Editing Urea cycle

{{short description|Set of biochemical reactions}}
The '''urea cycle''' (also known as the '''[[ornithine]] cycle''') is a cycle of [[Biochemistry|biochemical]] reactions that produces [[urea]] (NH<sub>2</sub>)<sub>2</sub>CO from [[ammonia]] (NH<sub>3</sub>). Animals that use this cycle, mainly amphibians and mammals, are called [[ureotelic]].

The urea cycle converts highly toxic ammonia to urea for excretion.<ref name=":0">{{Cite book|title=Lehninger Principles of Biochemistry|last=Cox |first=Michael|date=2013-01-01|publisher=Freeman|isbn=9781429234146|oclc=901647690}}</ref> This cycle was the first metabolic cycle to be discovered by [[Hans Adolf Krebs|Hans Krebs]] and [[Kurt Henseleit]] in 1932,<ref name="Krebs1932a">{{cite journal|last1=Krebs|first1=Hans Adolf|author-link1=Hans Krebs (biochemist)|last2=Henseleit|first2=Kurt|author-link2=Kurt Henseleit|title=Untersuchungen über die Harnstoffbildung im Tierkörper|journal=Klinische Wochenschrift|volume=11|number=18|pages=757–759|doi=10.1007/bf01757657|year=1932}}</ref><ref name="Krebs1932b">{{cite journal|last1=Krebs|first1=Hans Adolf|author-link1=Hans Krebs (biochemist)|last2=Henseleit|first2=Kurt|author-link2=Kurt Henseleit|title=Untersuchungen über die Harnstoffbildung im Tierkörper. II|journal=Klinische Wochenschrift|volume=11|number=27|pages=1137–1139|doi=10.1007/BF01758220|year=1932}}</ref><ref name="Krebs1932c">{{cite journal|last1=Krebs|first1=Hans Adolf|author-link1=Hans Krebs (biochemist)|last2=Henseleit|first2=Kurt|author-link2=Kurt Henseleit|title=Untersuchungen über die Harnstoffbildung im Tierkörper|journal=Hoppe-Seyler's Zeitschrift für physiologische Chemie|volume=210|number=1–2|pages=33–66|doi=10.1515/bchm2.1932.210.1-2.33|year=1932}}</ref> five years before the discovery of the [[TCA cycle]]. The urea cycle was described in more detail later on by Ratner and Cohen. The urea cycle takes place primarily in the [[liver]] and, to a lesser extent, in the [[kidney]]s.

==Function==
[[Amino acid catabolism]] results in waste ammonia. All animals need a way to excrete this product. Most [[Aquatic animal|aquatic organisms]], or [[Metabolic waste|ammonotelic]] organisms, excrete ammonia without converting it.<ref name=":0" /> Organisms that cannot easily and safely remove nitrogen as ammonia convert it to a less toxic substance, such as [[urea]], via the urea cycle, which occurs mainly in the liver. Urea produced by the liver is then released into the [[Circulatory system|bloodstream]], where it travels to the [[kidney]]s and is ultimately excreted in [[urine]]. The urea cycle is essential to these organisms, because if the nitrogen or ammonia is not eliminated from the organism it can be very detrimental.<ref name=":122" /> In species including [[bird]]s and most [[insect]]s, the ammonia is converted into [[uric acid]] or its [[Uric acid|urate]] salt, which is excreted in [[Salt|solid form]]. Further, the urea cycle consumes acidic waste carbon dioxide by combining it with the basic ammonia, helping to maintain a neutral pH.

==Reactions==
The entire process converts two amino groups, one from {{chem|NH|4|+}} and one from [[Aspartic acid|aspartate]], and a carbon atom from {{chem|HCO|3|-}}, to the relatively nontoxic excretion product [[urea]].<ref name=":2">{{Citation|last1=Mew|first1=Nicholas Ah|title=Chapter 57 - Urea Cycle Disorders|date=2015-01-01|url=http://www.sciencedirect.com/science/article/pii/B9780124105294000577|work=Rosenberg's Molecular and Genetic Basis of Neurological and Psychiatric Disease (Fifth Edition)|pages=633–647|editor-last=Rosenberg|editor-first=Roger N.|place=Boston|publisher=Academic Press|language=en|doi=10.1016/b978-0-12-410529-4.00057-7|isbn=978-0-12-410529-4|access-date=2020-11-10|last2=Pappa|first2=Maria Belen|last3=Gropman|first3=Andrea L.|editor2-last=Pascual|editor2-first=Juan M.|url-access=subscription}}</ref> This occurs at the cost of four "high-energy" [[phosphate]] bonds (3 ATP hydrolyzed to 2 [[Adenosine diphosphate|ADP]] and one [[Adenosine monophosphate|AMP]]). The conversion from ammonia to urea happens in five main steps. The first is needed for ammonia to enter the cycle and the following four are all a part of the cycle itself. To enter the cycle, ammonia is converted to [[carbamoyl phosphate]]. The urea cycle consists of four enzymatic reactions: one [[mitochondria]]l and three [[cytosol]]ic.<ref name=":0" /><ref name=":3">{{Citation|last=Walker|first=Valerie|title=Chapter Three - Ammonia Metabolism and Hyperammonemic Disorders|date=2014-01-01|url=http://www.sciencedirect.com/science/article/pii/S0065242314000031|journal=Advances in Clinical Chemistry|volume=67|pages=73–150|editor-last=Makowski|editor-first=Gregory S.|publisher=Elsevier|language=en|doi=10.1016/bs.acc.2014.09.002|pmid=25735860|access-date=2020-11-10|url-access=subscription}}</ref> This uses 6 enzymes.<ref name=":2" /><ref name=":3" /><ref name=":4">{{Citation |last=Pearl |first=Phillip L. |title=76 - Inherited Metabolic Epilepsies |date=2017-01-01 |work=Swaiman's Pediatric Neurology (Sixth Edition) |pages=594–599 |editor-last=Swaiman |editor-first=Kenneth F. |url=http://www.sciencedirect.com/science/article/pii/B978032337101800076X |access-date=2020-11-10 |publisher=Elsevier |language=en |doi=10.1016/b978-0-323-37101-8.00076-x |isbn=978-0-323-37101-8 |editor2-last=Ashwal |editor2-first=Stephen |editor3-last=Ferriero |editor3-first=Donna M. |editor4-last=Schor |editor4-first=Nina F. |editor3-link=Donna Ferriero|url-access=subscription }}</ref>

{| class="wikitable"
 |+ Reactions of the urea cycle
 ! Step || Reactants || Products || Catalyzed by || Location
 |-
 ! 1
 | NH<sub>3</sub> + {{chem|HCO|3|-}} + 2[[Adenosine triphosphate|ATP]] || [[carbamoyl phosphate]] + 2[[Adenosine diphosphate|ADP]] + [[Phosphate#Biochemistry of phosphates|P<sub>i</sub>]]  || [[Carbamoyl phosphate synthetase I|CPS1]] || mitochondria
 |-
 ! 2
 | [[carbamoyl phosphate]] + [[ornithine]] || [[citrulline]] + P<sub>i</sub>  || [[ornithine transcarbamylase|OTC]], zinc, biotin || mitochondria
 |-
 ! 3
 | [[citrulline]] + [[Aspartic acid|aspartate]] + [[Adenosine triphosphate|ATP]] || [[Arginosuccinic acid|argininosuccinate]] + [[Adenosine monophosphate|AMP]] + [[pyrophosphate|PP<sub>i</sub>]]  || [[Argininosuccinate synthetase|ASS]] ||  cytosol
 |-
 ! 4
 | [[Arginosuccinic acid|argininosuccinate]] || [[arginine]] + [[fumarate]]  || [[Argininosuccinate lyase|ASL]] || cytosol
 |-
 ! 5
 | [[arginine]] + H<sub>2</sub>O || [[ornithine]] + [[urea]]  || [[Arginase 1|ARG1]], manganese|| cytosol
|}

<blockquote>
::'''The reactions of the urea cycle'''
[[File:Urea cycle.svg|class=skin-invert-image|thumb|480px|left]]

1 <small>L</small>-[[ornithine]]<br>2 [[carbamoyl phosphate]]<br>3 <small>L</small>-[[citrulline]]<br>4 [[argininosuccinate]]<br>5 [[fumarate]]<br>6 <small>L</small>-[[arginine]]<br>7 [[urea]]<br> <small>L</small>-Asp <small>L</small>-[[aspartate]]<br>CPS-1 [[carbamoyl phosphate synthetase I]]<br>OTC [[Ornithine transcarbamoylase]]<br>ASS [[argininosuccinate synthetase]]<br>ASL [[argininosuccinate lyase]]<br>ARG1 [[Arginase|arginase 1]]
</blockquote>
{{clear}}

=== First reaction: entering the urea cycle ===
Before the urea cycle begins ammonia is converted to carbamoyl phosphate. The reaction is catalyzed by [[carbamoyl phosphate synthetase I]] and requires the use of two [[Adenosine triphosphate|ATP]] molecules.<ref name=":0" /> The carbamoyl phosphate then enters the urea cycle.

=== Steps of the urea cycle ===
# Carbamoyl phosphate is converted to [[citrulline]]. With catalysis by [[ornithine transcarbamylase]], the carbamoyl phosphate group is donated to ornithine and releases a phosphate group.<ref name=":0" />
# A [[condensation reaction]] occurs between the amino group of aspartate and the carbonyl group of citrulline to form [[argininosuccinic acid|argininosuccinate]]. This reaction is ATP dependent and is catalyzed by [[Argininosuccinate synthase|argininosuccinate synthetase]].<ref name=":0" />
# Argininosuccinate undergoes cleavage by [[Argininosuccinate lyase|argininosuccinase]] to form [[arginine]] and [[fumarate]].<ref name=":0" />
# Arginine is cleaved by [[arginase]] to form urea and ornithine. The ornithine is then transported back to the mitochondria to begin the urea cycle again.<ref name=":0" /><ref name=":3" />

=== Overall reaction equation ===
In the first reaction, {{chem|NH|4|+}} + {{chem|HCO|3|-}} is equivalent to [[Ammonia|NH<sub>3</sub>]] + [[Carbon dioxide|CO<sub>2</sub>]] + [[Water|H<sub>2</sub>O]].

Thus, the overall equation of the urea cycle is:
* [[Ammonia|NH<sub>3</sub>]] + [[Carbon dioxide|CO<sub>2</sub>]] + [[aspartate]] + 3 [[Adenosine triphosphate|ATP]] + 3 [[Water|H<sub>2</sub>O]] → [[urea]] + [[fumarate]] + 2 [[Adenosine diphosphate|ADP]] + 2 [[Phosphate|P<sub>i</sub>]] + [[Adenosine monophosphate|AMP]] + [[Pyrophosphate|PP<sub>i</sub>]] + [[Water|H<sub>2</sub>O]]
Since fumarate is obtained by removing NH<sub>3</sub> from aspartate (by means of reactions 3 and 4), and PP<sub>i</sub> + H<sub>2</sub>O → 2 P<sub>i</sub>, the equation can be simplified as follows:
* 2 [[Ammonia|NH<sub>3</sub>]] + [[Carbon dioxide|CO<sub>2</sub>]] + 3 [[Adenosine triphosphate|ATP]] + 3 [[Water|H<sub>2</sub>O]] → [[urea]] + 2 [[Adenosine diphosphate|ADP]] + 4 [[Phosphate|P<sub>i</sub>]] + [[Adenosine monophosphate|AMP]]
Note that reactions related to the urea cycle also cause the production of 2 [[NADH]], so the overall reaction releases slightly more energy than it consumes. The NADH is produced in two ways:
* One NADH molecule is produced by the enzyme [[glutamate dehydrogenase]] in the conversion of glutamate to ammonium and [[α-ketoglutarate]]. [[Glutamate]] is the non-toxic carrier of amine groups. This provides the ammonium ion used in the initial synthesis of carbamoyl phosphate.
* The fumarate released in the cytosol is hydrated to [[malate]] by cytosolic [[fumarase]]. This malate is then oxidized to [[oxaloacetate]] by cytosolic [[malate dehydrogenase]], generating a reduced NADH in the cytosol. [[Oxaloacetate]] is one of the keto acids preferred by [[transaminase]]s, and so will be recycled to [[aspartate]], maintaining the flow of nitrogen into the urea cycle.
We can summarize this by combining the reactions:
* CO<sub>2</sub> + [[glutamate]] + [[aspartate]] + 3 ATP + 2 NAD<sup>+</sup>+ 3 H<sub>2</sub>O → [[urea]] + [[α-ketoglutarate]] + [[oxaloacetate]] + 2 ADP + 2 P<sub>i</sub> + AMP + PP<sub>i</sub> + 2 NADH
The two NADH produced can provide energy for the formation of 5 [[Adenosine triphosphate|ATP]] (cytosolic NADH provides 2.5 ATP with the malate-aspartate shuttle in human liver cell), a net production of two high-energy phosphate bond for the urea cycle. However, if [[gluconeogenesis]] is underway in the cytosol, the latter reducing equivalent is used to drive the reversal of the [[GAPDH]] step instead of generating ATP.

The fate of oxaloacetate is either to produce aspartate via transamination or to be converted to [[Phosphoenolpyruvic acid|phosphoenolpyruvate]], which is a substrate for [[gluconeogenesis]].<!--
An excellent way to memorize the Urea Cycle is to remember the [[mnemonic]] phrase "Ordinarily Careless Crappers Are Also Frivolous About Urination." The first letter of each word corresponds to the first letter of each of the main reactants or products that are combined with each other or produced as one progresses through the five reactions of the cycle (Ornithine, Carbamoyl phosphate, Citrulline, Aspartate, Argininosuccinate, Fumarate, Arginine, Urea).-->

== Products of the urea cycle ==
As stated above many vertebrates use the urea cycle to create urea out of ammonium so that the ammonium does not damage the body. Though this is helpful, there are other effects of the urea cycle. For example: consumption of two ATP, production of urea, generation of H<sup>+</sup>, the combining of {{chem2|HCO3-}} and {{chem2|NH4+}} to forms where it can be regenerated, and finally the consumption of {{chem2|NH4+}}.<ref>{{cite journal|jstor=30158252|title=Functional Roles of Urea in Vertebrates|journal=Physiological Zoology|volume=65|issue=2|last1=Atkinson|first1=Daniel|date=September 20, 1991|publisher=The University of Chicago Press|edition=2|location=Los Angeles|pages=243–267|doi=10.1086/physzool.65.2.30158252|s2cid=87121092}}</ref>

==Regulation==

===''N''-Acetylglutamic acid===
The synthesis of carbamoyl phosphate and the urea cycle are dependent on the presence of [[N-Acetylglutamic acid|''N''-acetylglutamic acid]] (NAcGlu), which [[allosterically]] activates [[Carbamoyl phosphate synthase|CPS1]]. NAcGlu is an obligate activator of carbamoyl phosphate synthetase.<ref>Kaplan Medical USMLE Step 1 Biochemistry and Medical Genetics Lecture Notes 2010, page 261</ref> Synthesis of NAcGlu by [[N-Acetylglutamate synthase|''N''-acetylglutamate synthase]] (NAGS) is stimulated by both Arg, allosteric stimulator of NAGS, and Glu, a product in the transamination reactions and one of NAGS's substrates, both of which are elevated when free [[amino acid]]s are elevated. So Glu not only is a substrate for NAGS but also serves as an activator for the urea cycle.

===Substrate concentrations===
The remaining enzymes of the cycle are controlled by the concentrations of their substrates. Thus, inherited deficiencies in cycle enzymes other than [[Protein:ARG1|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 anomalous substrate buildup is not without cost, however. The substrate concentrations become elevated all the way back up the cycle to {{chem|NH|4|+}}, resulting in [[hyperammonemia]] (elevated [{{chem|NH|4|+}}]<sub>P</sub>).

Although the root cause of {{chem|NH|4|+}} toxicity is not completely understood, a high [{{chem|NH|4|+}}] puts an enormous strain on the {{chem|NH|4|+}}-clearing system, especially in the [[Human brain|brain]] (symptoms of urea cycle enzyme deficiencies include [[intellectual disability]] and [[lethargy]]). This clearing system involves [[Protein:GLUD1|GLUD1]] and [[Protein:GLUL|GLUL]], which decrease the [[2-oxoglutarate]] (2OG) and Glu pools. The brain is most sensitive to the depletion of these pools. Depletion of 2OG decreases the rate of [[TCAC]], whereas Glu is both a [[neurotransmitter]] and a precursor to [[GABA]], another neurotransmitter.<ref>{{Cite book |last=Voet |first=Donald |title=Biochemistry. Hauptbd. |last2=Voet |first2=Judith G. |date=1995 |publisher=Wiley |isbn=978-0-471-58651-7 |edition=2. rev. |location=New York |pages=734}}</ref>

== Link with the citric acid cycle ==
The urea cycle and the [[citric acid cycle]] are independent cycles but are linked. One of the nitrogen atoms in the urea cycle is obtained from the transamination of oxaloacetate to aspartate.<ref name=":1">{{Cite journal|last=Shambaugh|first=G. E.|date=1977-12-01|title=Urea biosynthesis I. The urea cycle and relationships to the citric acid cycle|journal=The American Journal of Clinical Nutrition|volume=30|issue=12|pages=2083–2087|issn=0002-9165|pmid=337792|doi=10.1093/ajcn/30.12.2083|doi-access=free}}</ref> The fumarate that is produced in step three is also an intermediate in the citric acid cycle and is returned to that cycle.<ref name=":1" />

==Urea cycle disorders==
Urea cycle disorders are rare and affect about one in 35,000 people in the [[United States]].<ref>{{Cite journal|last1=Summar|first1=Marshall L.|last2=Koelker|first2=Stefan|last3=Freedenberg|first3=Debra|last4=Le Mons|first4=Cynthia|last5=Haberle|first5=Johannes|last6=Lee|first6=Hye-Seung|last7=Kirmse|first7=Brian|date=2013|title=The incidence of urea cycle disorders|journal=Molecular Genetics and Metabolism|volume=110|issue=1–2|pages=179–180|doi=10.1016/j.ymgme.2013.07.008|issn=1096-7192|pmc=4364413|pmid=23972786}}</ref> [[Genetic disorder|Genetic defects]] in the enzymes involved in the cycle can occur, which usually manifest within a few days after birth.<ref name=":122">{{Cite book|title=BIOCHEMISTRY A Short Course|last1=Tymoczko|first1=John L.|last2=Berg|first2=Jeremy M.|last3=Stryer|first3=Lubert|publisher=W.H. Freeman and Company, New York|year=2013|isbn=978-1-4292-8360-1|pages=529}}</ref> The recently born child will typically experience varying bouts of [[vomiting]] and periods of [[lethargy]].<ref name=":122" /> Ultimately, the infant may go into a [[coma]] and develop [[brain damage]].<ref name=":122" /> New-borns with UCD are at a much higher risk of complications or death due to untimely [[Screening (medicine)|screening tests]] and [[Medical error|misdiagnosed]] cases. The most common misdiagnosis is [[neonatal sepsis]]. Signs of UCD can be present within the first 2 to 3 days of life, but the present method to get confirmation by test results can take too long.<ref name=":5" /> This can potentially cause complications such as coma or death.<ref name=":5">{{cite journal|last1=Merritt |first1=J. L. |last2=Brody |first2=L. L. |last3=Pino |first3=G. |last4=Rinaldo |first4=P. |date=2018 |title=Newborn screening for proximal urea cycle disorders: Current evidence supporting recommendations for newborn screening |journal=Molecular Genetics and Metabolism |volume=124 |issue=2 |pages=109–113 |doi=10.1016/j.ymgme.2018.04.006|pmid=29703588 |s2cid=13858458 }}</ref>

Urea cycle disorders may also be diagnosed in adults, and symptoms may include [[delirium]] episodes, [[lethargy]], and symptoms similar to that of a [[stroke]].<ref>{{Cite book|title=Genetic Disorders Sourcebook|last=Judd|first=Sandra|publisher=Omnigraphics|year=2010|isbn=978-0-7808-1076-1|pages=225}}</ref> On top of these symptoms, if the urea cycle begins to malfunction in the [[liver]], the patient may develop [[cirrhosis]].<ref name=":6" /> This can also lead to [[sarcopenia]] (the loss of muscle mass).<ref name=":6">{{Cite journal|last=Qiu|first=Jia|date=July 9, 2013|title=Hyperammonemia in cirrhosis induces transcriptional regulation of myostatin by an NF-κB–mediated mechanism|journal=Proceedings of the National Academy of Sciences of the United States of America|publisher=National Academy of Sciences|volume=110|issue=45|pages=18162–18167|jstor=23754730|doi=10.1073/pnas.1317049110|pmid=24145431|pmc=3831479|bibcode=2013PNAS..11018162Q|doi-access=free}}</ref> Mutations lead to deficiencies of the various enzymes and transporters involved in the urea cycle, and cause urea cycle disorders.<ref name=":0" /> If individuals with a defect in any of the six enzymes used in the cycle ingest [[amino acid]]s beyond what is necessary for the minimum daily requirements, then the ammonia that is produced will not be able to be converted to urea. These individuals can experience [[hyperammonemia]], or the build-up of a cycle intermediate.

=== Individual disorders ===
* [[N-Acetylglutamate synthase deficiency|N-Acetylglutamate synthase (NAGS) deficiency]]
* [[Carbamoyl phosphate synthetase I deficiency|Carbamoyl phosphate synthetase (CPS) deficiency]]
* [[Ornithine transcarbamoylase deficiency|Ornithine transcarbamoylase (OTC) deficiency]]
*  [[Citrullinemia|Citrullinemia type I]] (Deficiency of argininosuccinic acid synthase)
* [[Argininosuccinic aciduria]] (Deficiency of argininosuccinic acid lyase)
* [[Argininemia]] (Deficiency of arginase)
* [[Hyperornithinemia, hyperammonemia, homocitrullinuria syndrome|Hyperornithinemia, hyperammonemia, homocitrullinuria (HHH) syndrome]] (Deficiency of the mitochondrial ornithine transporter)<ref name=":4" /><ref>{{Citation|last1=Smith|first1=L. D.|title=Chapter 5: Urea cycle and other disorders of hyperammonemia|date=2017-01-01|url=http://www.sciencedirect.com/science/article/pii/B9780128028964000043|work=Biomarkers in Inborn Errors of Metabolism|pages=103–123|editor-last=Garg|editor-first=Uttam|place=San Diego|publisher=Elsevier|language=en|doi=10.1016/b978-0-12-802896-4.00004-3|isbn=978-0-12-802896-4|access-date=2020-11-10|last2=Garg|first2=U.|editor2-last=Smith|editor2-first=Laurie D.|url-access=subscription}}</ref>

All urea cycle defects, except OTC deficiency, are inherited in an [[autosomal recessive]] manner. OTC deficiency is inherited as an [[X-linked recessive]] disorder, although some females can show symptoms. Most urea cycle disorders are associated with [[hyperammonemia]], however argininemia and some forms of argininosuccinic aciduria do not present with elevated ammonia.

==Additional images==
<gallery class=skin-invert-image>
 File:Urea-Cycle scheme 2006-01.svg|Urea cycle.
 File:Urea cycle 2.png|Urea cycle colored.
</gallery>

==References==
{{reflist}}

==External links==
* [http://homepage.ufp.pt/pedros/bq/urea.htm The chemical logic behind the urea cycle]
* [https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=bnchm.figgrp.3102 ''Basic Neurochemistry''] - amino acid disorders

{{MetabolismMap}}
{{urea cycle}}
{{Urea cycle enzymes}}

{{DEFAULTSORT:Urea Cycle}}
[[Category:Biochemical reactions]]
[[Category:Urea cycle| ]]
[[Category:Nitrogen cycle]]