When Tyrosine becomes an essential amino acid

Answer to Question AM-06


Short answer: (g)


In patients with PKU, Tyrosine becomes essential, since it is formed from Phenylalanine in the reaction that is impaired in Phenylketonuria.


Additional information:


Most of the textbooks classify amino acids from the nutritional point of view, in two groups: essential or not essential.  Essential amino acids are considered those amino acids that can not be synthesized by an organism and so should be consumed in the diet; non essential amino acids are those amino acids that can be synthesized.  This classification is not related to the importance of the amino acids, but with the fact of them being required in the diet or not.


According to this classification, the essential amino acids are:


Arginine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine


















Non essential amino acids are:

Alanine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Proline, Serine, Tyrosine


Like most facts in biology, this “black and white” classification is not 100 % accurate. Actually, some amino acids are conditionally essential or partially essential, since some “essential” amino acids, like arginine,  can be synthesized by the body. Arginine is synthesized in the urea cycle, for example, but it is considered essential since the quantity of Arginine that is synthesized is not enough during the growing process.


 Tyrosine is an amino acid that is synthesized in the body from Phenylalanine, that is an essential amino acid. This reaction is catalyzed by the enzyme Phenylalanine Hydroxylase, that use as cofactor reduced tetrahydobiopterine.

If Phenylalanine is deficient in the diet, then the body requires tyrosine in the diet.


In Phenylketonuria there is an excess of Phenylalanine, since the body can not metabolize it, but Phenylketonuria is a consequence of a deficit of Phenylalanine Hydroxylase (Classic Phenylketonuria) or a deficit of Tetrahydrobiopterin Reductase. In both cases, the organism is not able to synthesize Tyrosine from Phenylalanine, so even when there is an accumulation of Phe in these patients, it can not be used to synthesize Tyrosine.


In fact, some of the signs and symptoms of Phenylketonuria, like mental retardation and other neurological symptoms, have been related to the unavailability of tyrosine for the synthesis of the neurotransmitters that derive from tyrosine.



The lack of pigmentation of PKU patients, has been related also to the lack of tyrosine, since Tyrosine is a precursor of melanine also.


It is obvious that if Tyrosine is formed in normal persons from phenylalanine through the reaction cited above, in case that this reaction can not be produced, like in PKU, it is necessary to supplement the patient with Tyrosine, since the patient can not synthesize it, so Tyrosine becomes an essential amino acid for these patients.




About Arginine

Answer to Biochemistry Question AM-05


(b) Arginine


Structure of arginine


                                                  Structure of Arginine



                                                                      Structure of Arginine  


Arginine is for humans a conditional essential amino acid, since we can synthesize, but it may not be enough for our requirements, depending of the health status and the stage of development. For infants, arginine is nutritionally essential, and in adults some must still be consumed through diet, especially in some conditions as trauma, burn injury, small-bowel resection and renal failure.


Arginine is synthesized from citrulline. Citrulline is formed mainly in the small intestine and is recovered from circulation by the kidney, that converts most of it in arginine (it explains the increased requirement of arginine in patients with renal failure of small-bowel resection).


 Not only the kidney and the liver, where Urea Cycle occurs, can produce arginine. In fact, several tissues can synthesize, in lower quantities, this amino acid, since it can yield important biologically active compounds.


As mentioned before, an important source of arginine is the diet. Arginine is found in a variety of foods including meats, dairy products and seafood. It appears also in vegetarian food as wheat germ, nuts, seeds, soybeans and others. Some energy drinks and body builder supplements are enriched with arginine.


Arginine, as stated in the question, is the precursor of Nitric Oxide and Urea.



The synthesis of Nitric Oxide occurs in a two steps reaction catalyzed by Nitric Oxide Synthase (NOS) that produces NwHydroxy-L Arginine (NOHLA) as an intermediary:


L-Arg + NADPH.H+ + O2  à [Nw-hydroxy-Larginine] + NADP+ +H2O

[Nw-hydroxy-Larginine] + NADPH.H+ + O2  à citrulline  + NO + NADP+



Nitric oxide synthase contains as cofactors FMN, FAD, tetrahydrobiopterin and Fe+++ Hem. There are three isoforms of this enzyme and it is present in many tissues and cell types: neurons, macrophages, hepatocytes, myocytes of smooth muscle, endothelial cells of the blood vessels and epithelial cells of the kidneys.



The synthesis of urea from arginine occurs in the last reaction of the Urea Cycle:


L-Arg + H2O —-à ornithine + Urea


This reaction is catalyzed by Arginase, an enzyme with two isoforms: Arginase I, expressed in the cytoplasm of the liver, and related to Urea Cycle, and Arginase II, that appears in several tissues and apparently act, as a competing enzyme for the same substrate, like some kind of regulator of the arginine available for the action of Nitric Oxide Synthase.


Besides the importance of Arginine as a precursor of Nitric Oxide and Urea, and its obvious role as one of the 20 amino acids that constitute the “building blocks” of proteins, Arginine is also precursor of Creatine, and can be interconverted with other amino acids as proline and glutamate. Arginine also can yield other nitrogenated compounds, depending on the specific tissue.


As described by Morris, (one of the authors that has focused on Arginine research during the last years): “L-arginine is catabolized by arginases, nitric oxide synthases, arginine: glycine amidinotransferase, and possibly also by arginine decarboxylase, resulting ultimately in the production of urea, proline, glutamate, polyamines, nitric oxide, creatine, or agmatine. There is considerable diversity in tissue-specific and stimulus-dependent regulation of expression within this group of enzymes, and the expression of several of them can be regulated at transcriptional and translational levels by changes in the concentration of L-arginine itself.” (Morris, S.M. Jr: Enzymes of Arginine Metabolism  (J Nutr.134 (10 Suppl):2743S-2747S; discussion 2765S-2767S, 2004) 



 More information about Arginine and Arginine metabolism in:


Morris, S.M. JR.: Arginine, Beyond Protein, Amer J Clin Nutr 83(2)  508S-512S, 2006



Morris, S.M. Jr. Arginine metabolism: boundaries of our knowledge (J Nutr 2007) 137(6 Suppl 2):1602S-1609S.


King, The Medical Biochemistry Page: amino acid derivatives


Nitric Oxide Synthase


Good graphics about Urea synthesis in:




 Arginine (Wikipedia)


 For the uses of Arginine based on scientific evidence:



MedlinePlus Herbs and Supplements: Arginine (L-arginine)



Ammonia Detoxification: From Muscle to Liver


Answer to Biochemistry Question AM-04


Answer:  (a) alanine and glutamine





                                                 Leonardo da Vinci muscle drawings 


At cellular pH NH3 exists as NH4+ ion. If the concentration of ammonium ions is very high, coma may result ( “Hepatic coma”).


There are mechanisms in our body to avoid hyperammonemia. Those mechanisms allow the transport of ammonia from muscle and other peripheral tissues to the liver and the kidneys.



                                                             Leonardo da Vinci Torso


 In the liver, the ammonia delivered by these mechanisms will form UREA, while in the kidneys these mechanism will allow the direct excretion of NH4+  in urine.


These mechanisms are:


– Glucose-alanine cycle (transport of  NH3 from muscle to liver).


– Glutamine synthase/glutaminase system (transport of NH3 from different tissues to kidney and liver)


  Ammonia Detoxification in Muscle:

 Alanine transaminase has an important function in the delivery of skeletal muscle carbon and nitrogen (in the form of alanine) to the liver. In the glucose-alanine cycle ammonium ion is transported from muscle cells to the liver in the form of alanine.


Through glycolysis, glucose becomes pyruvate in the muscle. The participation of this ketoacid (pyruvate) in transamination reactions produce the corresponding amino acid: alanine. Alanine is then transported to the liver, where it can be transaminated again producing pyruvate that can be used for gluconeogenesis yielding glucose that can be send again to the muscle for producing energy (glucose-alanine cycle).


The other mechanism for transporting nitrogen in a non toxic form from the muscle to the liver is in form of glutamine. The enzyme glutamine synthase (also present in the liver) catalyses the following reaction:


Glutamate + NH3 + ATP ———-à glutamine +ADP + (P)


This reaction allows the transportation of nitrogen in a non toxic form to the liver and kidney (this reaction is important for other things, also!). Glutamine is the major amino acid found in the circulatory system, followed by alanine. The role of glutamine in the blood is to carry ammonia to and from various tissues but principally from peripheral tissues like the muscle, to the kidney and liver, where the amide nitrogen is hydrolyzed by the enzyme glutaminase and the ammonia is released, forming H4+ ion. In the kidney, it can be excreted in the urine by direct renal excretion, while in the liver the ammonia released by glutaminase will be used mainly for the synthesis of urea.


Note that ammonia arising in muscle and other peripheral tissues is carried in a nonionizable form as alanine or glutamine from to the liver. In these forms, ammonia does not have the toxic properties of free ammonia.


 More information ca be found in:


Brosnan, J.T.: Interorgan Amino Acid Transport and its Regulation


 The medical biochemical page: Nitrogen metabolism


 Vey good graphics about the glucose-alanine cycle, can be found in this link.



About transamination, Vitamin B6 and Pyridoxal Phosphate

Answer to Biochemistry Question AM-03




         Interchange of the functional groups between an a-keto acid and one amino acid



         Aminotransferases or transaminases





         Pyridoxal Phosphate



Pyridoxal phosphate


                                                             Pyridoxal phosphate structure


Pyridoxal Phosphate is the active form of Vitamin B-6.  This vitamin has three active forms: pyridoxal, pyridoxine (or piridoxol) and  pyridoxamine. (sometimes pyridoxine is used as synonym of Vitamin B6)


Besides Transamination, Pyridoxal phosphate participates in several other reactions as cofactor, including:


         Glycogenolysis (cofactor of glycogen phosphorylase but participates with the Phosphate group)

         Hem synthesis





                        Non-oxidative deamination


Deficit of Vitamin B6:



         Deficit alone is uncommon. It usually appears associated to other nutritional deficits in alcoholics and elderly. Also in TB patients treated with Isoniazid. L-DOPA and Penicillamine also interfere with the metabolism of B6 and can produce deficiency.

         The deficit is characterized by dermatitis like eruption, neuropathy and frequently anemia.


Toxicity of Vitamin B6:


Vitamin B6 can also cause neuropathy when taken in excess. It has been established an upper tolerable intake level (UL) of  100 mg/day for adults. 



Participation of Pyridoxal Phosphate in the Mechanism of Transamination


Pyridoxal Phosphate acts as intermediary in the reaction:


a)     First, it takes the amino group of the original amino acid (amino acid 1), and gives the oxygen  to the carbon skeleton of the amino acid, yielding an a-ketoacid (a-ketoacid 1). Pyridoxal Phosphate becomes Pyridoxamine Phosphate in the process.


b)     In the second part of the reaction, the Pyridoxamine Phosphate gives the amino group to a ketoacid (ketoacid 2), yielding a new amino acid (amino acid 2) while the pirydoxal phosphate is regenerated.


             amino acid1 + pyridoxal Phosphate <—-> ketoacid1 + Pyridoxamine Phosphate


                 Pyridoxamine Phosphate + ketoacid2 <———-> amino acid 2 + Pyridoxal Phosphate


            amino acid1 + ketoacid2 <———–>  ketoacid1 + amino acid2



Important couples in Transamination reactions:


When the amino acid transaminated is Alanine it yields the ketoacid Pyruvate (and viceversa)


When the amino acid transaminated is Aspartate, the reaction yields the ketoacid Oxalacetate (and viceversa)


When the amino acid transaminated is Glutamate, the reaction yields the ketoacid a-ketoglutarate



Importance of Transamination:


         Funneling the a-amino group of amino acids to a-keto glutarate to get glutamate (glutamate plays a central rol in Nitrogen metabolism).


         Synthesis of non essential amino acids


         Interconexion between amino acid metabolism and Krebs Cycle.


The following reaction is a very good example of these three former observations:


a-amino acid + a-ketoglutarate ó a-ketoacid + glutamate


Clinical Importance of Transaminases (Aminotransferases) study:


Since amino transferases are intracellular enzymes, abundant in hepatic and cardiac tissues, serum aminotransferases such as serum glutamate-oxaloacetate-aminotransferase (SGOT) (also called aspartate aminotransferase, AST) and serum glutamate-pyruvate aminotransferase (SGPT) (also called alanine transaminase, ALT) classically have been used as clinical markers of these tissue damages, with increasing serum levels indicating an increased extent of damage.  



More information about these topics can be found in the following links:


Dietary Supplement fact Sheet: Vitamin B6


Linus Pauling Institute at Oregon State University. Micronutrient Information Center


Merck Manual: Vitamin B6





Transamination and Deamination


Transamination reaction


About the metabolic fate of the carbon skeleton of amino acids


Answer to Biochemistry Question AM-02 about Amino acid Metabolism.


Answer: (b) Ketogenic (Since the question only make reference to acetoacetyl CoA, we assume that it is the final product of the catabolism of this amino acid and no glucogenic metabolites are produced.)



                                                 General structure of an amino acid



Amino acids are used for different purposes in our body. Most of the metabolic pool of amino acids is used as building blocks of proteins, and a smaller proportion is used to synthesize specialized nitrogenated molecules as epinephrine and norepinephrine, neurotransmitters and the precursors of purines and pyrimidines.


Since amino acids can not be stored in the body for later use, any amino acid not required for immediate biosynthetic needs is deaminated and the carbon skeleton is used as metabolic fuel (10-20 % in normal conditions) or converted into fatty acids via acetyl CoA.


The main products of the catabolism of the carbon skeleton of the amino acids are pyruvate, oxalacetate, a-ketoglutarate, succinyl CoA, fumarate, acetyl CoA and acetoacetyl CoA.


When carbohydrates are not available (starvation, fasting) -or cannot be used properly, as in diabetes mellitus, amino acids can become a primary source of energy by oxidation of their carbon skeleton, but also by becoming an important source of glucose for those tissues that only can use this sugar as metabolic fuel.


The formation of glucose from amino acids (gluconeogenesis) in liver and kidney is intensified during starvation and this process becomes the most important source of glucose for the brain, RBC and other tissues.


Amino acids in skeletal proteins can be used, in a situation of prolonged starvation as an “emergency” energy store that can yield 25000 kcal.


Amino acids can be classified according to the metabolic fate of the carbon skeleton in:






         ketogenic and glucogenic


Ketogenics: Amino acids that yield acetyl CoA or acetoacetyl CoA ( e.g. they do not produce metabolites that can be converted in glucose).  

Lysine and Leucine are the only amino acids that are exclusively ketogenics.


Glucogenic: Amino acids whose catabolism yields to the formation of Pyruvate or Krebs Cycle metabolites, that can be converted in glucose through gluconeogenesis (Remember the pathway: pyruvate-àoxalacetate-à (P) enol pyruvate…etc.).

Glucogenic amino acids  are: Alanine, Arginine, Asparagine, Aspartate, Cysteine, Glutamate, Glycine, Histidine, Methionine, Proline, Serine, and Valine


Glucogenic and ketogenic: Amino acids that yield some products that can become glucose and others that yields acetyl CoA or Acetoacetyl CoA.

Amino acids of this kind are Isoleucine, Phenylalanine, Tryptophan, Tyrosine and Threonine.




A: About a baby with PKU (AM-01)

Original Question


Answer (a)


Phenylalanine, per se, can follow three metabolic pathways:


a)     incorporation to the process of synthesis of proteins

b)     hydroxylation  to tyrosine

c)      conversion to phenyl pyruvate and derivatives like phenyl lactic and phenyl acetic.


The incorporation of Phenylalanine to proteins depends on the requirements in the synthesis of proteins.


Normally, conversion of phenylalanine to phenyl pyruvate and derivatives occurs in small quantities, since most of the phenylalanine is used in the other two metabolic processes.


The hydroxylation of Phenylalanine to Tyrosine is catalyzed by the enzyme Phenylalanine Hydroxylase, as represented in this graphic from the NLM:


This reaction is impaired in PKU (Phenylketonuria), due to the lack of Phenyl alanine hydroxylase or to the lack of Tetrahydrobiopteryn reductase, an enzyme necessary for supplying the reduced cofactor (TH4) required for this reaction.


As a consequence, Phenylalanine accumulates and it is drained to the formation of Phenylpyruvate, in a transamination reaction.  Pyruvate can be reduced to Phenyllactate or decarboxylated to Phenylacetate, in a same way that Pyruvate can be reduced to Lactate or, by decarboxylation,  form the  Acetyl group of Acetyl CoA).


1) Phenylalanine + alpha-ketoglutarate <——–> Phenylpyruvate + glutamate


2) Phenyl lactate <———— Phenylpyruvate ———————–> Phenylacetate

                          (reduction)                            (decarboxylation)


These compounds, which are normally produced in very small amounts, accumulate in PKU and are eliminated by urine in increased quantities, where they can be detected.


The name Phenylketonuria corresponds to the finding of notable quantities of phenyl pyruvate and derived metabolites in urine of the patients and the detection of the metabolites was an important tool of diagnosis of this disease before the Guthrie test made available a screening test for newborns and the detection of phenylalanine in blood gave an appropriate diagnosis tool.


Note: questions very similar to the former one can be found frequently in different tests. The Step 1 Content description and General information 2008 (FSMB/NBME) includes a sample question in which the compound released in urine is phenylacetic. Copyrights issues do not allow me to show the question here, but you can find it as the question number 126 in the referred document. Observe that in these kind of questions the patient usually, for some circumstance, have escaped to mandatory screening for PKU)



The following site contains useful information and several links to other sites about Phenylketonuria: