Metabolism

Metabolism is the sum total of chemical changes that occur in living organisms and which are fundamental to life. All prokaryotic and eukaryotic cells are metabolically active. The sole exception is viruses, but even viruses require a metabolically active host for their replication.

Metabolism involves the use of compounds. Nutrients from the environment are used in two ways by microorganisms. They can be the building blocks of various components of the microorganism (assimilation or anabolism). Or, nutrients can be degraded to yield energy (dissimilation or catabolism). Some so-called amphibolic biochemical pathways can serve both purposes. The continual processes of breakdown and re-synthesis are in a balance that is referred to as turnover. Metabolism is an open system. That is, there are constant inputs and outputs. A chain of metabolic reactions is said to be in a steady state when the concentration of all intermediates remains constant, despite the net flow of material through the system. That means the concentration of intermediates remains constant, while a product is formed at the expense of the substrate.

Primary metabolism comprises those metabolic processes that are basically similar in all living cells and are necessary for cellular maintenance and survival. They include the fundamental processes of growth (e.g., the synthesis of biopolymers and the macromolecular structures of cells and organelles), energy production (glycolysis and the tricarboxylic acid cycle) and the turnover of cell constituents. Secondary metabolism refers to the production of substances, such as bile pigments from porphyrins in humans, which only occur in certain eukaryotic tissues and are distinct from the primary metabolic pathways.

Metabolic control processes that occur inside cells include regulation of gene expression and metabolic feedback or feed-forward processes. The triggers of differential gene expression may be chemical, physical (e.g., bacterial cell density), or environmental (e.g., light). Differential gene expression is responsible for the regulation, at the molecular level, of differentiation and development, as well as the maintenance of numerous cellular "house-keeping" reactions, which are essential for the day-to-day functioning of a microorganism. In many metabolic pathways, the metabolites (substances produced or consumed by metabolism) themselves can act directly as signals in the control of their own breakdown and synthesis. Feedback control can be negative or positive. Negative feedback results in the inhibition by an end product, of the activity or synthesis of an enzyme or several enzymes in a reaction chain. The inhibition of the synthesis of enzymes is called enzyme repression. Inhibition of the activity of an enzyme by an end product is an allosteric effect and this type of feedback control is well known in many metabolic pathways (e.g., lactose operon). In positive feedback, an endproduct activates an enzyme responsible for its own production.

Many reactions in metabolism are cyclic. A metabolic cycle is a catalytic series of reactions, in which the product of one bimolecular (involving two molecules) reaction is regenerated as follows: A + B → C + A. Thus, A acts catalytically and is required only in small amounts and A can be regarded as carrier of B. The catalytic function of A and other members of the metabolic cycle ensure economic conversion of B to C. B is the substrate of the metabolic cycle and C is the product. If intermediates are withdrawn from the metabolic cycle, e.g., for biosynthesis, the stationary concentrations of the metabolic cycle intermediates must be maintained by synthesis. Replenishment of depleted metabolic cycle intermediates is called anaplerosis. Anaplerosis may be served by a single reaction, which converts a common metabolite into an intermediate of the metabolic cycle. An example of this is pyruvate to oxaloacetate reaction in the tricarboxylic acid cycle. Alternatively, it may involve a metabolic sequence of reactions, i.e., an anaplerotic sequence. An example of this is the glycerate pathway which provides phosphoenol pyruvate for anaplerosis of the tricarboxylic acid cycle.

Prokaryotes exhibit a great diversity of metabolic options, even in a single organism. For example, Escherichia coli can produce energy by respiration or fermentation. Respiration can be under aerobic conditions (e.g., using O2 as the final electron acceptor) or anaerobically (e.g., using something other than oxygen as the final electron acceptor). Compounds like lactose or glucose can be used as the only source of carbon. Other bacteria have other metabolic capabilities including the use of sunlight for energy.

Some of these mechanisms are also utilized by eukaryotic cells. In addition, prokaryotes have a number of energy-generating mechanisms that do not exist in eukaryotic cells. Prokaryotic fermentation can be uniquely done via the phosphoketolase and Enter-Doudoroff pathways. Anaerobic respiration is unique to prokaryotes, as is the use of inorganic compounds as energy sources or as carbon sources during bacterial photosynthesis. Archaebacteria possess metabolic pathways that use H2 as the energy source with the production of methane, and a nonphotosynthetic metabolism that can convert light energy into chemical energy.

In bacteria, metabolic processes are coupled to the synthesis of adenosine triphosphate (ATP), the principle fuel source of the cell, through a series of membrane-bound proteins that constituent the electron transport system. The movement of protons from the inside to the outside of the membrane during the operation of the electron transport system can be used to drive many processes in a bacterium, such as the movement of the flagella used to power the bacterium along, and the synthesis of ATP in the process called oxidative phosphorylation.

The fermentative metabolism that is unique to some bacteria is evolutionarily ancient. This is consistent with the early appearance of bacteria on Earth, relative to eukaryotic organisms. But bacteria can also ferment sugars in the same way that brewing yeast (i.e., Saccharomyces cerevesiae ferment sugars to produce ethanol and carbon dioxide. This fermentation, via the so-called Embden Myerhoff pathway, can lead to different ends products in bacteria, such as lactic acid (e.g., Lactobacillus), a mixture of acids (Enterobacteriacaeae, butanediol (e.g., Klebsiella, and propionic acid (e.g., Propionibacterium).

See also Bacterial growth and division; Biochemistry