enzymes of the urea cycle are controlled by the concentrations of their substrates. Thus, inherited deficiencies in cycle enzymes other than ARG1 do not result in significant decreases in urea production if any cycle enzyme is entirely missing, death occurs shortly after birth.

Rather, the deficient enzyme's substrate builds up, increasing the rate of the deficient reaction to normal. The main purpose of the urea cycle is to eliminate toxic ammonia from the body. About 10 to 20 g of ammonia is removed from the body of a healthy adult every day.

A dysfunctional urea cycle would mean excess amount of ammonia in the body, which can lead to hyperammonemia and related diseases. The deficiency of one or more of the key enzymes catalyzing various reactions in the urea cycle can cause disorders related to the cycle. Defects in the urea cycle can cause vomiting, coma and convulsions in newborn babies.

This is often misdiagnosed as septicemia and treated with antibiotics in vain. Even 1mm of excess ammonia can cause severe and irreversible damages.

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