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Bioenergetics

The main overview should make a reference to the quantitative aspect of bioenergetics, bioenergetics focuses on quantifying energy transductions

Overview

In the living organisms section a clarification that cells get free energy from these processes which is transformed to ATP would be useful.

The bomb calorimeter mention seems irrelevant.

The sentence: "energy of hydration that results in energy release" is somewhat misleading. In most cases it is not just the hydrolysis that leads energy release, this leads to the release of heat. The transfer of the phosphoryl group leads to a higher free energy content and is a necessary component of the energy release.

This sentence: "An organism's stockpile of ATP is used as a battery to store energy in cells, for intermediate metabolism." is confusing. Could say "An organism's stockpile of ATP stores energy in cells and can be used for immediate metabolism".

Types of Reactions

Gibbs free energy should be explained or at least the page should be linked.

Cotransport It would be useful to state how this is related to bioenergetics. At this point it is not clear to a reader who does not know that much about bioenergetics.

Pentose Phosphate Pathway:

Overview: When discussing the products generated it should state that the products are generated from the oxidation of glucose-6-phosphate. Additionally, it should specifically state what the conditions of the Archaen ocean that allow for the non-enzymatic pathway.

Outcomes In the aromatic amino acids portion the reference to lignin in wood is unnecessary, irrelevant, and it is unclear what pathway biosynthetic pathway lignin is a precursor for.

A citation would be useful for the dietary pentose portion.

For the portion on mammals there is a typo: "in the human" should be "in humans". Potential citation for this portion is Lehninger Principles of Biochemistry.

Regulation the sentence: "Glucose-6-phosphate dehydrogenase is the rate-controlling enzyme of this pathway" is misleading. The pathway is inhibited by NADPH and the ratio of NADPH:NADP+ is what determines flux, not the enzyme itself.

= Urea Cycle =

The urea cycle (also known as the 'ornithine cycle') is a cycle of biochemical reactions that produces urea ((NH2)2CO) from ammonia (NH3). This cycle occurs in ureotelic organisms. The urea cycle converts highly toxic ammonia to urea for excretion. This cycle was the first metabolic cycle to be discovered (Hans Krebs and Kurt Henseleit, 1932), five years before the discovery of the TCA cycle. The urea cycle takes place primarily in the liver and, to a lesser extent, in the kidneys.

Function
Amino acid catabolism results in waste amino groups. All animals need a way to excrete this product. Most aquatic organisms, or ammonotelic organisms, excrete ammonia without converting it. Ammonia is toxic but upon excretion from aquatic species is diluted from water. Organisms that cannot easily and safely remove nitrogen as ammonia convert it to a less toxic substance: urea or uric acid. The urea cycle mainly occurs in the liver. The urea is then released into the bloodstream where it travels to the kidneys and is ultimately excreted in urine.

Reactions
The entire process converts two amino groups, one from NH4+ and one from Asp, and a carbon atom from HCO3−, to the relatively nontoxic excretion product urea at the cost of four "high-energy" phosphate bonds (3 ATP hydrolyzed to 2 ADP and one 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 carbomyl phosphate. The urea cycle consists of four enzymatic reactions: one mitochondrial and three cytosolic.
 * The reactions of the urea cycle

1 L -ornithine

2 carbamoyl phosphate 3 L -citrulline 4 argininosuccinate 5 fumarate 6 L -arginine 7 urea L -Asp L -aspartate CPS-1 carbamoyl phosphate synthetase I OTC Ornithine transcarbamoylase ASS argininosuccinate synthetase ASL argininosuccinate lyase ARG1 arginase 1

First Step: Entering the Urea Cycle
Before the urea cycle begins ammonia is converted to carbomyl phosphate. The reaction is catalyzed by carbamoyl phosphate synthetase I and requires the use of an ATP molecule. The carbomyl phosphate then enters the urea cycle.

4 Steps of the Urea Cycle
1) Carbomyl phosphate is converted to citrulline. With catalysis by ornithine transcarbamoylase, the carbomyl phosphate group is donated to ornithine and releases a phosphate group.

2) A condensation reaction occurs between the amino group of aspartate and the carbomyl group of citrulline to form arginosuccinate. This reaction is ATP dependent and is catalyzed by arginosuccinate synthetase.

3) Arginosuccinate undergoes cleavage by arginosuccinase to form arginine and fumarate.

4) 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.

Overall Reaction Equation
In the first reaction, NH4+ + HCO3− is equivalent to NH3 + CO2 + H2O.

Thus, the overall equation of the urea cycle is: Since fumarate is obtained by removing NH3 from aspartate (by means of reactions 3 and 4), and PPi + H2O → 2 Pi, the equation can be simplified as follows: 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: We can summarize this by combining the reactions: The two NADH produced can provide energy for the formation of 4 ATP (cytosolic NADH provides only 1.5 ATP due to the glycerol-3-phosphate shuttle which transfers the electrons from cytosolic NADH to FADH2 and that gives 1.5 ATP), a net production of one 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.
 * NH3 + CO2 + aspartate + 3 ATP + 2 H2O → urea + fumarate + 2 ADP + 2 Pi + AMP + PPi
 * 2 NH3 + CO2 + 3 ATP + H2O → urea + 2 ADP + 4 Pi + AMP
 * 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 transaminases, and so will be recycled to aspartate, maintaining the flow of nitrogen into the urea cycle.
 * CO2 + glutamate + aspartate + 3 ATP + 2 NAD++ 3 H2O → urea + α-ketoglutarate + oxalacetate + 2 ADP + 2 Pi + AMP + PPi + 2 NADH

The fate of oxaloacetate is either to produce aspartate via transamination or to be converted to phosphoenolpyruvate, which is a substrate for gluconeogenesis.

N-Acetylglutamic acid
The synthesis of carbamoyl phosphate and the urea cycle are dependent on the presence of NAcGlu, which allosterically activates CPS1. NAcGlu is an obligate activator of carbamoyl phosphate synthetase. Synthesis of NAcGlu by 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 acids 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 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 NH4+, resulting in hyperammonemia (elevated [NH4+]P).

Although the root cause of NH4+ toxicity is not completely understood, a high [NH4+] puts an enormous strain on the NH4+-clearing system, especially in the brain (symptoms of urea cycle enzyme deficiencies include intellectual disability and lethargy). This clearing system involves GLUD1 and 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. [1 ](p.734)

Linkage with the Citric Acid Cycle
The urea cycle and the citric acid cycle are independent cycles but are linked. The fumarate that is produced in step three is also an intermediate in the citric acid cycle.

Urea Cycle Disorders
Genetic defects in the enzymes involved in the cycle can occur. Mutations lead to deficiencies of the various enzymes and transporters involved in the urea cycle and cause urea cycle disorders. If individuals with a defect in any of the enzymes used in the cycle ingest amino acids beyond what is necessary for the minimum daily requirements the ammonia that is produced will not be able to be converted to urea. These individuals can experience hyperammonemia or the buildup of a cycle intermediate.

Types of urea cycle disorders
Most urea cycle disorders are associated with hyperammonemia, however argininemia and some forms of argininosuccinic aciduria do not present with elevated ammonia.
 * N-Acetylglutamate synthase deficiency
 * Carbamoyl phosphate synthetase deficiency
 * Ornithine transcarbamoylase deficiency
 * Citrullinemia (Deficiency of argininosuccinic acid synthase)
 * Argininosuccinic aciduria (Deficiency of argininosuccinic acid lyase)
 * Argininemia (Deficiency of arginase)
 * Hyperornithinemia, hyperammonemia, homocitrullinuria syndrome (Deficiency of the mitochondrial ornithine transporter)