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Metabolism and Catalysis

Life is a system that is not in equilibrium, as we pointed out in its attributes earlier; life is a very dynamic chemical system: parts are being moved, synthesized, broken apart, energy is stored and released. We call all of that action metabolism, or simply put: all chemical reactions that occur within a living system. Most metabolic reactions (or reaction networks, or cycles) relate to the extraction of energy and raw materials from the environment. Others lead to the synthesize of new molecules required for cellular functions, or help in the transport or disassembly of molecules.

Metabolism cannot occur in a system which is in thermodynamic equilibrium (life attribute # 2 from an earlier section), because equilibrium states have no transfer of energy or chemicals. Therefore, energy storage is essential for such a self-sustaining system. Earth life has evolved two generic ways to accomplish this:

The ATP (adenosine triphosphate) molecule is a small molecule that resembles the nucleotide unit of RNA (see figure below and the earlier section on nucletoids).

Attached to the ribose sugar unit is a phosphate group. In ATP this group consists of three phosphate groups connected by high-energy phosphate bonds (one Phosphorous-Oxygen bond between the outer and the middle group, and one P-O bond between the middle and the inner group). Removing the outer phosphate group breaks one of these bonds and releases substantial amount of energy (31 kJ/mole of phosphate). The remaining molecule with only 2 phosphate groups is called ADP (adenosine diphosphate).

The formation of ATP from ADP is a convenient way to store energy. In the example of photosynthesis, the energy from sunlight is captured and through a chain of chemical reactions generates ATP. The phosphate bond that is formed in the conversion of ADP to ATP is the result of a dehydration reaction: H and OH are removed from the molecule and together form water. It takes energy to remove the water and bond the phosphate to the ADP molecule. The generated bond "stores" that energy. When that bond is later broken, the energy can be harnessed. This energy is then spent on other metabolic processes, such as protein synthesis, membrane repair, or DNA replication. All life on Earth shares this core metabolism, one aspect of the unity of Earth biochemistry which is quite remarkable.

The proper functioning of the complex networks and cycles of metabolic reactions require control of the rates, often speeding rates up, sometimes the opposite. This is accomplished by catalysts - chemical entities that speed up the rate of a chemical reaction, but survive the reaction unchanged. Proteins that play the role of catalysts in living systems are known as enzymes.

Autocatalysis, when the product of a reaction actually catalyzes its own production, is extremely rare in nature. However, life does autocatalysis all the time, when enzymes catalyze their own synthesis in a chemical sequence of steps, involving DNA, RNA, and ribosomes. This is essential to remember when exploring pathways to the emergence of life and the first cells, and before any enzymes had evolved

Солнечная система и ее тайны