Fundamentals of Biochemistry - A. A. Anisimov 1986

Biological Oxidation and Bioenergetics
Pathways of Energy Utilization in the Cell

7.4.1. Energetics of Biosynthetic Reactions. Any manifestation of vital activity—such as movement, Respiration, reproduction, growth, and responses to stimuli—is associated with energy transformations. ATP serves as the direct energy source for the majority of endergonic processes. The potential chemical energy of ATP is utilized for the synthesis of Proteins, Fatty acids, Nucleic Acids, Steroids, and A number of Other Compounds. Biosynthetic reactions are coupled with the Cleavage of ATP. Activation typically occurs at the expense of The energy released upon the removal of a phosphoryl group from ATP. However, for the potential of the latter to be harnessed in driving an endergonic metabolic process, a coupling mechanism must exist; otherwise, ATP Hydrolysis within The Cell would simply result in the dissipation of heat.

Part of the coupling mechanism involves a nucleophilic Substitution at the Phosphorus Atom, followed by a substitution at the carbon atom. This process begins with The transfer of a portion of the ATP molecule to a nucleophilic compound. Nucleophilic attack can occur at the terminal phosphorus atom (γ), resulting in the displacement of ADP, whereby the phosphoester group is transferred and ADP is released; or at the middle phosphorus atom (β), leading to the transfer of the adenylyl group and the release of inorganic pyrophosphate; in rare cases, the pyrophosphate group is transferred and AMP is released. In very rare instances, substitution takes place at the inner (α) phosphorus atom, yielding adenosine and tripolyphosphate or its hydrolysis products. When Water acts as the nucleophile in substitution reactions, hydrolysis proceeds to completion, releasing all of ATP's constituent groups (phosphate, adenylyl, or pyrophosphate). This is accompanied by a significant decrease in Free energy, rendering these stages virtually irreversible.

A wide variety of BIOSYNTHETIC PROCESSES IN living organisms typically begin with the interaction between ATP and the precursor compound for Biosynthesis. Upon acquiring the energy of one of ATP's high-energy bonds, this compound becomes activated and capable of entering into biosynthetic pathways. It is through this mechanism, for example, that Amino Acids are activated during METABOLISM/35.html">Protein Biosynthesis, initially forming aminoacyl adenylates. The biosynthesis of Polysaccharides similarly begins with The formation of nucleoside diphosphate sugars with the participation of ATP or UTP. In addition to UTP, other equivalent nucleoside triphosphates—GTP and CTP—function in place of ATP in certain biosynthetic pathways.

7.4.2. Muscle contraction and Other Contractile Structures. In living organisms, the movement of Organs, Tissues, individual Cells and their Organelles, protoplasm, flagella, cilia, etc., occurs continuously. As early as 1939, V. A. Engelhardt and M. N. Lyubimova discovered that Myosin, the contractile protein of muscle, possesses ATPase activity. During the hydrolysis of ATP, the energy released drives its contraction and conformational changes—allowing the muscle to perform work. Thus, the contractile protein of muscle extracts the energy required for its work directly from ATP molecules. Later, these same authors demonstrated that elevated ATPase activity is also observed in a number of other instances where movement occurs in living organisms (such as the movement of the leaves of the sensitive plant, Mimosa pudica).

At present, there is no doubt that various movements in living organisms (muscle contraction, the beating of flagella and cilia in Protozoa, sperm motility, leaf movements in certain plants, and cytoplasmic streaming) are driven by the energy of ATP, which is extracted by the contractile proteins themselves that execute the movement. This phenomenon clearly illustrates the well-known tenet of dialectical materialism regarding Life as a form of the movement of matter that is qualitatively higher than Physical and Chemical forms, yet incorporates them in a 'sublated' (aufgehoben) form.

Muscle contraction is a biological phenomenon, yet it encompasses both chemical processes (ATP hydrolysis) and physical ones (the utilization of energy for movement). The molecules involved in movement are typically assembled into contractile structures. In some cases, apart from generating movement, they provide structural strength and shape to cells, forming the so-called Cytoskeleton.

In Eukaryotic cells, contractile structures are subdivided into microtubules and microfilaments (from Latin filamentum — thread). The former consist primarily of the protein tubulin, while the latter contain large amounts of the protein Actin. A characteristic feature of muscle cells is the presence of contractile myofibrils, which are bundles of protein molecules organized in a specific manner.

Under an Electron microscope, Two Types of filaments—thick and thin—can be observed within myofibrils. The backbone of thin filaments is the protein actin, which can exist in two forms: a monomeric, globular form (G-actin) and a polymeric, filamentous form (F-actin). G-actin consists of 375 amino acid residues, and its polymerization into F-actin obligatorily consumes ATP to form a double-stranded helix. In the Cytoplasm of other cells, actin exists as an equilibrium mixture of F- and G-forms. Actin has undergone remarkably little change throughout evolution. The second major muscle protein is myosin. Bundles of its myosin molecules form the thick filaments of myofibrils. Myosin is a very large protein (up to 160 nm in length) composed of two heavy chains folded into α-helices (M = 212,000) and two to four light chains (M = 20,000). Toward its C-terminus, the myosin molecule forms a fibrillar 'tail,' while its N-terminus features a 'HEAD' region where the short chains are located.

Associated with actin filaments are the regulatory Muscle Proteins Tropomyosin and troponin. Tropomyosin has the shape of a long α-Helix that coils around the actin filament. Troponin binds to tropomyosin to form a complex termed native tropomyosin.

Many aspects of the Molecular Mechanism of muscle contraction remain insufficiently clear, but in broad terms, the process is envisioned as follows. Actin and myosin form an Actomyosin complex in the muscle—actomyosin—in which actin filaments bind to the myosin heads. The ATPase activity of myosin increases significantly within this complex. The signal for muscle contraction is an electrical impulse from a motor nerve, which triggers the release of Ca²⁺ cations and their efflux from specialized membrane vesicles—'cisterns'—into the sarcoplasm (the intracellular fluid of Muscles). Calcium activates the hydrolysis of ATP by myosin. The Free energy of ATP hydrolysis is stored in the form of Conformational Changes in the myosin heads, which cause the actin filament to slide by approximately 10 nm relative to the myosin filament. Concurrently, the cross-bridges between the myosin heads and the actin filaments detach; these cross-bridges are stable only in the absence of ATP. Meanwhile, other cross-bridges formed by the myosin heads attach to the actin filaments, preventing them from slipping back into their original position. Upon the rephosphorylation of ADP to ATP, the process repeats. As cross-bridges continuously form and break, the sliding of actin filaments continues; they are pulled further between the myosin filaments and may even overlap (Fig. 7.7), ultimately leading to the shortening and contraction of the muscle. This mechanism, though still hypothetical in certain details, has been termed the 'rowing model' because the repetitive, transient action of cross-bridges in actomyosin resembles the strokes of a multi-oared boat propelling it forward. Muscle relaxation occurs after the impulse from the motor nerve ceases. During this phase, Ca²⁺ ions are pumped back and sequestered within the cisternae by a Ca²⁺-dependent ATPase (see Section 9.2).

Although ATP serves as the immediate energy source for a working muscle, its intracellular concentration is low. The reserve high-energy compounds in mammalian muscles are represented by creatine phosphate, and in invertebrates, by Arginine phosphate. The high-energy bonds of these compounds allow for the regeneration of ATP from ADP within the muscle.

In addition to muscle contraction, actin—as the primary component of microfilaments—participates in stabilizing and altering cell shape, mitosis, cell motility (such as amoeboid movement), cytoplasmic streaming, organelle transport, phagocytosis, secretory activity, membrane protein distribution, and other processes. In plants, Chloroplasts are not isolated from one another but are, as it were, strung along actin filaments, which drive their movement.

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Fig. 7.7. Model of muscle contraction:

I — resting state, II — moderate contraction, III — maximum contraction; A — thin filaments (actin), M — thick filaments (myosin)

Actomyosin structures responsible for the pulsating movement of protoplasm have been discovered in myxomycetes. Actin-like filaments have been found in the sieve tubes of plants, and it has been suggested that they play a role in the translocation of assimilates. Eukaryotic microfilaments are long, thread-like structures 5–7 nm in thickness. They typically form bundles, clusters, or mesh-like structures. Whereas actin filament bundles form a stable Structure in muscle fibers and intestinal microvilli, in most other instances their shape and intracellular localization change depending on the developmental phase and other factors. Actin is present in virtually all eukaryotic cells, but is particularly abundant (accounting for up to 20–30% of total protein) in actively moving cells (amoebae, macrophages, platelets), where it predominates among cell extract proteins. In most non-muscle cells, as in muscle fibers, the energy transducer possessing ATPase activity is myosin, which is structurally similar to muscle myosin.

Alongside actin-containing microfilaments, tubulin-containing microtubules are found in all eukaryotic cells. They participate in the following processes: 1) the beating of flagella and cilia; 2) chromosome movement during Mitosis and Meiosis; 3) Intracellular Transport of granules and vesicles; 4) movement of melanin granules in melanocytes; 5) substance transport along the axons and dendrites of Neurons; and 6) communication between the cell interior and the external environment.

In plants, microtubules have been found, for instance, in Molds and in the chloroplasts of Crassulaceae. Among prokaryotes, microtubular structures are present in spirochetes. The Morphology of microtubules is quite standard: they are long, hollow cylinders with an outer diameter of about 24 nm and an inner diameter of 15 nm. Their major protein, tubulin, is remarkably similar in Primary Structure and conformation across Representatives of the most distant taxonomic groups, indicating that it has undergone very little change during evolution. Dimeric globular subunits of tubulin (M = 115,000) polymerize to form long protofibrils, which make up the microtubules. While tubulin functionally corresponds to actin, The Role of the ATP energy transducer (i.e., the function of myosin) in microtubules is fulfilled by the protein dynein.

Unlike eukaryotes, Bacteria lack a wide variety of motility types and move using a uniform structure—the flagellum. The body of the flagellum, the filament, is a hollow cylinder formed by two rows of identical subunits consisting of a single protein: flagellin. The energy source for bacterial flagellar motility is not ATP (with rare exceptions), but rather the electrochemical proton gradient — ΔμH⁺.

7.4.3. The Role of the Transmembrane Electrochemical Potential in Bioenergetics. According to the concept developed by V. P. Skulachev, the transmembrane electrochemical potential of hydrogen ions (ΔμH⁺) occupies a paramount position in The system of energy transformations (Fig. 7.8). The energy derived from external sources (light or respiratory substrates) is converted into ΔμH⁺, which can then be utilized for a variety of processes occurring within coupling membranes. Thus, according to V. P. Skulachev, ΔμH⁺ represents a second (alongside ATP) convertible form of energy within the cell. It powers chemical work, most notably the synthesis of high-energy phosphates—ATP and inorganic pyrophosphate.

Fig. 7.8. The role of ATP and the electrochemical proton gradient in cellular energetics

The transmembrane potential is also consumed by the cell for a number of other endergonic processes. As noted earlier, bacterial cells in some instances utilize it directly to perform mechanical work (flagellar motion). Osmotic work—the accumulation of cations and anions in Mitochondria against a concentration gradient—is likewise driven by the electrochemical potential. Along with ATP, the electrochemical potential of hydrogen ions is expended on thermogenesis (heat production).