Biochemistry and Molecular Biology - Belyasova N.A. 2002

Metabolism. Energy-Requiring Processes
Metabolism of Nitrogenous Compounds
Amino Acid Biosynthesis

The biosynthetic pathways of proteinogenic (protein-forming) Amino Acids are quite complex and multifaceted—the same amino acid can be synthesized via different routes—and may vary significantly across different organisms. Nevertheless, these processes share a considerable number of common regularities, and for convenience, all 20 Proteinogenic Amino Acids can be divided into five biosynthetic families. Amino acids belonging to the same family typically share common precursors generated in the TCA cycle, Glycolysis, or the Pentose Phosphate Pathway.

Non-Essential Amino Acids are synthesized through relatively simple reactions, whereas the biosynthetic pathways of essential amino acids are highly complex. For white rats, essential amino acids include valine, isoleucine, leucine, Threonine, Methionine, Lysine, phenylalanine, Tryptophan, Histidine, and Arginine. Eight of these Ten amino acids are also not synthesized by The Human Body; whether histidine and arginine are essential for humans remains a subject of debate.

Biosynthesis of the glutamate family of amino acids. This family includes glutamate, glutamine, Proline, and arginine. The first Two amino acids are formed from a-ketoglutarate, with their amino groups originating from ammonia molecules (Fig. 16.3). Proline is synthesized from glutamate through a four-step reaction: the g-carboxyl group of glutamate reacts with ATP to form an acyl phosphate. The latter is reduced to an aldehyde in the presence of NADPH, and subsequently converted into a cyclic compound—pyrroline-carboxylate—via spontaneous dehydration. This product is then reduced by NADPH to form proline (Fig. 16.4).

The synthesis of arginine (Fig. 16.5) also originates from glutamate, which is first acetylated at its amino group and then subjected to the aforementioned phosphorylation and semialdehyde formation reactions. However, unlike the proline biosynthetic pathway, the g-semialdehyde of N-acetylglutamate does not cyclize; instead, it undergoes Transamination involving glutamate (Glu). This reaction yields a-ketoglutarate (KG) and N-acetylornithine. The latter is deacetylated to form Ornithine. Ornithine is subsequently converted into arginine through a series of reactions comprising The Urea Cycle.

Biosynthesis of the aspartate family of amino acids. The aspartate family includes aspartate, asparagine, lysine, threonine, isoleucine, and methionine. The latter Five amino acids are synthesized from aspartate, which in turn is produced from oxaloacetate—an intermediate of the TCA cycle—via a transamination reaction where glutamate acts as the amino group donor (Fig. 16.6).

Aspartate serves as the precursor for asparagine synthesis. In many Bacteria, direct amination of aspartate can take place via an ATP-dependent reaction mediated by asparagine synthetase (16.2).

Class="center">Aspartate + NH₃ + ATP → Asparagine + AMP + PP_i     (16.2)

Fig. 16.4. Biosynthesis of proline (details in text)

Fig. 16.5. Biosynthesis of arginine (details in text)

In mammalian Cells, a different reaction takes place (Fig. 16.6), in which glutamine serves as the amino group donor during asparagine formation.

Fig. 16.6. Biosynthesis of aspartate and asparagine (details in text)

Lysine, methionine, and threonine are synthesized from aspartate derivatives (Fig. 16.7), whereas isoleucine is synthesized from threonine.

In bacterial and plant cells, lysine is synthesized via an aldol Condensation of aspartate semialdehyde and Pyruvate, followed by reduction, addition of a succinate residue, transamination involving glutamate, intramolecular rearrangement, and decarboxylation. Fungal cells utilize an alternative pathway for lysine biosynthesis starting from a-ketoglutarate and acetyl-CoA.

The carbon Skeleton of methionine is derived from homoserine, the sulfur atom originates from Cysteine, and N-methyltetrahydrofolic acid serves as the methyl group donor.

Threonine provides four of the six carbon atoms in the isoleucine molecule. In the first step of synthesis, threonine is deaminated to form 2-ketobutyrate, which then reacts with pyruvate, undergoes structural rearrangements, and participates in a transamination reaction with glutamate acting as the amino group donor.

Biosynthesis of the pyruvate family of amino acids. Alanine, valine, and leucine are synthesized from pyruvate.

Alanine is formed via a transamination reaction in which glutamate acts as the amino group donor (Fig. 16.8).

The synthesis of valine and leucine shares several common steps and begins with The formation of acetolactate. This metabolite is formed from two pyruvate molecules: one is decarboxylated, and the resulting active acetate is transferred to the second molecule (Fig. 16.8). This reaction is catalyzed by acetolactate synthase in the presence of thiamine pyrophosphate. 2-Acetolactate is reduced to dihydroxyisovalerate, accompanied by the migration of a methyl group. Dihydroxyisovalerate is then dehydrated to 2-ketoisovalerate. This product can either be converted into valine through a Transamination reaction involving glutamate, or condense with acetyl-CoA to yield leucine through a series of reactions (isomerization, reduction, decarboxylation, transamination). Glutamate also serves as the amino group donor in the formation of leucine (Fig. 16.8).

Fig. 16.7. Biosynthesis of threonine. Outline of the biosynthetic pathways for methionine, lysine, and isoleucine (dashed arrows)

Biosynthesis of the Serine family of amino acids. This family includes serine, cysteine, and Glycine. The precursor for these amino acids is 3-phosphoglycerate, an intermediate of glycolysis.

Fig. 16.8. Biosynthesis of alanine, valine, and leucine. Glu — glutamate; KG — a-ketoglutarate; the dashed arrow denotes multiple steps of synthesis (explained in the text)

3-Phosphoglycerate is oxidized to 3-phosphohydroxypyruvate, then aminated with the participation of glutamate to yield 3-phosphoserine, and dephosphorylated to serine (Fig. 16.9). An alternative pathway also exists, in which the phosphate group is cleaved prior to the oxidation reaction:

3-Phosphoglycerate → Glycerate → Hydroxypyruvate → Serine

Serine serves as a precursor for the synthesis of glycine and cysteine. During glycine formation, the ß-carbon atom of the serine side chain is accepted by a one-carbon carrier—the cofactor tetrahydrofolate—in a reaction catalyzed by serine hydroxymethyltransferase (Fig. 16.9). Another pathway for glycine synthesis also exists: from CO₂, NH₄⁺, and methylenetetrahydrofolate, catalyzed by glycine synthase.

Fig. 16.9. Biosynthesis of serine, cysteine, and glycine. The dashed arrow indicates the multistep conversion of methionine to homocysteine; the dashed line in the cystathionine molecule represents the bond attacked by cystathionine-y-lyase

The conversion of serine into cysteine involves the replacement of the side-chain oxygen atom with a sulfur atom, provided by methionine as the sulfur donor. First, methionine undergoes a series of ATP-dependent reactions to form its activated form (S-adenosylmethionine), loses its methyl group at the sulfur atom, and is converted into homocysteine:

L-methionine + ATP + Methyl group acceptor →

→ Homocysteine + Adenosine + PP_i + P_i + Methylated acceptor

Homocysteine then reacts with serine to form cystathionine, which is cleaved by cystathionine-y-lyase into cysteine and a-ketobutyrate (Fig. 16.9).

In some microorganisms, an alternative pathway for cysteine synthesis exists, in which hydrogen sulfide serves as the sulfur donor. In this case, serine is first acetylated by acetyl-CoA (catalyzed by serine transacetylase), and then acetylserine reacts with hydrogen sulfide in a reaction catalyzed by O-acetylserine sulfhydrylase:

Acetylserine + H₂S → Cysteine + Acetate

Biosynthesis of the pentose Amino acid family. The amino acids belonging to this family (histidine, tryptophan, phenylalanine, and Tyrosine) are synthesized with the participation of ribose-5-phosphate, a five-carbon intermediate of The pentose phosphate pathway, which is why they are grouped into the pentose family. Figure 16.10 illustrates the pathways of ribose-5-phosphate conversion that lead to the Formation of the compounds from which these amino acids are synthesized.

The biosynthesis of histidine is quite complex and proceeds with the participation of 5-phosphoribosyl-1-pyrophosphate, ATP, and glutamine. Figure 16.10 shows the Water/144.html">Origin of the carbon and nitrogen atoms within the histidine molecule: one nitrogen atom of the imidazole ring originates from the amide group of glutamine, another nitrogen atom and one of the ring carbon atoms originate from ATP, while the remaining carbon atoms derive from 5-phosphoribosyl-1-pyrophosphate.

The biosynthesis of aromatic amino acids begins with the condensation of erythrose-4-phosphate with phosphoenolpyruvate. The resulting seven-carbon compound (7-phospho-2-keto-3-deoxy-D-arabinoheptulosonate) is dephosphorylated, cyclized, dehydrated, and reduced with NADPH to yield shikimic acid. Shikimic acid undergoes another condensation with phosphoenolpyruvate and, following the elimination of a phosphate group, is converted into Chorismic acid (Fig. 16.11). Chorismate serves as the primary precursor for the tryptophan biosynthesis pathway, which is depicted in Fig. 16.11.

Chorismic acid is also used for the synthesis of phenylalanine; that is, at this branch point, the biosynthetic Pathways of the two essential aromatic amino acids—tryptophan and phenylalanine—diverge (hence the name chorismate, derived from the Greek word meaning "fork").

Phenylalanine is produced via three sequential reactions: the isomerization of chorismate to prephenate, the dehydration and decarboxylation of prephenate to phenylpyruvate, and the transamination of phenylpyruvate with glutamate.

The non-essential amino acid tyrosine can be synthesized from phenylalanine via hydroxylation catalyzed by phenylalanine-4-monooxygenase, as well as from prephenic acid following its decarboxylation and amination.

Fig. 16.10. General scheme of histidine, tryptophan, phenylalanine, and tyrosine biosynthesis. Dashed arrows indicate multistep processes

Fig. 16.11. Tryptophan biosynthesis pathway. Dashed arrows indicate multistep processes

GENERAL PATTERNS OF Amino acid biosynthesis. An Overview of the biosynthetic pathways of proteinogenic amino acids reveals several key regularities in these processes: 1) the carbon skeletons of amino acids originate from glycolytic intermediates (3-phosphoglycerate, phosphoenolpyruvate, pyruvate), pentose phosphate pathway intermediates (ribose-5-phosphate and erythrose-4-phosphate), and TCA cycle intermediates (oxaloacetate and a-ketoglutarate); 2) glutamate serves as the amino group donor for most proteinogenic amino acids, and less frequently glutamine; reactions in which an amino group is transferred to a keto acid are termed "transamination reactions"; 3) the biosynthesis of many amino acids occurs in "families" that share common precursors, and many amino acids themselves act as substrates for the synthesis of others; 4) many stages of amino acid biosynthesis require an energy input and are accompanied by ATP Hydrolysis (e.g., synthesis of histidine, proline, methionine, asparagine, glutamine, and arginine); furthermore, the energy of activated Molecules Participating in the synthesis is utilized, and intermediates that would otherwise provide energy storage for The Cell are diverted from catabolic and amphibolic processes; 5) many steps of amino acid biosynthesis require reducing equivalents (NADH and NADPH) that could otherwise be oxidized in the Respiratory Chain to yield metabolic energy.

Thus, amino acid biosynthesis is energetically costly for the cell. It is therefore not surprising that this process in every Organism (cell) is subject to highly complex regulation (Chapter 19). On the one hand, this regulation is dictated by the complexity and branching of the biosynthetic pathways of proteinogenic amino acids themselves, while on the other hand, it must ensure strict conservation of cellular resources (energy, reducing equivalents, and building blocks). Consequently, it is entirely logical that in the presence of exogenous amino acids, microbial cells, for example, do not perform de novo synthesis, but instead utilize preformed environmental sources.