The excretion of ammonium ions
A part of the NH4+ that is formed in the degradation of amino acid is used for the biosynthesis of nitrogen compounds. In most of the land living vertebrate animals (including human) the excess NH4+ is converted in urea and in that form it is excreted. You can read more about this metabolic process on the page urea cycle. In birds and living reptiles NH4+ is converted in urine acid for the excretion. In many in water living animals NH4+ is excreted directly in the water.
Destination of degraded amino acid in the metabolism
The carbon atoms of degraded amino acids are found in important intermediate products of the metabolism. The strategy of the amino acid degradation is the formation of important intermediate products that can be converted in glucose or can be oxidised in the citric acid cycle. The carbon skeletons of the twenty amino acids are brought back to only seven molecules: pyruvate, acetyl CoA, acetoacetyl CoA, alpha-ketoglutarate, succinyl CoA, fumarate and oxaloacetate. Amino acids that are degraded to acetyl CoA or acetoacetyl CoA are called ketogenic amino acids because they can be converted in ketone bodies. The amino acids that are converted in the remaining of the seven molecules are called glucogenic amino acids because they can be converted in phospho-enol pyruvate and from there in glucose (via the gluconeogenesis).
Destinations of the carbon chain of amino acids. Glucogenic amino acids are in a red frame, the ketogenic amino acids in a yellow frame. Some amino acids (ile, try, phe, tyr) are as well glucogenic as ketogenic amino.
The C3 family: alanine, serine and cysteine is converted in pyruvate. Pyruvate is the entry point for alanine, serine, cysteine, glycine, threonine and tryptophan. Cysteine can be converted in pyruvate through different paths, by which the sulphur atom returns in H2S, SO32-, or SCN-. Also carbon atoms of the amino acids glycine, threonine and tryptophan can be converted in pyruvate.
The C4 family: aspartate and asparagine are converted in oxaloacetate. Aspartate can also be converted in fumarate by the urea cycle. Fumarate is an entry point for half of the carbon atoms of tyrosine and phenylalanine.
The C5 family: glutamine, proline, arginine and histidine are converted to alpha-ketoglutarate via glutamate. Alpha-ketoglutarate is the entry point of glutamine, proline, arginine and histidine that are first converted to glutamate.
Succinate CoA is an entry point for single apolar amino acids by the transformation of methionine, isoleucine and valine via propionyl CoA in succinate CoA. The pathway of propionyl CoA to succinate CoA is also present in the oxidation of fatty acids with an odd number carbon atoms. Fatty acids with an odd number of carbon atoms are thus partial glucogenic; three of their carbon atoms can go in glucose.
Degradation of phenylalanine and tyrosine in acetylacetate and fumarate
The first step in the degradation of phenylalanine is the hydroxylation of phenylalanine to tyrosine by the enzyme phenylalanine hydroxylase. This enzyme is called a monooxygenase or mixed-function oxygenase because one atom of O2 is found in the product (tyrosine) and the other in H2O.
The second step is the transamination of tyrosine in p-hydroxyphenylpyruvate. This alpha-keto acid reacts with O2 and forms homogentisate (the acid rest of homogentisin acid). The enzyme p-hydroxyphenylpyruvate hydroxylase is a dioxygenase because both atoms of O2 are built in the product (one in the ring and one in the carboxyl group).
The aromatic ring is then broken by O2 under formation of 4-maleylacetylacetate. This reaction is catalysed by another dioxygenase enzyme.
4-Maleylacetylacetate is then isomerised to 4-fumarylacetylacetate. Ultimately 4-fumarylacetylacetate is hydrolysed in fumarate and acetylacetate. See the figure below for the path of the degradation of phenylalanine and tyrosine.
A blockade in the degradation of phenylalanine can lead to mental retardation
The absence or insufficient activity (deficiencies) of phenylalaninehydroxylase (or its cofactor tetrahydrobiopterine) causes an accumulation of phenylalanine in all bodies liquids and therefore an excretion in the urine of the transformation product phenylpyruvate (phenylketon).
The biochemical background of the mental retardation is still a riddle.
An early diagnosis is essential and is reached by screening on newborn. The concentration phenylalanine in the blood, obtained by a heel prick, is determined.
The frequency of phenylketonuria is 1 on 20,000 of all newborn. The illness is inherited autonomic recessive.
The mental retardation is prevented by a diet with little phenylalanine. For that proteins with a low content of phenylalanine, like the milk protein casein, is hydrolysed. From the hydrolysate, phenylalanine is removed by adsorption.
. Stryer, Lubert;- Biochemistry - fourth edition; New York: W. H. Freeman and Company (1995). ISBN 0-7167-2009-4