Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 432


Spring 2009

Lecture Notes: 9 February

© R. Paselk 2006


Nitrogen Metabolism, cont.


Pyridoxal-P catalyzes a variety of other reactions involving amino acids involving destabilization of bonds to the alpha-carbon:

In addition, Pyridoxal-P catalyzes the direct deamination of serine and threonine via the destabilization of the side chain hydroxyl group. This reaction is favored by the excellent leaving group (water) on the beta-carbon. Thus PLP catalyzes the removal of water in Serine dehydratase:

The resulting aminoacrylate is then hydrated to give pyruvate as the product. The analogous reaction is catalyzed by Threonine dehydratase to give 2-oxobutyrate.

Other, non PLP catalyzed, direct deaminations include the hydrolysis of the amide nitrogens of glutamine and asparagine, and the deamination of histidine by histidase to give urocanate and ammonium.

L- & D-Amino acid oxidases are flavoproteins which catalyze the direct oxidation of amino acids in what can be considered detoxification reactions. The aa oxidases exhibit broad specificities. These enzymes occur in the peroxisomes of liver and kidney, where the hydrogen peroxide produced can be eliminated by catalase without damaging the cell:

Note here that unlike mixed function oxidases we are going to peroxide instead of water, and oxygen in peroxide has an oxidation state of -1, so only two electrons are required. So this reaction is not energy intensive - no NADH required, no ATP equiv. lost. But a very toxic product, hydrogen peroxide is produced! (Generally done in isolation in organelles such as peroxisomes which contain catalase to destroy peroxide.)

Urea Cycle

Let's next look over the Kreb's Urea Cycle (this is his first cycle, the TCA cycle came later). Urea is synthesized from ammonia, carbon dioxide, and aspartate nitrogen using Kreb's Urea Cycle:

Note that two ATP's are required to synthesize carbamyl phosphate, the first to activate bicarbonate, the second to provide the activated phosphate on the carbamyl-P itself. Carbamyl-P is itself a high-energy compound with a mixed anhydride bond much like we saw in 1,3-bis PGA. The carbamyl group is then transferred onto ornithine which acts as a carrier for the growing urea molecule. Addition of the aspartate nitrogen requires two additional ATP equivalents to drive the condensation to argininosuccinate. Lysis results in the formation of a fumerate and arginine, which is then hydrolyzed to give our product, Urea, and regenerate the ornithine carrier.

Note a total of four ATP equivalents has been consumed. How many ATP equivalents are then required to convert the nitrogen of two amino acids into urea? The flow diagram supplied below may help in this calculation:

To solve this problem we can first note the four ATP equivalents consumed in the biosynthesis of one urea from two amino acids. But the fumerate produced must be taken back to regenerate the oxalacetate used to pick up the nitrogen from one amino acid):

fumerate + H2O malate; malate +NAD+ oxaloacetate + NADH + H+

This will provide an NADH via malate DH. This is equivalent to 2.5 ATP's, so we have -4 + 2.5 = -1.5. Next, while the second nitrogen enters via two transaminations through aspartate:

we also have to produce the ammonia from the first amino acid via glutamate using Glutamate DH,

This also produces an NADH, providing another 2.5 ATP's. thus the final tally is -4 + 2.5 + 2.5 = +1 ATP to produce one urea from two amino acid nitrogens. Of course for mammals this does not take into account the physiological costs of excreting the urea, which can be significant.

Pathway Diagrams

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Last modified 10 February 2008