Fundamentals of Biochemistry - A. A. Anisimov 1986

General Biochemical Characteristics of Living Organisms
Main Features of Metabolic Processes

The METABOLISM of a living Cell essentially consists of two streams of reactions: Catabolic and anabolic.

Catabolic pathways (Catabolism) are degradative, dissimilatory processes. These include various Cleavage reactions (Hydrolysis, phosphorolysis) and oxidations. Large organic molecules are broken down into simple substances with the simultaneous release of the free chemical energy they contain. This Energy is stored by the Organism in the form of ATP and A number of Other Compounds, and is subsequently used to fuel vital life processes (see Fig. 7.8).

Anabolic pathways (anabolism) are synthetic, assimilatory processes. In this case, complex Organic compounds are built from relatively simple molecules. These pathways often involve reduction reactions and proceed with the consumption of energy.

Due to the distinct localization of catabolic and anabolic Enzymes, these opposing metabolic processes occur simultaneously within The Cell. They are linked by central, or amphibolic, processes (Fig. 1.1), The Tricarboxylic Acid Cycle being a prime example (see Section 6.9.5).

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Fig. 1.1. The connection between catabolic and anabolic pathways: Ф_H stands for orthophosphoric acid, ФФ_Н stands for pyrophosphoric acid

The close relationship between anabolism and catabolism manifests itself on three levels.

1. At the carbon source level: the products of catabolism can serve as initial substrates for anabolic reactions.

2. At the energy level: catabolism generates ATP and other high-energy compounds, whereas anabolic processes consume them.

3. At the level of reduction equivalents: catabolic reactions are predominantly oxidative, while anabolic processes, conversely, consume reduction equivalents.

The interplay between anabolism and catabolism illustrates one of the fundamental laws of dialectical materialism—the unity and struggle of opposites as the internal source of development (in this case, of living matter).

The core biochemical reactions and their sequences are remarkably similar across all life forms. They presumably emerged at Cytology/cytology/16.html">Early stages of evolution and reached perfection by the time speciation began. Central Metabolic pathways are particularly conserved.

Metabolism carries out four specific Functions: 1. Extracting energy from the environment (either in the form of chemical energy from organic matter or as sunlight). 2. Converting exogenous substances into "building blocks," i.e., biopolymer precursors. 3. Assembling Proteins, Nucleic Acids, Lipids, Polysaccharides, and other cellular components from these building blocks. 4. Degrading "obsolete" Biomolecules that have already fulfilled their functions in the cell.

From a purely chemical standpoint, metabolism represents a vast assemblage of diverse reactions: oxidation, reduction, cleavage, molecular Condensation, intermolecular group transfer, etc. What is specific to the metabolism of a living organism is the spatial and temporal coordination of individual reactions. Protoplasm possesses a complex internal Organization and Structure. Specific biochemical processes are localized in certain Regions of the cell, Organelles, and membrane structures. For instance, Protein Synthesis occurs in Ribosomes, energy production in a readily usable form takes place in Mitochondria, the anaerobic phase of Respiration (Glycolysis) occurs in the Cytoplasm, and plant Photosynthesis happens in Chloroplasts, etc. Numerous membranes effectively partition the cell into compartments, allowing various biochemical reactions—often of opposing nature—to proceed simultaneously within the cell without interfering with one another due to this spatial Separation, known as compartmentalization. This exemplifies the spatial coordination of biochemical reactions.

Their temporal coordination is no less important. An orchestra's performance only yields a harmonious, pleasing combination of sounds when each musician plays their instrument at the precise moment prescribed by the score. Similarly, within a cell, individual biochemical reactions unfold in a strictly defined temporal sequence, often forming long chains of interrelated reactions. For example, carbohydrate glycolysis proceeds through 11 sequential reactions, with each preceding step creating the conditions necessary for the next. Crucially, this spatial and temporal coordination and harmony of biochemical reactions are directed toward a single goal: the self-renewal and self-preservation of the living system—the organism or cell. This is characteristic of any living organism, even a microscopic one.

At first glance, a question arises: does the foregoing contradict The Second Law of Thermodynamics, according to which spontaneous processes tend toward an increase in Entropy, i.e., disorder and randomness? No, living organisms also obey this law. They consume energy from the environment in the form of nutrients, partially utilize the Free energy of the latter, and return energy to the environment as heat and Other forms of energy of little or no use to life. As a result, environmental entropy increases, while living organisms create and maintain the order characteristic of them.

By absorbing nutrients from the external environment, living organisms acquire not only energy but also building Materials; the End products of Metabolism are excreted back into the environment. Systems in which the continuous intake and removal of substances, as well as the exchange of energy with the environment, take place are called open systems. Their characteristic feature is the absence of equilibrium with the external environment.

In a thermodynamic equilibrium state, all system parameters remain constant over time, and there are no stationary fluxes driven by external sources. The entropy of thermodynamic equilibrium is maximal, and free energy is zero. Unlike thermodynamic equilibrium, biosystems maintain a stationary state, in which The rate of mass and energy transfer from the environment into the system precisely matches the rate of transfer out of the system. A leading modern bioenergetics specialist, A. Lehninger, describes the living cell as "a non-equilibrium open system, a machine for extracting free energy from the external environment, resulting in an increase in environmental entropy." Understanding the living cell as an open system in a stationary state reflects the fundamental property of all living things—a continuous metabolism with the environment.

Viewing a living organism as an open stationary system neatly explains The phenomenon of Homeostasis—the constancy of the organism's internal environment and the stability of its biochemical parameters. For example, Blood glucose levels in a healthy person fluctuate within a fairly narrow range (around 5 mM), blood pH is consistently maintained at 7.40 ±0.05, and so on.

A living cell not only consumes substances but also excretes breakdown products, functioning as an open system. A complex, often branched system of intermediate reactions bridges the intake of nutrients and The excretion of waste products. If the rates of formation and breakdown of these intermediates are equal, a stationary state is established. However, the external availability of certain nutrients may suddenly increase or decrease, altering their rate of uptake into the cell. Various factors can likewise accelerate or slow down specific intermediate reactions or the rate of substance efflux from the cell, leading to significant shifts in the stationary concentrations of the system's components.

Nevertheless, living Cells and organisms possess numerous sensitive mechanisms that "detect" concentration shifts, compensate for them, and restore normal values. When the conditions of the stationary state change in an open system, processes are triggered to preserve the system's properties—a phenomenon known as the dynamic stabilization of the stationary state. In most cases, these mechanisms operate via feedback loops. For instance, when blood glucose levels drop (e.g., due to starvation), a specific Brain center is stimulated, activating a complex hormonal-enzymatic mechanism that breaks down stored Liver Glycogen into glucose, which is then released into the bloodstream. As soon as blood glucose returns to normal, the corresponding brain center ceases to be stimulated, and the glycogen breakdown mechanism shuts down. This is one of many Examples of a living organism functioning as a self-regulating system.

Thus, the relative constancy of the biochemical parameters of a living organism is not static and passive (like the stability of a granite cliff or a reinforced concrete bridge), but active and dynamic. Substances continuously enter the organism from the environment, undergo assimilation, and are converted into the organism's own components. Concurrently, older molecules gradually "age," catabolic and dissimilatory reactions take place, and breakdown products are eliminated. All these reactions are governed by the organism's genetic apparatus, ensuring that newly synthesized substances conform to hereditary traits.

Over short time intervals, an organism's external features may remain unchanged while its molecular constituents undergo substantial turnover. Using radioactive tracer techniques, it has been established, for example, that half of all proteins are replaced within 80 days, while Water is completely turned over in 30 days. The prominent British researcher and progressive public figure J. Bernal¹ wrote: "The molecules in our bodies and in every organism are in a state of continuous reconstruction, and atoms flow through them in an almost continuous stream. It is highly probable that none of us retains more than a few of the atoms with which we began our lives, and that even as adults we probably replace the greater part of our body material in the course of a few months." The great ancient Greek dialectician Heraclitus expressed this thought succinctly: "Our bodies flow like rivers; the matter in them is renewed like water in a stream." The continuous renewal of substances in a living organism manifests the dialectical law of negation: the new negates the old, then becomes old itself and is in turn negated by the newer.

A crucial feature of all biochemical reactions is their exceptionally high rate, driven by the presence of enzymes—biological catalysts. The same reactions outside the organism, mediated by chemical catalysts, proceed at rates orders of magnitude lower. As catalysts, enzymes are vastly superior to chemical ones.

¹ Bernal, J. Science in History. London, 1954 (or Moscow, 1956, p. 483).

Metabolic processes are also characterized by multistepness and coupling. Many cellular reactions typically proceed through a series of intermediate stages or steps. For instance, The oxidation of CARBOHYDRATES (such as Cellulose, starch, etc.) during combustion outside a living organism occurs in a single step—O₂ is added, immediately yielding the final oxidation products СO₂ and Н₂O.

In a living organism, the oxidation of carbohydrates during respiration to СO₂ and Н₂O proceeds step-by-step through more than 20 intermediate reactions. Individual reactions are very frequently coupled and interdependent. Thus, many biosynthetic reactions, being energy-consuming, are typically coupled with exergonic reactions that release free energy in an easily usable form. Coupling is also prominent in multi-stage chain processes, where the products of each preceding reaction serve as the starting compounds for the next.

In recent years, the literature has increasingly reported on the liquid-crystalline state of many crucial Biopolymers in aqueous environments (including proteins, nucleic acids, lipids, and polysaccharides), as well as the liquid-crystalline properties of cellular structures (such as Biomembranes). This new aspect of biochemical research provides a deeper and more comprehensive understanding of numerous metabolic processes and explains The behavior of various substances in living systems.

In the liquid-crystalline state, a substance simultaneously exhibits The properties of both a liquid (The ability to flow and form droplets) and a solid (strict ordering of the crystal structure). At the same time, liquid crystals possess unique properties inherent only to them (such as the ability to form single crystals in an external electromagnetic field and exceptionally high optical activity). Understanding biochemical phenomena relies heavily on the extreme sensitivity of liquid crystals to various external influences. Liquid crystals, characterized by one- or two-dimensional ordering, possess the capacity for self-organization, spontaneous formation of ordered structures, and their reproduction. This is of great interest for studying and explaining structure formation in living cells.

None of the aforementioned features of metabolic processes can claim to be the sole factor conferring the property of life upon a system. Life, as a qualitatively unique and most complex form of the motion of matter, can be understood and explained only by considering the totality of all features characteristic of this mode of existence of protein bodies, with their continuous metabolism with the surrounding environment.