General Microbiology - Schlegel H. 1987

Basic mechanisms of metabolism and energy conversion
Biosynthesis of certain low-molecular-weight substances

Amino acid Biosynthesis. Most microorganisms and green plants are capable of synthesizing de novo all twenty Amino Acids required for protein building. The carbon skeletons of Amino acids are derived from Intermediary METABOLISM intermediates. Amino groups are introduced via direct amination or Transamination. The conversion of inorganic nitrogen into Organic compounds always proceeds via ammonia. Nitrates, nitrites, and molecular nitrogen are first reduced to ammonia (assimilation nitrate reduction) and only subsequently incorporated into organic compounds (Fig. 7.16, a, b, c).

Only a few amino acids are formed through the direct amination by free NH₄⁺ ions. Primary ammonia assimilation involves L-Glutamate dehydrogenase (Fig. 7.16, e) and L-Alanine Dehydrogenase (f), which catalyze the reductive amination of 2-oxo acids; ATP is not consumed in this process. The Synthesis of Glutamine from glutamate is catalyzed by Glutamine Synthetase (d). This enzyme exhibits a substantially higher affinity for ammonium ions (a lower K_M constant) than the aforementioned dehydrogenases, rendering it active even at extremely low NH₄⁺ concentrations; ATP is required for glutamine formation. Glutamate synthase (e) allows the amide group of glutamine to be transferred to 2-oxoglutarate. This pathway for incorporating ammonium nitrogen into organic compounds is presumably established and utilized by many Bacteria and plants when the ambient ammonium ion concentration is very low (below 1 mM/L), as well as during N₂ fixation.

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Fig. 7.16. Major pathways of nitrogen assimilation. Ammonium ions present in the nutrient medium are taken up directly by Cells (a). Nitrate ions via assimilatory nitrate reduction (b), and molecular nitrogen (N₂) via Nitrogen Fixation (c), are reduced to ammonium ions. Ammonium nitrogen is incorporated into organic compounds either with ATP expenditure via glutamine formation, or without ATP consumption via the direct reductive amination of 2-oxoglutarate or Pyruvate.

Most Other Amino Acids acquire their amino group from one of the primary amino acids via transamination. Glutamic acid is quantitatively predominant among the free amino acids in the Cytoplasm, accounting for over half of the total amino acid pool.

The biosynthetic pathways for all twenty Amino acids have been thoroughly elucidated in A number of microorganisms. Simple metabolic intermediates (pyruvate, 2-oxoglutarate, oxaloacetate or fumarate, erythrose-4-phosphate, ribose-5-phosphate, and ATP) serve as the starting Materials. In the synthesis of Most amino acids, the amino group is introduced only at The final stage via transamination. Certain amino acids are formed through a series of transformations of other amino acids, bypassing the transamination step. Amino acids can be categorized into groups based on their biosynthetic routes (Fig. 7.17). The synthesis of various amino acids involves a varying number of enzyme-catalyzed steps. Notably, amino acids that must be obtained ready-made by humans are synthesized via particularly lengthy pathways.

The relatively prompt elucidation of biosynthetic pathways for Amino Acids and Other Compounds was facilitated by The Use of auxotrophic mutants of Fungi and, notably, bacteria. Auxotrophy in many mutants stems from the loss of ability to produce a specific enzyme involved in biosynthesis. Consequently, the growth of such a mutant requires the end product of the biosynthetic pathway that has been blocked due to the enzymatic defect. These mutants possess another valuable trait: they can grow not only in the presence of the end product of the blocked pathway, but also in the presence of intermediates generated between the blocked step and the end product. Concurrently, the substrate for the blocked reaction often accumulates; for instance, if enzyme b is missing, intermediate product B is excreted into the medium:

Fig. 7.17. The twenty amino acids essential for Protein Synthesis are derived from simple compounds—products of intermediary metabolism.

Consequently, certain mutants with blocks at different steps of the same synthetic pathway can supply each other with the missing substances. A mutant with a later block (lacking enzyme d) provides the necessary intermediate to the cells of another mutant with an earlier block (lacking enzyme b). Such experiments have enabled researchers to arrange specific mutants into a sequence where each preceding mutant Supports the growth of all subsequent ones. Through the analysis of accumulating intermediates, the Isolation and Purification of Enzymes, and other Methods, many biosynthetic pathways have successfully been charted.

Nucleotide biosynthesis. Purine and pyrimidine NUCLEOTIDES serve as the structural building blocks for Nucleic Acids; they are also constituents of numerous Coenzymes and participate in the activation and transfer of amino acids, sugars, Cell wall components, and Lipids. The synthesis of all purine nucleotides proceeds via a common pathway that diverges only at the inosine acid stage, subsequently yielding either adenylic or guanylic acid. The pyrimidine nucleotide biosynthetic pathway is similarly shared, branching at the uridylic acid level.

Ribose-5-phosphate serves as the starting compound for the pentose moiety of nucleotides. It can be synthesized via two routes: 1) the oxidative pathway, from glucose-6-phosphate via the oxidative Pentose Phosphate Pathway, and 2) the non-oxidative pathway, from fructose-6-phosphate and glyceraldehyde-3-phosphate through transaldolase- and transketolase-catalyzed reactions (Section 7.2.2). Ribose-5-phosphate is utilized for purine and pyrimidine nucleotide synthesis in its high-energy form as phosphoribosyl pyrophosphate. The reduction of ribose to deoxyribose occurs at the ribonucleotide level and can proceed via various mechanisms.

Fatty acid and Lipid Biosynthesis. Fats and lipids in general function both as essential components of plasma Membranes and Cell Walls, and as reserve storage materials. Bacterial lipids are predominantly composed of long-chain Fatty acids (C₁₄–C₁₈), both saturated and monounsaturated. Polyunsaturated Fatty Acids and Steroids appear to be absent, and triglycerides are likewise uncommon. Complex Lipids are of major significance. These are glycerol esters in which two hydroxyl groups are esterified with fatty acids¹, while the third is linked to a phosphoric acid residue or a sugar. The phosphoric acid residue, in turn, is bonded to Serine, ethanolamine, or glycerol. Such lipids have been identified in numerous bacteria; this group of compounds includes, specifically, phosphatidylinositol, phosphatidylglycerol, and phosphatidylethanolamine.

¹ Lipids containing fatty acids have not been found in archaea. — Transl. note.

Long-chain Fatty acids are synthesized through the Condensation and reduction of acetate units. To enhance reactivity, the methyl group of acetyl-CoA is initially carboxylated in a biotin-dependent reaction to yield malonyl-CoA:

In subsequent condensation steps, the carboxyl group is released again as CO₂. Fatty acid synthesis is carried out by a multienzyme complex According to the equation