Biochemistry and Molecular Biology - Belyasova N.A. 2002

Metabolism. Processes Leading to Energy Storage
Catabolic Pathways
Carbohydrate Catabolism

CARBOHYDRATES serve as the primary sources of carbon and energy—and consequently as nutritional substrates—for the vast majority of organisms (excluding plants). Among them, Cellulose, its derivatives, and starch are the most widespread on the planet. Besides these Polysaccharides, Glycogen, inulin, Chitin, xylans, pectic substances, and others are of great importance. Most of these polysaccharides are broken down by specific Enzymes into Monosaccharides, with hexoses and pentoses predominating. Frequently, the Cleavage of poly- and Oligosaccharides is mediated by phosphorylases, resulting in phosphorylated reaction products.

A distinctive feature of sugars is the presence of an oxygen atom attached to every carbon atom, which allows chemical attack on these substrates at virtually any point within the molecule. Furthermore, monosaccharides—and primarily their phosphorylated forms—are capable of isomerization: carbonyl groups and hydrogen atoms can readily shift to adjacent positions or alter their spatial configuration within the molecule through the action of isomerases. Thus, a transition becomes possible from any hexose or pentose to any other isomeric sugar. For this reason, despite the diversity and complexity of Carbohydrate METABOLISM, several distinct pathways of their transformation—in particular, Catabolism—can be identified, each with pronounced distinguishing characteristics. These pathways include Glycolysis, the Pentose Phosphate Pathways, and the Entner–Doudoroff pathway.

A general characteristic of monosaccharide catabolism is the obligatory initial activation stage of free monoses, which occurs via phosphorylation. This process yields sugar phosphates capable of entering subsequent biochemical transformations.

Glycolysis. This pathway of sugar catabolism is also known as the fructose-1,6-bisphosphate pathway (named after its key intermediate) or the Embden–Meyerhof–Parnas pathway (after its discoverers).

Glycolysis is considered the most universal and energetically efficient pathway of hexose catabolism. Discovered in 1897 by the Buchner brothers, the term originates from two Greek roots: glicos meaning sugar, and lysis meaning to dissolve. During glycolysis, hexoses undergo a multi-step conversion into Pyruvate that does not require molecular oxygen, accompanied by the synthesis of ATP and reduction equivalents.

The reactions of The Glycolytic Pathway take place in the Cytosol. All intermediate compounds occur in phosphorylated forms. Energy is conserved via substrate-level phosphorylation.

The conversion of glucose to pyruvate (Fig. 9.3) requires ten enzymes and proceeds through the following stages: preparation for hexose chain cleavage, chain cleavage yielding glyceraldehyde-3-phosphate, and the First and Second substrate-level phosphorylations.

The process begins with the phosphorylation of glucose (molecular activation) involving ATP (as a phosphate group donor) and the enzyme hexokinase. The resulting glucose-6-phosphate is subsequently isomerized by glucose phosphate isomerase into fructose-6-phosphate, which undergoes a second phosphorylation utilizing ATP to yield fructose-1,6-bisphosphate.

Fructose-1,6-bisphosphate is a key intermediate in the glycolytic pathway: this specific compound distinguishes glycolysis from other sugar catabolism pathways. Furthermore, the overall rate of glycolysis is regulated at the level of this metabolite. The activity of The enzyme catalyzing this reaction (Phosphofructokinase) is inhibited by high concentrations of ATP, which lowers the affinity of phosphofructokinase for its substrate, fructose-6-phosphate. Additionally, phosphofructokinase is inhibited by citrate, an early intermediate of The Tricarboxylic Acid Cycle. Activation of phosphofructokinase is also well documented: it is stimulated by ADP and inorganic phosphate. Thus, phosphofructokinase is most active under conditions where cellular ATP is low (ADP is high) and building blocks are scarce.

In the next step of glycolysis, fructose bisphosphate is cleaved by fructose bisphosphate aldolase into two triose phosphates: dihydroxyacetone phosphate and glyceraldehyde-3-phosphate. These products are isomers and readily interconvert under the action of triose phosphate isomerase. However, the equilibrium of this reaction is shifted toward the Formation of glyceraldehyde-3-phosphate because it is continuously consumed in downstream reactions. Glyceraldehyde-3-phosphate serves as the substrate for the first substrate-level phosphorylation.

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Fig. 9.3. The glycolytic pathway of hexose catabolism. Zigzag lines denote high-energy chemical bonds

Unlike the preceding steps, energy is released and conserved in the form of ATP during the remaining stages of glycolysis. One such reaction is The oxidation of glyceraldehyde-3-phosphate. The enzyme catalyzing this reaction (glyceraldehyde-3-phosphate dehydrogenase) utilizes NAD as a coenzyme and is characterized by a high content of sulfhydryl (SH) groups. Oxidation begins with the binding of glyceraldehyde-3-phosphate to an SH group of the enzyme, forming an enzyme–substrate complex. Next, the enzyme catalyzes The transfer of hydrogen from the substrate to NAD⁺, and the reduced coenzyme dissociates. This dehydrogenation reaction serves as the oxidative step that supplies energy, generating an energy-rich enzyme–acyl complex (a thioester). This is followed by phosphorolysis—the transfer of the glyceraldehyde-3-phosphate residue, along with the high-energy bond, to phosphoric acid, resulting in The formation of 1,3-bisphosphoglycerate and the regenerated enzyme. 1,3-Bisphosphoglycerate is a mixed anhydride of phosphoric and carboxylic acids and possesses a high Phosphate group transfer potential. The energy-rich phosphate group is transferred from 1,3-bisphosphoglycerate to ADP via phosphoglycerate kinase, yielding 3-phosphoglycerate and ATP. This marks the first substrate-level phosphorylation in glycolysis.

The final stage of glycolysis—the second substrate-level phosphorylation—begins with an intramolecular rearrangement in which 3-phosphoglycerate is isomerized to 2-phosphoglycerate by phosphoglycerate mutase. 2-Phosphoglycerate is then dehydrated to phosphoenolpyruvate by enolase. This reaction yields a compound characterized by a high phosphate group transfer potential; thus, the elimination of a Water molecule from 2-phosphoglycerate is accompanied by an intramolecular redistribution of energy, converting the phosphate bond at carbon atom 2 from a low-energy to a high-energy bond. The final reaction of glycolysis is catalyzed by pyruvate kinase, which transfers the phosphate group to a molecule of ADP, producing the pathway's end product: pyruvate.

The glycolytic breakdown of a single glucose molecule leads to the formation of 4 ATP molecules (two per each glyceraldehyde-3-phosphate molecule), of which 2 are consumed during the Formation of fructose bisphosphate. Consequently, a net yield of 2 ATP molecules is conserved. Furthermore, 2 molecules of NADH are generated per glucose molecule oxidized (via the oxidation of 2 glyceraldehyde-3-phosphate molecules). The overall balance of glycolysis is expressed as follows:

1 С₆Н₁₂О₆ → 2 С₃Н₄О₃ + 2 АТР + 2NADH

The glycolytic process serves The Cell for the storage of energy and reduction equivalents, while also supplying building blocks in the form of a three-carbon, partially oxidized compound—pyruvic acid—along with certain intermediates, notably glyceraldehyde-3-phosphate.

Pentose phosphate pathways. These pathways of sugar catabolism are quite diverse. Depending on environmental conditions and the Organism's species, the outcome of these processes can yield various substances. The operation of The pentose phosphate pathways in reverse is utilized by Cells during CO₂ fixation. Their principal distinguishing feature is the formation of five-carbon sugars as intermediates, as well as the sequential cleavage of single carbon atoms from a six-carbon phosphorylated sugar, which are released into the medium as CO₂.

The pentose phosphate pathways (also known as the Warburg–Dickens–Horecker shunt, the hexose monophosphate shunt, or the phosphogluconate pathway) are utilized by organisms less frequently than glycolysis and are most commonly found in bacterial cells.

Following the conventional activation reaction of glucose via phosphorylation, the resulting glucose-6-phosphate undergoes dehydrogenation. This reaction is catalyzed by glucose-6-phosphate dehydrogenase, with its coenzyme NADP⁺ acting as the electron acceptor for reduction equivalents, yielding 6-phosphoglucono-δ-lactone (Fig. 9.4). This compound undergoes ring-opening Hydrolysis mediated by gluconolactonase, and the resulting 6-phosphogluconic acid undergoes a second dehydrogenation (catalyzed by phosphogluconate dehydrogenase), which is immediately followed by decarboxylation to form ribulose-5-phosphate. Ribulose-5-phosphate is subsequently isomerized into two five-carbon sugars: xylulose-5-phosphate and ribose-5-phosphate (Fig. 9.4).

The next stage of the pentose phosphate pathways involves multiple intermolecular rearrangements and isomerizations of intermediates derived from ribulose-5-phosphate. These reactions are directed toward the synthesis of a six-carbon compound (glucose-6-phosphate), which can once again undergo oxidation and decarboxylation. As a result, 6 molecules of ribulose-5-phosphate yield 5 molecules of glucose-6-phosphate (Fig. 9.5).

The sugar rearrangement system involves two enzymes—transketolase and transaldolase—which catalyze the transfer of two- and three-carbon fragments by cleaving C–C bonds at two positions: adjacent to the carbonyl carbon (α) and at the carbon atom adjacent to the carbonyl-adjacent carbon (β) (in Fig. 9.5, the sites of bond cleavage are indicated by dashed lines).

During the Complete oxidation of glucose via the pentose phosphate pathways, the glyceraldehyde-3-phosphate molecule produced at the final stage is isomerized by triose phosphate isomerase into dihydroxyacetone phosphate. This intermediate then participates in an aldol Condensation with a second molecule of glyceraldehyde-3-phosphate to form fructose bisphosphate. This reaction is the reverse of the fructose bisphosphate cleavage that occurs in glycolysis (Fig. 9.3), with the enzyme fructose bisphosphate aldolase catalyzing both the forward and reverse transformations. The fructose-1,6-bisphosphate molecule is dephosphorylated to yield fructose-6-phosphate (via a phosphatase enzyme), which in turn is isomerized into glucose-6-phosphate, thereby returning to the initial dehydrogenation stage.

Fig. 9.4. Formation and isomerization of ribulose-5-phosphate during the pentose phosphate pathways. Since 6 molecules of CO₂ can be generated from a single hexose molecule, for convenience in balance calculations, the process is presented based on 6 molecules of glucose-6-phosphate

Thus, the complete oxidation of a single glucose molecule via the Pentose Phosphate Pathway consumes 1 molecule of ATP and yields 6 molecules of CO₂ and 12 molecules of NADPH. Consequently, The primary function of the pentose phosphate pathway is to supply the cell with NADPH, which is utilized in biosynthetic processes.

Complete oxidation of glucose does not necessarily occur during the pentose phosphate pathway. In such cases, glyceraldehyde-3-phosphate undergoes alternative transformations, such as Substrate-Level Phosphorylation Reactions catalyzed by glycolytic enzymes.

The pentose phosphate pathway is of great importance for biosynthetic processes, as it generates intermediates that serve as precursors for numerous substances. Specifically, erythrose-4-phosphate is used by Bacteria and plants to synthesize aromatic Amino Acids. Ribose-5-phosphate acts as a substrate for the synthesis of nitrogenous bases and Certain amino acids.

Fig. 9.5. Transformations of ribulose-5-phosphate isomers during the pentose phosphate pathway upon complete oxidation of glucose (per 6 molecules of glucose-6-phosphate). Explanations are provided in the text

The Entner-Doudoroff Pathway (2-keto-3-deoxy-6-phosphogluconate pathway). This process represents another mechanism of hexose catabolism and is predominantly found in microorganisms. This pathway is of particular significance for the degradation of gluconate. The Initial Stages of glucose-6-phosphate conversion are identical to those of the pentose phosphate pathway, up to the formation of 6-phosphogluconic acid. Subsequently, however, 6-phosphogluconate undergoes dehydration rather than oxidation, mediated by the enzyme 6-phosphogluconate dehydratase. This yields the key intermediate of this pathway, 2-keto-3-deoxy-6-phosphogluconate. The dehydration stage proceeds via the formation of an intermediate compound (enol), which tautomerizes into 2-keto-3-deoxy-6-phosphogluconate (Fig. 9.6).

Next, aldolase catalyzes the cleavage of this key intermediate into pyruvate and glyceraldehyde-3-phosphate. The latter can enter the glycolytic pathway and undergo further transformations.

Fig. 9.6. The Entner-Doudoroff pathway and associated processes

As indicated by the Stoichiometry of the Entner-Doudoroff pathway, this process is energetically less efficient than glycolysis: only 1 molecule of ATP is conserved per glucose molecule (of the two synthesized, one is consumed in the phosphorylation of glucose).

An Overview of the major Catabolic pathways demonstrates that The breakdown of fuel molecules via incomplete oxidation leads to the formation of two key metabolites: pyruvic acid and acetyl-CoA. These compounds can either serve as building blocks in biosynthetic pathways or undergo further transformations to ensure cellular energy storage. Since this section focuses on energy-yielding processes, it should be noted that the metabolic fate of pyruvate and acetyl-CoA depends primarily on the availability of molecular oxygen within the cell, as well as its enzymatic Complement. For instance, in the cells of anaerobic microorganisms and Tissues of higher organisms, pyruvate and acetyl-CoA can undergo various Types of Fermentation that complete the catabolic degradation of substrates. In aerobic and facultatively anaerobic cells, in the presence of molecular oxygen, pyruvate can undergo oxidative decarboxylation, and the resulting acetyl-CoA enters the tricarboxylic acid cycle, where it is completely oxidized to CO₂ and H₂O, while the generated reducing equivalents enter the Respiratory Chain. These processes will be discussed in the subsequent chapters.