Amino acids metabolic pathways, ammonia

The physiological relevance together with chnical importance of transamination and deamination is wide-ranging. As an aid to understanding the somewhat complex nature of amino acid metabolism, it can be considered (or imagined) as a metabolic box (represented in Figure 8.13). Some pathways feed oxoacids into the box whereas others remove oxoacids and the ammonia that is released is removed to form urea. The box illustrates the role of transdeamination as central to a considerable amount of the overall metabolism in the liver cell (i.e. protein, carbohydrate and fat metabohsm, see below). 

Amino acids derived from dietary or body proteins are also potential fuels that can be oxidized to acetyl CoA, or converted to glucose and then oxidized (see Fig. 2). These oxidation pathways, like those of fatty acids, generate NADH or FAD(2H). Ammonia, which can be formed during amino acid oxidation, is toxic. It is therefore converted to urea in the liver and excreted in the urine. There are more than 20 different amino acids, each with a somewhat different pathway for oxidation of the carbon skeleton and conversion of its nitrogen to urea. Because of the complexity of amino acid metabolism, use of amino acids as fuels is considered separately in Section Seven, Nitrogen Metabolism. 

N-Amino Acms. In addition to its use in studies of ammonia metabolism, NH3 is useful as a synthetic precursor for preparation of labeled amino acids. Because amino acids are optically active and chemical syntheses invariably result in racemic mixtures, enzymatic reactions provide the best synthetic route to N-labeled amino acids. Enzymatic pathways are characterized by speed, a high degree of chemical specificity under mild reaction conditions, and a product involving only the optical isomer of interest. It is not the purpose of this chapter to detail the many amino acid syntheses that have been described in the literature and recently reviewed exhaustively by Straatmann (53). 

The first example of a dynamic flux analysis was a study performed in the 1960s [269]. In the yeast Candida utilis, the authors determined metabolic fluxes via the amino acid synthesis network by applying a pulse with 15N-labeled ammonia and chasing the label with unlabeled ammonia. Differential equations were then used to calculate the isotope abundance of intermediates in these pathways, with unknown rate values fitted to experimental data. In this way, the authors could show that only glutamic acid and glutamine-amide receive their nitrogen atoms directly from ammonia, to then pass it on to the other amino acids. 

When soybean leaves and pine needles were exposed to ozone, there was an initial decrease in the levels of soluble sugars followed by a subsequent increase. Ozone exposure also caused a decrease in the activity of the glycolytic pathway and the decrease in the activity was reflected in a lowered rate of nitrate reduction. Amino acids and protein also accumulated in soybean leaves following exposure. Ozone increased the activities of enzymes involved in phenol metabolism (phenylalanine ammonia lyase and polyphenoloxidase). There was also an increase in the levels of total phenols. Leachates from fescue leaves exposed to ozone inhibited nodulation. 

Figure 18-2a provides an overview of the catabolic pathways of ammonia and amino groups in vertebrates. Amino acids derived from dietary protein are the source of most amino groups. Most amino acids are metabolized in the liver. Some of the ammonia generated in this... 

Some of the pathways of animal and bacterial metabolism of aromatic amino acids also are used in plants. However, quantitatively more important are the reactions of the phenylpropanoid pathway,173-1743 which is initiated by phenylalanine ammonia-lyase (Eq. 14-45).175 As is shown at the top of Fig. 25-8, the initial product from phenylalanine is trails-cinnam-ate. After hydroxylation to 4-hydroxycinnamate (p-coumarate) and conversion to a coenzyme A ester,1753 the resulting p-coumaryl-CoA is converted into mono-, di-, and trihydroxy derivatives including anthocyanins (Box 21-E) and other flavonoid compounds.176 The dihydroxy and trihydroxy methylated products are the starting materials for formation of lignins and for a large series of other plant products, many of which impart characteristic fragrances. Some of these are illustrated in Fig. 25-8. 

Free amino acids are further catabolized into several volatile flavor compounds. However, the pathways involved are not fully known. A detailed summary of the various studies on the role of the catabolism of amino acids in cheese flavor development was published by Curtin and McSweeney (2004). Two major pathways have been suggested (1) aminotransferase or lyase activity and (2) deamination or decarboxylation. Aminotransferase activity results in the formation of a-ketoacids and glutamic acid. The a-ketoacids are further degraded to flavor compounds such as hydroxy acids, aldehydes, and carboxylic acids. a-Ketoacids from methionine, branched-chain amino acids (leucine, isoleucine, and valine), or aromatic amino acids (phenylalanine, tyrosine, and tryptophan) serve as the precursors to volatile flavor compounds (Yvon and Rijnen, 2001). Volatile sulfur compounds are primarily formed from methionine. Methanethiol, which at low concentrations, contributes to the characteristic flavor of Cheddar cheese, is formed from the catabolism of methionine (Curtin and McSweeney, 2004 Weimer et al., 1999). Furthermore, bacterial lyases also metabolize methionine to a-ketobutyrate, methanethiol, and ammonia (Tanaka et al., 1985). On catabolism by aminotransferase, aromatic amino acids yield volatile flavor compounds such as benzalde-hyde, phenylacetate, phenylethanol, phenyllactate, etc. Deamination reactions also result in a-ketoacids and ammonia, which add to the flavor of... 

In addition to being incorporated into tissue proteins, amino acids, after losing their nitrogen atoms by deamination and/or transamination, may be catabolized to yield energy or to form glucose. Conversely, the nonessential amino acids may be synthesized from carbohydrate metabolism intermediates and ammonia or from essential amino acids. This section is devoted to the mechanisms of such metabolic processes and their interrelationships with carbohydrate and lipid metabolic pathways. 

One of the major waste products of glucose metabolism in peripheral tissues is the amino acid alanine and its use as a substrate for glucpnepgenesis requires the disposal of ammonia in the urea cycle In the following discussion we will illustrate how the flow of the label from alanine into products byproducts and intermediates of gluconeogenesis can be used to obtain qualitative and quantitative information about the relative activities of these pathways ... 

Treatment involves a low-protein diet (0.5-0.7 g/kg BW/day) with a sufficient supply of calories. Substitution of essential amino acids (in about the same quantity) is required. The administration of benzoate (0.1-0.25 g/kg BW/day), arginine hydrochloride (1 mmol/kg BW/day) or sodium phenylacetate (0.3-0.5 g/ kg BW/day) (phenylbutyrate tends to be more effective) facilitates nitrogen excretion via other metabolic pathways. (168-170) With an enhanced excretion of orotate or other metabolites of pyrimidine synthesis, the administration of allopurinol leads to an increase in the excretion of nitrogen via metabolites from pyrimidine synthesis. Ammonia and urea precursors are eliminated by haemodialysis. In individual cases, liver transplantation is indicated. (I7l)... 

L-Phenylalanine,which is derived via the shikimic acid pathway,is an important precursor for aromatic aroma components. This amino acid can be transformed into phe-nylpyruvate by transamination and by subsequent decarboxylation to 2-phenylacetyl-CoA in an analogous reaction as discussed for leucine and valine. 2-Phenylacetyl-CoA is converted into esters of a variety of alcohols or reduced to 2-phenylethanol and transformed into 2-phenyl-ethyl esters. The end products of phenylalanine catabolism are fumaric acid and acetoacetate which are further metabolized by the TCA-cycle. Phenylalanine ammonia lyase converts the amino acid into cinnamic acid, the key intermediate of phenylpropanoid metabolism. By a series of enzymes (cinnamate-4-hydroxylase, p-coumarate 3-hydroxylase, catechol O-methyltransferase and ferulate 5-hydroxylase) cinnamic acid is transformed into p-couma-ric-, caffeic-, ferulic-, 5-hydroxyferulic- and sinapic acids,which act as precursors for flavor components and are important intermediates in the biosynthesis of fla-vonoides, lignins, etc. Reduction of cinnamic acids to aldehydes and alcohols by cinnamoyl-CoA NADPH-oxido-reductase and cinnamoyl-alcohol-dehydrogenase form important flavor compounds such as cinnamic aldehyde, cin-namyl alcohol and esters. Further reduction of cinnamyl alcohols lead to propenyl- and allylphenols such as... 

Amino acids differ from carbohydrates and fats in that they contain nitrogen as part of their molecular structure. For the carbons in amino acids to enter into the energy generating metabolic pathways, the amino groups must first be removed so that they can be detoxified and excreted. The amino acid nitrogen is excreted predominantly as urea, but some is also excreted as free ammonia in order to buffer the urine. 

It is unknown when and how cooperation with amino acids, peptides, and proteins started to evolve into an RNA-protein world. However, there is an upper size limit of RNAs, which is due to a threshold error of RNA replication. The heart of the core necessary to launch the process of chemical evolution towards the RNA world must have consisted of a number of pathways for the synthesis of organic molecules from CO2, N2, and H2. Additional pathways for the synthesis of amino acids, ribose, purines, pyrimidines, coenzymes, and lipids likely combined into this core. Overall, the number of pathways required to generate nucleotides is relatively small. Pyruvate, ammonia, carbon dioxide, ATP, and glyoxalate suffice to synthesize virtually the compounds required for metabolic cycles. It seems likely that once the RNA world existed that thereafter an RNA-Peptide world developed. Details are on the following website http //www.sciencedirect.com - Cell, Volumel36, Issue 4, page 599, and a description follow below. 

In this chapter we examine maintenance of nitrogen balance. This includes pathways and controls of nitrogen excretion as urea or ammonia. The method the body has for transferring nitrogen from one carbon skeleton to another is described. The metabolism of several amino acids, their physiological role, and their metabolic products are considered. Specific tissue metabolism and tissue-tissue interactions related to several amino acids are discussed. 

Serine is one of the two hydroxyamino acids, the other being threonine. Serine has two major pathways of catabolism. The first, and apparently predominant, direction in many mammals is catalyzed by serine dehydratase, where water is removed between the alpha and beta carbons of serine. A rearrangement of the double bond forms an amino acid with spontaneous hydrolysis to form pyruvate and ammonia. Pyruvate then can be metabolized as discussed in previous chapters. This enzyme is primarily active in the liver, where the ammo-... 

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