Transformation of Energy to Maintain a Low Entropy State and Perform Work
A biological system in a state of energetic equilibrium is dead. The consumption of energy is required to drive and maintain the system far from equilibrium. That prerequisite is needed in order to allow the system to promptly change its configuration, according to the system's needs. In turn, the dissipative energy provides the thermodynamic driving force for the self-organization processes.
A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery. When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The energy is used to do work by the cell, usually by the released phosphate binding to another molecule, activating it. Since ATP plays a key role in the vital activities of all organisms, analysis of abiogenesis pathways for this compound becomes an important issue within the context of the problem of the origin of life.
Cell metabolism is impossible in the absence of nucleoside triphosphates because transcription and translation processes depend on them. ATP occupies a special place, because it was selected for the role of universal energy currency, that is, for coupling catabolic and anabolic reactions in the cell.
Modeling of Abiotic ATP Synthesis in the Context of Problems of Early Biosphere Evolution May 13, 2014
https://sci-hub.ren/10.1134/S0016702914130084
The pathway of adenosine triphosphate (ATP) synthesis in living organisms consists of two autonomous stages; The first stage is construction of an adenine heterocycle linked to a ribose-5-phosphate molecule to yield AMP, while the following stage is the attachment of phosphoryl residues to the nucleotide molecule by macroergic phosphoanhydride bonds. Involvement of the same set of precursor molecules in both de novo biosynthesis of AMP and abiogenesis of this nucleotide is a very important issue for the analysis of metabolic pathways.
Phosphoanhydride bonds in ATP and other nucleoside phosphates, as well as some other types of bonds with high hydrolysis energy, are referred to as high-energy (or macroergic) bonds in the biochemical literature. The presence of such bonds accounts for the involvement of ATP in intracellular transfer of chemical energy. However, strictly speaking, the energy balance between the molecules of the initial participants and products of the
reaction, rather than the energy of the bond itself, is relevant, since the breakage of any chemical bond is an endergonic process.
The complete biosynthetic pathway from ribose-5-phosphate to AMP consists of 13 consecutive “steps,” i.e., individual enzymatic reactions. None of the intermediate reaction products have an independent value in metabolism. Photophosphorylation during photosynthesis, oxidative phosphorylation coupled to cellular respiration, and substrate-level phosphorylation are the three principal ATP sources in living organisms.
Implementation of the first two mechanisms requires the presence of a lipid membrane incorporating the ATP synthase which catalyzes the attachment of a phosphoryl residue to ADP. The energy of the transmembrane electrochemical ion gradient (usually proton gradient) is the immediate source of energy for this process.
Abiotic formation of nucleosides in a chemical reaction of the bases with sugar molecules turned out to be quite problematic. The yield of purine nucleosides in such reactions was low, while pyrimidine nucleosides were not formed at all. The absence of a realistic mechanism for the specific synthesis of ribose under abiogenous conditions constituted an additional problem. The absence of a realistic mechanism for the specific synthesis of ribose under abiogenous conditions constituted an additional problem, arising both from the low specificity of the formose reaction (which is usually considered an abiotic pathway of sugar formation) and instability of the “desirable” configurations of carbohydrate molecules under the conditions of a model experiment. This complication has not been completely circumvented even today.
Spontaneous instantaneous emergence of multienzyme complexes that are capable of catalyzing a series of sequential reactions resulting in the conversion of a substrate into the target product is highly unlikely. The modern views on the development of such multistep metabolic pathways imply gradual replacement of abiotic synthesis by more efficient biocatalytic reactions in protobionts. The occurrence of identical reactions during the chemical (abiogenic) and enzymatic conversion of the precursor molecules into the product molecule is a prerequisite for such substitution, that is, a reaction catalyzed by the newly formed enzyme can only replace a chemical reaction involving completely analogous substrates and products. Therefore, the initial substrates for abiogenic synthesis and biosynthesis of the final product (specifically, AMP) must be the same in this case.
The structure of the biochemical pathways is completely determined by the genetic machinery of the cell. The existence of profound structural differences between abiotic and enzyme driven systems is an important issue.
Maintenance of the low entropy state of living systems requires the persistent infusion of energy (Morowitz 1968), first, to enable the system to maintain its complex organization and resist dissipation toward randomness. The second requirement for an input of energy derives from the fact that living processes perform work by growing and retracting, moving through the environment, emitting energy, counteracting concentration gradients, transforming materials, erecting and breaking down structures, and other endogenous activities. While energy transformations are characteristic of all dynamic physical and chemical systems, energy flow in non-living systems tends to result in greater disorder among all elements of the system. Energy released through different stages of the rock and water cycles, for instance, generally erodes land and distributes water to increase the entropy of the total collection of water and land toward equilibrium (lower mountains, more dispersed water and soil). The energy transformations of living systems, on the other hand, serve primarily to harvest and store the levels of free energy necessary for maintaining the highly ordered structure of the organism and performing the work that living cells carry out. The net effect for living systems, in contrast to that for non-living systems, is to maintain and often increase order at local levels and on microscopic scales.
There are two consequences to the way in which life transforms energy. One is that much of the energy is used to create and sustain a level of complexity that supports emergent functions that in their totality exceed the sum of the parts of the system. A mountain may be structurally complex but its role in the rock cycle is not dependent on the detailed organization of its individual rocks and sediments. The mountain is in essence a simple conglomerate of its component parts. The function of a living organism, on the other hand, depends critically on precisely how it is put together. Its component parts function in a coordinated manner, to generate a complex array of emergent properties, both structurally and functionally. The generation and maintenance of this complexity is one of the primary uses of the energy that living systems transform. A second consequence of biological energy transformations is to create one or more additional microenvironments within the natural environment. The Eh (redox-potential), pH, solute composition, and structural complexity of the living cell is maintained at levels different from the extracellular environment because of the autonomous functions carried out by the cell, but not in the abiotic environment surrounding the cell. New environments can also be created on a larger scale by colony forming organisms such as stromatolites and corals, which can alter the topography of large amounts of habitat.
Life-induced changes can occur even on a planetary scale, such as the change in atmospheric oxygen composition brought about by oxygen-producing microbes on Earth, beginning with the emergence of photosynthesis as a uniquely biological form of energy transformation (Knoll 1999; Schopf 1994). This innovation enabled life to become autotrophic (manufacturer of its own food from the simple and abundant molecule, CO2) on a global scale. Thus, not only is the transformation of energy a characteristic of life, but so is the ability of life to alter conditions in the natural environment. Note the dual requirement of living systems: to resist an increase in entropy, and to perform work. Both requirements are essential for the definition of a living entity. Any fabrication or machine is, for the time being, at a lower state of entropy than, and in disequilibrium with, its environment. Indeed, such objects are known to exist on other worlds: the lifeless Huygens lander rests on Titan, and the surfaces of Mars and the Moon are littered with man-made objects. When a cell or organism can no longer maintain steady disequilibrium conditions it approaches equilibrium with its environment and therefore dies
A biological system in a state of energetic equilibrium is dead. The consumption of energy is required to drive and maintain the system far from equilibrium. That prerequisite is needed in order to allow the system to promptly change its configuration, according to the system's needs. In turn, the dissipative energy provides the thermodynamic driving force for the self-organization processes.
A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery. When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The energy is used to do work by the cell, usually by the released phosphate binding to another molecule, activating it. Since ATP plays a key role in the vital activities of all organisms, analysis of abiogenesis pathways for this compound becomes an important issue within the context of the problem of the origin of life.
Cell metabolism is impossible in the absence of nucleoside triphosphates because transcription and translation processes depend on them. ATP occupies a special place, because it was selected for the role of universal energy currency, that is, for coupling catabolic and anabolic reactions in the cell.
Modeling of Abiotic ATP Synthesis in the Context of Problems of Early Biosphere Evolution May 13, 2014
https://sci-hub.ren/10.1134/S0016702914130084
The pathway of adenosine triphosphate (ATP) synthesis in living organisms consists of two autonomous stages; The first stage is construction of an adenine heterocycle linked to a ribose-5-phosphate molecule to yield AMP, while the following stage is the attachment of phosphoryl residues to the nucleotide molecule by macroergic phosphoanhydride bonds. Involvement of the same set of precursor molecules in both de novo biosynthesis of AMP and abiogenesis of this nucleotide is a very important issue for the analysis of metabolic pathways.
Phosphoanhydride bonds in ATP and other nucleoside phosphates, as well as some other types of bonds with high hydrolysis energy, are referred to as high-energy (or macroergic) bonds in the biochemical literature. The presence of such bonds accounts for the involvement of ATP in intracellular transfer of chemical energy. However, strictly speaking, the energy balance between the molecules of the initial participants and products of the
reaction, rather than the energy of the bond itself, is relevant, since the breakage of any chemical bond is an endergonic process.
The complete biosynthetic pathway from ribose-5-phosphate to AMP consists of 13 consecutive “steps,” i.e., individual enzymatic reactions. None of the intermediate reaction products have an independent value in metabolism. Photophosphorylation during photosynthesis, oxidative phosphorylation coupled to cellular respiration, and substrate-level phosphorylation are the three principal ATP sources in living organisms.
Implementation of the first two mechanisms requires the presence of a lipid membrane incorporating the ATP synthase which catalyzes the attachment of a phosphoryl residue to ADP. The energy of the transmembrane electrochemical ion gradient (usually proton gradient) is the immediate source of energy for this process.
Abiotic formation of nucleosides in a chemical reaction of the bases with sugar molecules turned out to be quite problematic. The yield of purine nucleosides in such reactions was low, while pyrimidine nucleosides were not formed at all. The absence of a realistic mechanism for the specific synthesis of ribose under abiogenous conditions constituted an additional problem. The absence of a realistic mechanism for the specific synthesis of ribose under abiogenous conditions constituted an additional problem, arising both from the low specificity of the formose reaction (which is usually considered an abiotic pathway of sugar formation) and instability of the “desirable” configurations of carbohydrate molecules under the conditions of a model experiment. This complication has not been completely circumvented even today.
Spontaneous instantaneous emergence of multienzyme complexes that are capable of catalyzing a series of sequential reactions resulting in the conversion of a substrate into the target product is highly unlikely. The modern views on the development of such multistep metabolic pathways imply gradual replacement of abiotic synthesis by more efficient biocatalytic reactions in protobionts. The occurrence of identical reactions during the chemical (abiogenic) and enzymatic conversion of the precursor molecules into the product molecule is a prerequisite for such substitution, that is, a reaction catalyzed by the newly formed enzyme can only replace a chemical reaction involving completely analogous substrates and products. Therefore, the initial substrates for abiogenic synthesis and biosynthesis of the final product (specifically, AMP) must be the same in this case.
The structure of the biochemical pathways is completely determined by the genetic machinery of the cell. The existence of profound structural differences between abiotic and enzyme driven systems is an important issue.
Maintenance of the low entropy state of living systems requires the persistent infusion of energy (Morowitz 1968), first, to enable the system to maintain its complex organization and resist dissipation toward randomness. The second requirement for an input of energy derives from the fact that living processes perform work by growing and retracting, moving through the environment, emitting energy, counteracting concentration gradients, transforming materials, erecting and breaking down structures, and other endogenous activities. While energy transformations are characteristic of all dynamic physical and chemical systems, energy flow in non-living systems tends to result in greater disorder among all elements of the system. Energy released through different stages of the rock and water cycles, for instance, generally erodes land and distributes water to increase the entropy of the total collection of water and land toward equilibrium (lower mountains, more dispersed water and soil). The energy transformations of living systems, on the other hand, serve primarily to harvest and store the levels of free energy necessary for maintaining the highly ordered structure of the organism and performing the work that living cells carry out. The net effect for living systems, in contrast to that for non-living systems, is to maintain and often increase order at local levels and on microscopic scales.
There are two consequences to the way in which life transforms energy. One is that much of the energy is used to create and sustain a level of complexity that supports emergent functions that in their totality exceed the sum of the parts of the system. A mountain may be structurally complex but its role in the rock cycle is not dependent on the detailed organization of its individual rocks and sediments. The mountain is in essence a simple conglomerate of its component parts. The function of a living organism, on the other hand, depends critically on precisely how it is put together. Its component parts function in a coordinated manner, to generate a complex array of emergent properties, both structurally and functionally. The generation and maintenance of this complexity is one of the primary uses of the energy that living systems transform. A second consequence of biological energy transformations is to create one or more additional microenvironments within the natural environment. The Eh (redox-potential), pH, solute composition, and structural complexity of the living cell is maintained at levels different from the extracellular environment because of the autonomous functions carried out by the cell, but not in the abiotic environment surrounding the cell. New environments can also be created on a larger scale by colony forming organisms such as stromatolites and corals, which can alter the topography of large amounts of habitat.
Life-induced changes can occur even on a planetary scale, such as the change in atmospheric oxygen composition brought about by oxygen-producing microbes on Earth, beginning with the emergence of photosynthesis as a uniquely biological form of energy transformation (Knoll 1999; Schopf 1994). This innovation enabled life to become autotrophic (manufacturer of its own food from the simple and abundant molecule, CO2) on a global scale. Thus, not only is the transformation of energy a characteristic of life, but so is the ability of life to alter conditions in the natural environment. Note the dual requirement of living systems: to resist an increase in entropy, and to perform work. Both requirements are essential for the definition of a living entity. Any fabrication or machine is, for the time being, at a lower state of entropy than, and in disequilibrium with, its environment. Indeed, such objects are known to exist on other worlds: the lifeless Huygens lander rests on Titan, and the surfaces of Mars and the Moon are littered with man-made objects. When a cell or organism can no longer maintain steady disequilibrium conditions it approaches equilibrium with its environment and therefore dies
Last edited by Otangelo on Sun Feb 07, 2021 9:58 am; edited 2 times in total
