Fundamentals of Biochemistry - A. A. Anisimov 1986

General biochemical characteristics of living organisms
Energy sources for living organisms, high-energy compounds

1.3.1. Energy and Carbon Sources for Living Organisms. All living organisms can be divided into two large groups depending on the chemical form in which they obtain carbon from the environment. Autotrophs (from Greek autos — self, trophe — Nutrition), or self-feeders, can use carbon dioxide (IV), CO₂, as their sole carbon source, from which they are capable of synthesizing all their carbon-containing compounds. Autotrophs include plants, photosynthetic Bacteria, and chemosynthetic bacteria. The process of METABOLISM/21.html">Chemosynthesis, i.e., the assimilation of CO₂ utilizing energy released during The oxidation of Inorganic Compounds, was first discovered in the late 19th century by S. N. Vinogradsky.

Heterotrophs (from Greek heteros — other, trophe — nutrition) must obtain carbon in the form of preformed, relatively complex Organic compounds (such as CARBOHYDRATES). This group includes animals and the majority of microorganisms. All heterotrophic organisms are capable of assimilating small amounts of CO₂. However, the carbon is fixed via carboxylation of carboxylic keto acids already present in The Cell; thus, a heterotrophic Organism requires preformed organic compounds.

Living organisms can also be classified according to their Energy Sources. For a large group of phototrophs, the direct energy resource is light. They utilize sunlight energy to form high-energy compounds that act as unique energy stores. This group includes higher plants, Algae, and photosynthetic bacteria.

Chemotrophs utilize oxidation-reduction reactions as their energy source. Chemotrophs include animals and the majority of microorganisms. This mode of energy acquisition is also characteristic of non-photosynthetic plant Cells. Both phototrophs and chemotrophs can, in turn, be subdivided into groups depending on the substances that serve as electron Donors in oxidation-reduction processes. In lithotrophs, these are inorganic compounds, whereas in organotrophs, they are organic compounds. Thus, depending on the energy sources and electron donors utilized, four MAIN TYPES OF organisms can be distinguished (Table 1.2).

Chemotrophic organisms are also grouped by the type of electron acceptors they use. When oxygen is used for oxidation, the energetics are of the aerobic, or respiratory, type. Under anaerobic Energy Metabolism, oxygen is replaced by a range of other substances acting as oxidants, i.e., alternative electron acceptors.

Many organisms can exist under both aerobic and anaerobic conditions. Under aerobic conditions, they use oxygen as an electron acceptor, carrying out Respiration. Under anaerobic conditions, their electron acceptors are organic compounds, resulting in Fermentation. Such organisms are termed facultative anaerobes. This group includes most organotrophic cells (Yeasts, cells of higher organisms). When oxygen is available in the environment, they prefer to use it. Anaerobes incapable of utilizing oxygen are called obligate anaerobes; oxygen is toxic to them. Since all free oxygen in Earth's atmosphere originated from Photosynthesis, it is evident that anaerobic energy metabolism is evolutionarily older than aerobic metabolism. Consequently, fermentation is a more ancient process than respiration.

Class="center">Table 1.2. Classification of organisms based on energy sources and electron donors utilized

1.3.2. High-Energy Compounds. High-energy compounds include ATP and substances capable of generating ATP in enzymatic group-transfer reactions without the involvement of oxidative processes. The molecules of such compounds contain bonds whose Hydrolysis releases a large amount of Free energy. These reactions occur under various conditions that affect the magnitude of free energy change. Therefore, biochemistry uses the term Standard Free Energy change — ∆G°. This refers to the free energy change under standard conditions: pressure of 1 atm¹, initial substrate concentrations of 1 M, and Temperature of 25°C. ∆G° at pH 7.0 is denoted as ∆G°'. The value of ∆G° is used to quantitatively characterize both metabolic pathways and individual Chemical Reactions; as in Thermodynamics, a minus sign indicates the release of energy, while a plus sign indicates its uptake. If the ∆G° of a given reaction is negative, the reaction can proceed spontaneously with the release of free energy — an exergonic reaction. If ∆G° is positive, the reaction proceeds with the absorption of energy (an endergonic reaction). Among metabolic reactions, entirely endergonic ones are known. They depend on an influx of free energy from an external source (e.g., light) or from other exergonic metabolic reactions (e.g., oxidation). A system of high-energy compounds Functions as a mediator between processes associated with ENERGY GENERATION AND utilization. The standard Free energy of hydrolysis for high-energy bonds exceeds —21 kJ⋅mol^-1 (Table 1.3); such bonds are denoted by the symbol ∽.

¹ According to the International System of Units (SI), pressure is measured in pascals:

1 atm = 101.3 kPa. In biology, it is standard practice to measure pressure in atmospheres.

Table 1.3. Standard free energy of hydrolysis for various compounds (in kJ⋅mol^-1)

High-energy compounds typically contain a high-energy phosphate group in their Structure and can transfer it to other substances. Numerous experiments have shown that the transferred moiety is not the phosphate group but the phosphoryl group Although the expression "Phosphate group transfer" is commonplace, it is more accurate to speak of phosphoryl group transfer. High-energy phosphoryl groups are denoted as ∽ Ф or ∽ Р.

Five main types of high-energy compounds are distinguished: ribonucleoside-5'-diphosphates and triphosphates (ATP, GTP, UTP, CTP, ADP, etc.), carboxyl phosphates (e.g., acetyl phosphate), acyl thiol esters (e.g., acetyl-CoA), phosphoramidate compounds (creatine phosphate), and enol phosphates (phosphoenolpyruvate).

At the core of cellular energy metabolism lies the adenylate system: ATP and its hydrolysis products — ADP, AMP, P_i, PP_i. It functions like a rechargeable battery that is charged with energy from various generators and supplies it to numerous machines and devices (which correspond to Organs, Tissues, and biochemical reactions in a living organism). In this regard, "battery charging" consists in the synthesis of ATP:

whereas "battery discharging" is accompanied by ATP hydrolysis:

where E₁ and E₂ are Enzymes catalyzing the respective reactions.

During ATP hydrolysis, the phosphoryl group is transferred to a hydroxide ion, with the standard free energy of hydrolysis at pH 7.0 being —34.5 kJ⋅mol^-1. The hydrolysis of the terminal phosphoryl group of ADP is characterized by a similar value. The Cleavage of the phosphoryl group from AMP is characterized by a lower value of —9.6 kJ⋅mol^-1. Consequently, only the last two phosphoanhydride bonds in the ATP molecule are high-energy bonds. However, it should be borne in mind that in specific reactions, The amount of energy released depends on temperature, pH, and the concentrations of substrates and magnesium ions.

The majority of adenylyl NUCLEOTIDES in the cell are present as magnesium complexes, MgATP^2- and MgADP^-. It is in this form that they participate in most enzymatic reactions, acting as donors of phosphoryl groups and energy. A certain amount of ATP and ADP exists in The Cell as free anions. In this state, ATP contains four ionizable OH groups, possessing a maximum charge of ATP^4-, while ADP contains three OH groups, with a charge of ADP^3-.

In the ATP molecule, the charges are located in close proximity, generating strong repulsion between them. This repulsion decreases when the terminal phosphoryl group is cleaved. The reaction products — HPO₄^2- and ADP^3- — cannot reassociate because their approach is hindered by the repulsion of like charges. This is precisely what accounts for the large negative value of the standard free energy of ATP hydrolysis.

It should also be kept in mind that in the terminal phosphoanhydride bond of the ATP molecule, the phosphorus and oxygen atoms are surrounded by A large number of electrons. They compete with each other for energetically most favorable orbitals. This competition prevents all electrons from occupying the lowest energy levels. In the products of ATP hydrolysis — ADP^3- and HPO₄^2- — electrons occupy lower energy levels, which stabilizes the products and renders the overall reaction irreversible. This factor also contributes to the large negative value of ∆G° for ATP hydrolysis.

In terms of its standard free energy of hydrolysis, ATP occupies an intermediate position between high-energy and low-energy phosphate compounds. This unique feature allows ATP to act as a universal mediator and carrier of phosphoryl groups and energy, transferring it from high-energy compounds (listed above ATP in Table 1.3) to low-energy compounds during the Synthesis of the latter (listed below ATP in Table 1.3).

Cells never execute a direct transfer of phosphoryl groups from high-energy compounds to low-energy ones; practically all such transfer reactions are mediated by the ATP—ADP system acting as an intermediary carrier. Other nucleoside 5'-triphosphates (UTP, GTP, CTP) are also high-energy compounds, yet they do not play the universal role of ATP, instead fulfilling specialized functions as energy donors: UTP supplies phosphoryl groups and energy for Polysaccharide synthesis, CTP for lipid synthesis, and GTP selectively accelerates peptide bond formation during Protein Biosynthesis.

The transfer of phosphoryl groups and energy from ATP to Other Compounds is catalyzed by enzymes commonly known by the short trivial name Kinases (e.g., hexokinase, pyruvatekinase; from the Greek kineo, meaning to move or transport). Consequently, a kinase implies an activator, since the phosphorylation of any compound increases its chemical reactivity and activates it.

All living organisms capture energy from external resources via energy-accumulation systems and convert it into the energy of high-energy compounds. Energy-accumulation systems fall into two types based on their energy-coupling mechanisms. The first type involves phosphorylation reactions that do not require insoluble membrane structures, known as substrate-level (or non-membrane) phosphorylation. Here, ATP is generated by transferring an active phosphoryl group from a substrate oxidation product to ADP, as seen in Glycolysis and fermentation. The second type comprises phosphorylation reactions occurring within coupling membranes, known as membrane phosphorylation. In this process, ATP is synthesized via the phosphorylation of ADP with inorganic phosphate, driven by the energy of the electrochemical proton gradient across the membrane. Examples include ATP formation during photosynthesis or the aerobic phase of respiration. Membrane phosphorylation takes place in The inner mitochondrial membrane, the thylakoid membranes of Chloroplasts, the chromatophores of photosynthetic bacteria, and the Cytoplasmic membranes of bacteria. These membranes, which house electron transport enzymes and coupled phosphorylation machinery, are referred to as coupling membranes.