FUNDAMENTALS OF MICROBIOLOGY - V. M. Samygin - 2015

CHAPTER 7. METABOLISM AND BASIC MECHANISMS OF METABOLIC PROCESSES AND ENERGY CONVERSION IN MICROBES

The totality of biochemical processes occurring within a Cell is called METABOLISM, which is sustained through Nutrition and Respiration. It comprises two main processes: Catabolism (or dissimilation) and anabolism (or assimilation).

During catabolism, complex Organic compounds are broken down or converted into simpler ones. Proteins may degrade into Peptides, Amino Acids, ammonia, and carbon dioxide; complex CARBOHYDRATES into di- and Monosaccharides; and Complex Lipids into glycerol and Fatty acids. Catabolic processes are accompanied by the release of a significant amount of energy, which is why they are also referred to as Energy Metabolism. Anabolism, on the other hand, involves The Biosynthesis of bacterial cell components from various organic and Inorganic Compounds. For instance, proteins are synthesized from amino acids, while carbohydrates are formed from CO₂ and other carbon compounds. Anabolism, or biosynthetic processes, requires an input of energy. Polymerization and Condensation processes—that is, The formation of large molecules from simpler compounds (such as the formation of Cellulose from glucose molecules)—play a crucial role in biosynthesis.

All the diverse and numerous processes in microbial Cells associated with metabolism, growth, and reproduction occur with the participation of Enzymes, which act as biological catalysts. Enzymes accelerate chemical reactions by millions of times. As catalysts, they possess A number of unique properties. First and foremost is their extraordinarily high catalytic activity: The addition of a minute amount of an enzyme (10^-7-10^-9 mol) can accelerate the catalyzed reaction more than 10¹⁰-fold. Another vital property is reaction Specificity. In some cases, enzymes exhibit absolute specificity, catalyzing the transformation of only a single substance. This specificity is also manifested with respect to reaction conditions.

Enzymes accelerate reactions at various, often very low (from a chemical perspective) temperatures: from 0°C in invertebrates and cold-blooded organisms of arctic seas, and 37–40°C in warm-blooded animals, up to 70°C in organisms inhabiting hot springs. Each enzyme has its own optimum pH at which its catalytic activity is at its maximum. A drastic change in the ambient pH can inactivate enzymes As a result of irreversible Denaturation (alteration of conformation, unwinding).

Enzymes may consist solely of a high-molecular-weight protein or possess a more complex Structure. In the latter case, enzymes consist of a protein part (apoenzyme) loosely bound to a cofactor (coenzyme), which Functions as an activator. The cofactor can be a low-molecular-weight inorganic substance (metal) or an organic compound. The non-protein portion of the enzyme (often various Vitamins) can be tightly bound to the apoenzyme, in which case it is termed a prosthetic group.

The Classification of Enzymes is based on the types of reactions they catalyze. Accordingly, enzymes are divided into 6 groups:

- oxidoreductases, which catalyze oxidation-reduction reactions (e.g., dehydrogenases);

- transferases, which catalyze The transfer of amino, phosphoryl, or methyl groups from one compound to another;

- Hydrolases, which cleave various compounds via Hydrolysis;

- lyases, which cleave various groups (CO₂, H₂O, SH₂, etc.) from substrates by non-hydrolytic means, catalyzing Cleavage reactions with the formation of double bonds or addition across double bonds;

- isomerases, which catalyze intramolecular rearrangements within a substrate, i.e., compound isomerization reactions;

- ligases (synthetases), which effect the joining of molecules together (forming C-C, C-O, C-N, and C-S bonds), i.e., accelerating synthetic reactions.

Microorganisms produce exoenzymes, which are secreted into the external environment and play a crucial role in preparing nutrients and facilitating their uptake into The Cell, damaging host Tissues, and performing a protective function. For example, hydrolases ensure the hydrolysis of Polysaccharides, proteins, and lipids, while the enzyme penicillinase inactivates the antibiotic penicillin, protecting Bacteria from destruction. Endoenzymes are tightly bound to the microbial cell and catalyze intracellular metabolic processes.

The majority of enzymes are associated with specific structures of the bacterial cell. For instance, oxidoreductases, which ensure the delivery of nutrients, are localized in the Cytoplasm. Enzymes associated with Cell Division are located in mesosomes and The Cell wall at the site of septum formation.

Enzymes that are synthesized by the cell continuously are called constitutive enzymes. Inducible (adaptive) enzymes are synthesized only in the presence of the corresponding substrate in the environment. For example, the ability of *Escherichia coli* to break down lactose manifests only when this sugar is present in the medium. Inducible enzymes predominate in bacteria, as they play the primary role in adaptation to changing environmental conditions.

To perform their functions, enzymes must possess high specificity and a high degree of substrate affinity. Enzyme Specificity refers to The ability to interact with only one or a few substrates that are closely related in chemical structure. Consequently, enzyme determination is a valuable diagnostic technique for identifying various species of microorganisms. Microbial enzymes are widely used in a number of industries: winemaking, brewing, baking, and the Production of organic acids such as acetic, citric, and oxalic acids.

Anabolic and catabolic reactions occurring within cells with the participation of enzymes are interrelated. The End products of these reactions are called metabolites. At certain stages of metabolism, intermediate Reactions Involving the conversion of one substance into another take place. These are termed amphibolic reactions, and their products, amphibolites, can be utilized in both anabolic and catabolic processes.

Initially, nutrients entering the cell are broken down into small fragments, after which they are converted during amphibolia into a series of organic acids and phosphate esters. These two pathways transition seamlessly into one another. From the resulting diverse low-molecular-weight compounds, monomers are synthesized—amino acids, purine and pyrimidine bases, phosphorylated sugars, organic acids, and other metabolites, which are the end products of biosynthetic chains. From these, polymeric macromolecules are built—Nucleic Acids, proteins, reserve substances, cell wall components, and the like, which comprise the cell. These two stages of cellular substance biosynthesis—the synthesis of monomers and polymers—constitute the synthetic branch of metabolism, or anabolism.

The vital activities of a microbial cell are coupled with Energy Expenditure and require its replenishment, which is accomplished through exothermic biochemical oxidation reactions of various organic and inorganic substances. These energy-metabolism processes (catabolism), which restore the cell's energy, are driven by respiration. In this process, the same compounds that are used to build Structural components of the cell—sugars, alcohols, organic acids, fats, etc.—are consumed.

The oxidation of substances can occur via different pathways:

- direct oxidation, when oxygen is added to a substance with the aid of oxidase enzymes. In this case, direct oxidation of an inorganic substrate—molecular hydrogen, carbon monoxide, or sulfur—by atmospheric oxygen takes place. Direct oxidation is observed in many Saprophytes;

- indirect oxidation, through the removal of two hydrogen atoms or two electrons from the substrate, i.e., via dehydrogenation. The hydrogen removed from the oxidized substrate-donor is transferred to another substance, the acceptor, which is thereby reduced. The process of hydrogen and electron transfer is accompanied by the release of energy, which is utilized by the cell and accumulated in high-energy compounds (predominantly ATP).

Enzymes that Abstract hydrogen atoms from a substrate are called dehydrogenases. In bacteria, several dehydrogenases participate in the transfer process. They are named after the hydrogen donor (e.g., Lactate dehydrogenase). They transfer hydrogen to one of two Coenzymes—NAD⁺ or NADP⁺. These coenzymes readily dissociate from the dehydrogenase and transfer the hydrogen to another acceptor.

The oxidation processes of organic substances occurring in living cells have specific features. First, living cells carry out oxidation in several stages, ultimately releasing the same amount of energy (heat) as would be produced by instant one-step oxidation. Second, not all The energy released during these reactions is dissipated as heat; part of it is stored in the form of ATP. To achieve this, an energy-releasing reaction is «coupled» with an energy-consuming reaction—specifically, the formation of ATP from ADP and inorganic phosphate. Third, organic substances are not always oxidized completely, i. e., down to carbon dioxide. Fourth, living cells are capable of oxidizing organic substances even in the absence of free oxygen (for instance, in anaerobic microorganisms).

The numerous Chemical Reactions taking place within a cell are not independent of one another. Most often, they are linked into complex sequences sharing common intermediates, such that the product of the first reaction serves as a substrate or reactant for the second reaction, and so on. Such sequences may consist of several reactions which, in turn, are interconnected to form complex networks of converging and diverging pathways. The Biological Significance of such systems is multifaceted. First, these sequential reaction systems ensure the directionality of biochemical processes. Second, the existence of such reaction sequences makes it possible to transfer chemical energy under isothermal conditions.

Living cells obtain energy from their external environment in various forms (such as radiant energy or energy derived from the oxidation of chemical compounds); however, they store and utilize it primarily in a single form—namely, as adenosine triphosphate (ATP). ATP serves as the primary carrier of chemical energy in the cells of All living organisms, acting as a universal energy currency (the «energy currency» of the cell).

ATP is a mononucleotide and, like all NUCLEOTIDES, consists of a nitrogenous base (adenine), a five-carbon sugar ribose, and three phosphoric acid residues. The hydrolysis of an ATP molecule, catalyzed by specialized enzymes known as ATPases, results in the cleavage of one phosphoric acid residue and the formation of ADP (adenosine diphosphate). This reaction is accompanied by the release of a significant amount of energy (approximately 40 kJ/mol or 10 kcal/mol):

АТФ —> АДФ + Ф + 40 кДж

Bonds whose hydrolysis is accompanied by the release of a substantial amount of energy are termed high-energy (or macroergic) bonds. The energy of high-energy bonds significantly exceeds the energy of any other chemical bonds.

An ATP molecule contains two high-energy bonds—one between the First and Second, and another between the second and third phosphoric acid residues. Consequently, the cleavage of two phosphoric acid residues (pyrophosphate) from ATP, resulting in the formation of AMP (adenosine monophosphate), is likewise accompanied by the release of energy. The energy liberated in this process is utilized by cells for the transport of sodium, potassium, or Calcium Ions across Introduction/36.html">Biological Membranes against their concentration gradient, as well as for various biosynthetic processes.

In addition to ATP, cells contain other nucleotides that differ in The structure of their nitrogenous base: GTP (guanosine triphosphate), UTP (uridine triphosphate), and CTP (cytidine triphosphate). These are also high-energy compounds whose energy is utilized, for instance, in Protein Synthesis (GTP), Polysaccharide synthesis (UTP), and phospholipid synthesis (CTP). All of these nucleotides are essential for RNA Synthesis.

Based on their pathways of Biological Oxidation, bacteria are classified into several groups:

- obligate aerobes: bacteria in which the ultimate hydrogen and electron acceptor is free molecular oxygen from the air;

- microaerophiles: aerobic bacteria whose GROWTH AND REPRODUCTION are optimal at a reduced partial pressure of oxygen. Examples include Leptospira, Actinomyces, etc. Some microaerophilic bacteria (such as Neisseria and Brucella) grow better in an environment with an elevated CO₂ concentration. They are referred to as «capnophilic» microorganisms;

- obligate anaerobes: bacteria that derive energy from the oxidation of organic or inorganic substances (such as hydrogen, sulfur, iron, and hydrogen sulfide) in the absence of free atmospheric oxygen, or via anaerobic Photosynthesis;

- facultative anaerobes: microorganisms capable of extracting energy from substrates through both aerobic and anaerobic pathways of biological oxidation, depending on the availability of oxygen.

The term Anaerobic respiration refers to those pathways of biological oxidation in which the ultimate electron acceptors are organic compounds (such as fumarate) or inorganic substances (such as nitrates, sulfates, sulfur, iron, and carbonates) rather than free atmospheric oxygen. Anaerobic respiration is coupled with the functioning of an Electron Transport Chain. All types of anaerobic respiration are classified According to the specific terminal electron acceptor utilized.

Energy-generating processes in which organic compounds serve simultaneously as both electron Donors and electron acceptors are called Fermentation. Oxygen does not participate in fermentation processes. Carbohydrates most commonly serve as the energy substrate. Hydrogen acceptors are intermediate breakdown products of the resulting organic compounds, which become reduced and accumulate in the medium. Hydrogen may also be partially released in free form. Depending on the predominant or most characteristic end products, fermentation is classified into alcoholic (carried out by Yeasts and mucoralean Fungi), lactic acid (caused by bacteria of the family Lactobacillaceae), butyric acid (caused by the genus Clostridium), and propionic acid (caused by the genus Propionibacterium) fermentation.

Regardless of the specific type of microorganisms, the core principle of energy metabolism remains the same: obtaining energy generated through biological oxidation under both aerobic and anaerobic conditions. Therefore, the term «biological oxidation» more accurately and correctly reflects the respiration process in microbes. Respiration involving oxygen is merely a special case of biological oxidation. During respiration, oxidative processes occur with the participation of molecular oxygen and the release of a large amount of energy. For example, the oxidation of 1 g-mol of glucose releases 688.5 kcal.

С₆Н₁₂О₆ + 6О₂ = 6СО₂ + 6Н₂О + Q

Anaerobic degradation of organic substances is also accompanied by energy release, albeit in significantly smaller quantities. For instance, the fermentation of 1 g-mol of glucose to ethanol under anaerobic conditions yields 31.2 kcal of energy.

С₆Н₁₂O₆ —> 2СН₃СН₂ОН + 2СO₂ + Q

It follows from this that the aerobic type of oxidation has a significant energetic advantage over the anaerobic type.

The bulk of the energy obtained by microorganisms during respiration is dissipated into the environment as heat, and only a fraction is utilized in vital metabolic processes. Aerobes utilize about 50% of this energy and lose the rest. Anaerobes utilize considerably less.