8.1 Energy, Matter, and Enzymes
- Metabolism includes chemical reactions that break down complex molecules (catabolism) and those that build complex molecules (anabolism).
- Organisms may be classified according to their source of carbon. Autotrophs convert inorganic carbon dioxide into organic carbon; heterotrophs use fixed organic carbon compounds.
- Organisms may also be classified according to their energy source. Phototrophs obtain their energy from light. Chemotrophs get their energy from chemical compounds. Organotrophs use organic molecules, and lithotrophs use inorganic chemicals.
- Cellular electron carriers accept high-energy electrons from foods and later serve as electron donors in subsequent redox reactions. FAD/FADH2, NAD+/NADH, and NADP+/NADPH are important electron carriers.
- Adenosine triphosphate (ATP) serves as the energy currency of the cell, safely storing chemical energy in its two high-energy phosphate bonds for later use to drive processes requiring energy.
- Enzymes are biological catalysts that increase the rate of chemical reactions inside cells by lowering the activation energy required for the reaction to proceed.
- In nature, exergonic reactions do not require energy beyond activation energy to proceed, and they release energy. They may proceed without enzymes, but at a slow rate. Conversely, endergonic reactions require energy beyond activation energy to occur. In cells, endergonic reactions are coupled to exergonic reactions, making the combination energetically favorable.
- Substrates bind to the enzyme’s active site. This process typically alters the structures of both the active site and the substrate, favoring transition-state formation; this is known as induced fit.
- Cofactors are inorganic ions that stabilize enzyme conformation and function. Coenzymes are organic molecules required for proper enzyme function and are often derived from vitamins. An enzyme lacking a cofactor or coenzyme is an apoenzyme; an enzyme with a bound cofactor or coenzyme is a holoenzyme.
- Competitive inhibitors regulate enzymes by binding to an enzyme’s active site, preventing substrate binding. Noncompetitive (allosteric) inhibitors bind to allosteric sites, inducing a conformational change in the enzyme that prevents it from functioning. Feedback inhibition occurs when the product of a metabolic pathway noncompetitively binds to an enzyme early on in the pathway, ultimately preventing the synthesis of the product.
8.2 Catabolism of Carbohydrates
- Glycolysis is the first step in the breakdown of glucose, resulting in the formation of ATP, which is produced by substrate-level phosphorylation; NADH; and two pyruvate molecules. Glycolysis does not use oxygen and is not oxygen dependent.
- After glycolysis, a three-carbon pyruvate is decarboxylated to form a two-carbon acetyl group, coupled with the formation of NADH. The acetyl group is attached to a large carrier compound called coenzyme A.
- After the transition step, coenzyme A transports the two-carbon acetyl to the Krebs cycle, where the two carbons enter the cycle. Per turn of the cycle, one acetyl group derived from glycolysis is further oxidized, producing three NADH molecules, one FADH2, and one ATP by substrate-level phosphorylation, and releasing two CO2 molecules.
- The Krebs cycle may be used for other purposes. Many of the intermediates are used to synthesize important cellular molecules, including amino acids, chlorophylls, fatty acids, and nucleotides.
8.3 Cellular Respiration
- Most ATP generated during the cellular respiration of glucose is made by oxidative phosphorylation.
- An electron transport system (ETS) is composed of a series of membrane-associated protein complexes and associated mobile accessory electron carriers. The ETS is embedded in the cytoplasmic membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes.
- Each ETS complex has a different redox potential, and electrons move from electron carriers with more negative redox potential to those with more positive redox potential.
- To carry out aerobic respiration, a cell requires oxygen as the final electron acceptor. A cell also needs a complete Krebs cycle, an appropriate cytochrome oxidase, and oxygen detoxification enzymes to prevent the harmful effects of oxygen radicals produced during aerobic respiration.
- Organisms performing anaerobic respiration use alternative electron transport system carriers for the ultimate transfer of electrons to the final non-oxygen electron acceptors.
- Microbes show great variation in the composition of their electron transport systems, which can be used for diagnostic purposes to help identify certain pathogens.
- As electrons are passed from NADH and FADH2 through an ETS, the electron loses energy. This energy is stored through the pumping of H+ across the membrane, generating a proton motive force.
- The energy of this proton motive force can be harnessed by allowing hydrogen ions to diffuse back through the membrane by chemiosmosis using ATP synthase. As hydrogen ions diffuse through down their electrochemical gradient, components of ATP synthase spin, making ATP from ADP and Pi by oxidative phosphorylation.
- Aerobic respiration forms more ATP (a maximum of 34 ATP molecules) during oxidative phosphorylation than does anaerobic respiration (between one and 32 ATP molecules).
- Fermentation uses an organic molecule as a final electron acceptor to regenerate NAD+ from NADH so that glycolysis can continue.
- Fermentation does not involve an electron transport system, and no ATP is made by the fermentation process directly. Fermenters make very little ATP—only two ATP molecules per glucose molecule during glycolysis.
- Microbial fermentation processes have been used for the production of foods and pharmaceuticals, and for the identification of microbes.
- During lactic acid fermentation, pyruvate accepts electrons from NADH and is reduced to lactic acid. Microbes performing homolactic fermentation produce only lactic acid as the fermentation product; microbes performing heterolactic fermentation produce a mixture of lactic acid, ethanol and/or acetic acid, and CO2.
- Lactic acid production by the normal microbiota prevents growth of pathogens in certain body regions and is important for the health of the gastrointestinal tract.
- During ethanol fermentation, pyruvate is first decarboxylated (releasing CO2) to acetaldehyde, which then accepts electrons from NADH, reducing acetaldehyde to ethanol. Ethanol fermentation is used for the production of alcoholic beverages, for making bread products rise, and for biofuel production.
- Fermentation products of pathways (e.g., propionic acid fermentation) provide distinctive flavors to food products. Fermentation is used to produce chemical solvents (acetone-butanol-ethanol fermentation) and pharmaceuticals (mixed acid fermentation).
- Specific types of microbes may be distinguished by their fermentation pathways and products. Microbes may also be differentiated according to the substrates they are able to ferment.
8.5 Catabolism of Lipids and Proteins
- Collectively, microbes have the ability to degrade a wide variety of carbon sources besides carbohydrates, including lipids and proteins. The catabolic pathways for all of these molecules eventually connect into glycolysis and the Krebs cycle.
- Several types of lipids can be microbially degraded. Triglycerides are degraded by extracellular lipases, releasing fatty acids from the glycerol backbone. Phospholipids are degraded by phospholipases, releasing fatty acids and the phosphorylated head group from the glycerol backbone. Lipases and phospholipases act as virulence factors for certain pathogenic microbes.
- Fatty acids can be further degraded inside the cell through β-oxidation, which sequentially removes two-carbon acetyl groups from the ends of fatty acid chains.
- Protein degradation involves extracellular proteases that degrade large proteins into smaller peptides. Detection of the extracellular proteases gelatinase and caseinase can be used to differentiate clinically relevant bacteria.
- Heterotrophs depend on the carbohydrates produced by autotrophs, many of which are photosynthetic, converting solar energy into chemical energy.
- Different photosynthetic organisms use different mixtures of photosynthetic pigments, which increase the range of the wavelengths of light an organism can absorb.
- Photosystems (PSI and PSII) each contain a light-harvesting complex, composed of multiple proteins and associated pigments that absorb light energy. The light-dependent reactions of photosynthesis convert solar energy into chemical energy, producing ATP and NADPH or NADH to temporarily store this energy.
- In oxygenic photosynthesis, H2O serves as the electron donor to replace the reaction center electron, and oxygen is formed as a byproduct. In anoxygenic photosynthesis, other reduced molecules like H2S or thiosulfate may be used as the electron donor; as such, oxygen is not formed as a byproduct.
- Noncyclic photophosphorylation is used in oxygenic photosynthesis when there is a need for both ATP and NADPH production. If a cell’s needs for ATP outweigh its needs for NADPH, then it may carry out cyclic photophosphorylation instead, producing only ATP.
- The light-independent reactions of photosynthesis use the ATP and NADPH from the light-dependent reactions to fix CO2 into organic sugar molecules.
8.7 Biogeochemical Cycles
- The recycling of inorganic matter between living organisms and their nonliving environment is called a biogeochemical cycle. Microbes play significant roles in these cycles.
- In the carbon cycle, heterotrophs degrade reduced organic molecule to produce carbon dioxide, whereas autotrophs fix carbon dioxide to produce organics. Methanogens typically form methane by using CO2 as a final electron acceptor during anaerobic respiration; methanotrophs oxidize the methane, using it as their carbon source.
- In the nitrogen cycle, nitrogen-fixing bacteria convert atmospheric nitrogen into ammonia (ammonification). The ammonia can then be oxidized to nitrite and nitrate (nitrification). Nitrates can then be assimilated by plants. Soil bacteria convert nitrate back to nitrogen gas (denitrification).
- In sulfur cycling, many anoxygenic photosynthesizers and chemoautotrophs use hydrogen sulfide as an electron donor, producing elemental sulfur and then sulfate; sulfate-reducing bacteria and archaea then use sulfate as a final electron acceptor in anaerobic respiration, converting it back to hydrogen sulfide.
- Human activities that introduce excessive amounts of naturally limited nutrients (like iron, nitrogen, or phosphorus) to aquatic systems may lead to eutrophication.
- Microbial bioremediation is the use of microbial metabolism to remove or degrade xenobiotics and other environmental contaminants and pollutants. Enhanced bioremediation techniques may involve the introduction of non-native microbes specifically chosen or engineered for their ability to degrade contaminants.