Prokaryotic Metabolism

Core Concepts

Classifying metabolism: energy source × carbon source

Every organism needs energy (to drive reactions) and carbon (to build molecules), and these are independent choices, giving four categories:

• Photoautotrophs get energy from light and carbon from CO₂. Examples: cyanobacteria, purple and green sulfur bacteria. They are primary producers — making organic matter from inorganic carbon using sunlight.
• Chemoautotrophs get energy from oxidizing inorganic chemicals (hydrogen sulfide, ammonia, ferrous iron, hydrogen) and carbon from CO₂. Examples: sulfur-oxidizing bacteria at deep-sea vents, nitrifying soil bacteria. They need no sunlight and no organic food — the base of food webs in dark, chemically rich environments.
• Photoheterotrophs get energy from light but carbon from organic molecules. Examples: green and purple nonsulfur bacteria.
• Chemoheterotrophs get both energy and carbon from organic molecules — the category humans belong to, including most pathogens, gut microbes, and decomposers.

"Autotroph" describes carbon source, not energy source: a chemoautotroph is not photosynthetic, and a photoautotroph is not a chemoheterotroph. The two axes are independent — the classic exam trap.

Aerobic respiration, anaerobic respiration, and fermentation

All three strategies start with glycolysis, which splits glucose into pyruvate and yields a small amount of ATP. What happens next defines the strategy:

• Aerobic respiration uses the electron transport chain (ETC) with oxygen as the final electron acceptor. The ETC builds a proton gradient across the membrane, and ATP synthase uses it to make ATP (oxidative phosphorylation). Because oxygen is a powerful electron acceptor, aerobic respiration extracts far more energy per glucose than the alternatives — commonly taught textbook figures are roughly 36–38 ATP per glucose for aerobic respiration versus about 2 for fermentation (reference values to verify against current texts).
• Anaerobic respiration also uses an ETC, but the final electron acceptor is something other than oxygen: nitrate (reduced to nitrite or nitrogen gas — denitrification), sulfate (reduced to hydrogen sulfide — sulfate reduction), carbon dioxide (reduced to methane — methanogenesis), or ferric iron. These acceptors yield less energy than oxygen but let organisms respire in oxygen-free environments. The products matter globally: denitrification removes fixed nitrogen from ecosystems, sulfate reduction produces the rotten-egg smell of hydrogen sulfide in swamps, and methanogenesis (done by archaea) produces methane.
• Fermentation skips the ETC entirely. Without it, the cell must regenerate NAD⁺ from the NADH built up in glycolysis, so pyruvate (or a derivative) is reduced to a waste product: lactic acid (yogurt, muscles under oxygen debt) or ethanol and CO₂ (beer, wine, bread). Fermentation yields only the small ATP from glycolysis, but it needs no oxygen and no ETC, so it works anywhere — which is why facultative anaerobes switch to it when oxygen runs out.

The key distinction: anaerobic respiration uses an ETC with an alternative electron acceptor; fermentation uses no ETC at all and relies on substrate-level phosphorylation alone.

Oxygen relationships: who can live where

Prokaryotes differ in oxygen tolerance — predictable, testable biology. Obligate aerobes require oxygen (aerobic respiration). Obligate anaerobes are killed or inhibited by oxygen; they ferment or respire anaerobically (Clostridium species are classic). Facultative anaerobes prefer oxygen but switch to fermentation or anaerobic respiration when it is absent (E. coli, many gut bacteria). Aerotolerant anaerobes don't use oxygen but tolerate it (many lactic acid bacteria). Microaerophiles require oxygen only at low concentrations (Campylobacter).

Why is oxygen toxic to obligate anaerobes? Oxygen metabolism generates reactive oxygen species (superoxide, hydrogen peroxide), and cells need enzymes — superoxide dismutase and catalase — to neutralize them. Obligate anaerobes typically lack adequate defenses, so oxygen damages them; aerobes and facultative anaerobes have the enzymes. This biochemical difference is another favorite exam comparison.

Nitrogen fixation: turning air into food

All organisms need nitrogen for proteins and nucleic acids, but almost none can use the N₂ that makes up 78% of the atmosphere — its triple bond is too strong. Nitrogen fixation converts N₂ into ammonia (NH₃), and only certain prokaryotes do it, using the enzyme nitrogenase. Fixers come in two flavors: free-living (Azotobacter in soil, cyanobacteria in water) and symbiotic (Rhizobium living in root nodules of legumes such as soybeans, peas, and clover). In the symbiosis, the plant feeds the bacteria carbohydrates and the bacteria supply ammonia for building amino acids. Nitrogenase is poisoned by oxygen, which is why root nodules maintain low-oxygen conditions (with leghemoglobin, a plant protein that binds oxygen) and why fixers have various tricks to protect the enzyme. The fixed ammonia feeds the rest of the nitrogen cycle — nitrification (ammonia → nitrite → nitrate), assimilation by plants, and denitrification (nitrate → N₂ gas, closing the loop). Crop rotation with legumes is, in essence, farming nitrogen-fixing bacteria.

Metabolic diversity in action: cycles and symbiosis

Prokaryotic metabolism stitches ecosystems together: decomposers (chemoheterotrophs) break down dead organic matter and release CO₂; methanogens finish the job in oxygen-free sediments; nitrifiers and denitrifiers move nitrogen between forms; sulfate reducers drive sulfur cycling; chemoautotrophs at hydrothermal vents support entire communities with no sunlight. Symbioses range from mutualism (rumen microbes digest cellulose for cattle; gut microbes make vitamins and break down fiber for us; Rhizobium feeds legumes), to commensalism (skin microbes that neither help nor harm), to parasitism (pathogens exploiting host resources). Humans harness this versatility: fermentation for food, microbes for wastewater treatment, and bioremediation — bacteria that degrade petroleum hydrocarbons help clean up oil spills, and others transform toxic metals.

Common Confusions