Metabolism in Microbes

Metabolism is the sum of biological process that builds or breaks molecules to provide cells with the capacity to acquire and utilize energy. Metabolism is a series of reactions in living cells aimed at producing energy from food to run cellular functions, producing building blocks for cellular growth, and excreting wastes. In metabolic pathways, the products of one step are the reactants for the next step and many pathways are cyclic in that the final product created is the initial reactant.

Eukaryotic microorganisms (yeast, algae, protozoa, helminths), or microbes, typically require organic materials to produce energy. The metabolic pathways of microscopic eukaryotes are very similar to those of larger multicellular plants and animals. Prokaryotic microbes can metabolize a wide range of organic and also inorganic molecules in order to thrive in various environments. Many microbial metabolic pathways are amphibolic—they are functional in both catabolic (breaking down molecules to produce energy) and anabolic (building complex compounds that require energy) directions. In amphibolic pathways, a sequence of chemical reactions constructs or synthesizes molecules from smaller units, and the pathway can operate in reverse and through a sequence of chemical reactions that break down or decompose molecules into smaller units while generating energy.

Catabolism is a sequence of chemical reactions that breaks down or decomposes molecules into smaller units while generating energy. The production of ATP and energization of electron carriers such as NAD⁺ require catabolism. Some examples include glycolysis, fermentation, and cellular respiration.

Anabolism is a sequence of chemical reactions that constructs or synthesizes molecules from smaller units. Anabolic reactions need energy to occur. These processes typically use the molecule adenosine triphosphate (ATP) as the biological energy source. Some examples of anabolic reactions are protein synthesis, DNA replication and repair, and the Calvin cycle—the production of glucose from carbon dioxide.

Catabolism and anabolism are complementary pathways. For example, cellular respiration is a catabolic process that breaks down glucose (C₆H₁₂O₆) into carbon dioxide, water, and cellular energy in the form of ATP. Photosynthesis is the complementary pathway to respiration, using the energy from the sun to build glucose from water (H₂O) and carbon dioxide (CO₂).

The spontaneous occurrence of metabolic reactions is typically too slow to be useful for an organism because of the activation energy required. Activation energy is the minimum energy needed for a chemical reaction to initiate. A catalyst is a substance that causes the rate of a chemical reaction to increase. It does this by lowering the activation energy required for the reaction to take place. Catalysts are not consumed in the reaction. Most reactions will proceed without a catalyst, but far too slowly for biological relevance, and therefore, catalysts are essential to life.

An enzyme is a substance that speeds up a biological reaction without being consumed in the reaction. All living microbes utilize enzymes made of proteins or RNA as catalysts in their metabolic pathways. Most viruses do not use enzymes but some viruses, called retroviruses, carry genes to produce viral-specific enzymes to catalyze reactions in host cells. Human immunodeficiency virus (HIV) is an example of a retrovirus.

An enzyme's active site is the place on an enzyme where the substrate binds and the reaction occurs. A substrate is a molecule that is acted upon by an enzyme by binding to the enzyme's active site. Enzymes commonly are named according to their respective substrates, with the suffix -ase appended. Reverse transcriptase is the enzyme used by HIV. Reverse transcriptase uses RNA (the substrate) to encode new DNA (the product), which can then be inserted in the host's genome.

An apoenzyme is an inactive enzyme that requires a cofactor for activation. A cofactor is a nonprotein compound or metallic ion whose presence is essential for the activity of an enzyme. A cofactor can be a coenzyme, a nonprotein chemical that helps an enzyme function, or it may be an inorganic ion. When an apoenzyme combines with its cofactor(s), it becomes a holoenzyme, the active form of an enzyme, which is a complex resulting from the combination of an enzyme and the necessary cofactor(s). Enzymes are specific to certain substrates. According to the induced-fit model of specificity, the enzyme changes shape to fit a matching substrate more closely. Cofactors and coenzymes are essential for creating the correct shape in a holoenzyme. Because enzymes are proteins, they are susceptible to denaturation, the alteration of a protein's shape through some form of external stress resulting in lack of function. The enzymes of human pathogenic microbes are adapted to the temperature, pH, and oxygenic levels found in the human body. Microbes whose enzymes are capable of functioning under extreme environmental conditions are known as extremophiles. An important example of an extremophile enzyme is the DNA replicating enzyme Taq polymerase from the deep sea hydrothermal vent bacteria Thermus aquaticus. Taq polymerase is used in the polymerase chain reaction to replicate DNA in the laboratory.

Adenosine triphosphate (ATP) is the biological unit of energy, which consists of an adenosine (an adenine group and a ribose sugar) and three phosphate groups. Because each phosphate group is negatively charged, energy is required to maintain these high-energy bonds. When ATP is used in a reaction, these bonds break, releasing energy. Removing one phosphate group forms adenosine diphosphate (ADP). Removing phosphate groups yields adenosine monophosphate (AMP), which is used to regenerate ADP and in RNA synthesis.

Throughout the metabolic process, ATP and ADP cycle. ATP is converted to ADP to release energy and ADP is converted to ATP to store energy for later use. The addition of a phosphate is called phosphorylation. Phosphorylation of ADP into ATP is often accomplished by the creation of a proton gradient, a different amount of hydrogen ions on each side of a membrane. For cyanobacteria and algae, which possess chlorophyll that absorbs light energy from the sun, light-dependent photosynthesis and cellular respiration are major sites of ATP generation. For bacteria, fungi, and protozoa, which do not possess chlorophyll, cellular respiration alone is the major site of ATP creation. In all cases, ATP is generated where a proton gradient is created across an internal membrane. This occurs in the cytoplasm in prokaryotes and in both chloroplasts and mitochondria in eukaryotes.