Metabolism and Energy Pathways

Other Types of Microbial Metabolism


Photosynthesis is the process of converting light energy from the sun into chemical energy and then using that energy to synthesize glucose through the Calvin cycle.

Photosynthesis is the process by which photoautotrophs convert light energy into chemical energy that is stored in organic compounds, such as sugars. In eukaryotes, there are two phases to photosynthesis: the light-dependent reactions and the light-independent reactions (also known as the Calvin cycle). In the light-dependent reactions, photons of light are captured to drive electron transport to establish a proton gradient and produce ATP and NADPH. In the light-independent reaction, the electron carriers and ATP generated by the light-dependent reactions drive the fixation of carbon dioxide to glucose.

Light energy is captured by chlorophyll, a green pigment used in photosynthesis. All photosynthetic organisms use chlorophyll a in their photosynthetic reaction centers. Photosynthetic accessory pigments can be used to differentiate groups of organisms. In green algae, as well as land plants, the main accessory pigments are chlorophyll b and carotenes. In red algae and cyanobacteria—bacteria capable of photosynthesis—the main accessory pigment is phycobiliprotein. In brown algae the main accessory pigment is fucoxanthin.

Chlorophyll and accessory pigments are incorporated in dense complexes of light-capturing pigments called photosystems. These photosystems are embedded in lipid membranes. In eukaryotic algal cells this process occurs inside the thylakoid membranes, highly folded membranes found inside the chloroplast. A chloroplast is a membrane-bound organelle found in plants and some other organisms that captures energy from light and converts it into chemical energy. The light-dependent reactions occur on the thylakoid membrane, while the light-independent reactions take place in the space inside the thylakoid called the lumen. In prokaryotic cells that perform photosynthesis, such as cyanobacteria, the photosystems are embedded in internal membranes also called thylakoid membranes that are folded and provide compartmentation similar to eukaryotic organelles.

The two photosystems, photosystem I (PSI) and photosystem II (PSII), form the backbone of light-dependent photosynthesis. Every photoautotroph can utilize the PSI pathway to phosphorylate ADP to ATP. There are five groups of bacteria capable of performing photosynthesis in the absence of oxygen that solely use PSI in their light-dependent reactions. Cyanobacteria, along with algae and all other eukaryotic photoautotrophs, use both PSI and PSII. This is because PSII splits water to generate oxygen. The evolution of PSII water splitting to produce molecular oxygen is thought to have created the oxygenic environment currently present on Earth.

In photosynthesis, light is absorbed by a large surface area of pigments called the light-harvesting complex. When light is absorbed, the energy is transferred between pigments until it reaches the central chlorophyll reaction center. The electron in the reaction center is excited and is passed through an a series of electron carriers called the electron transport chain from the PSII reaction center to PSI. During electron transport, protons are transported across the thylakoid membrane creating a proton concentration gradient that drives ADP phosphorylation to ATP. This process also produces NADPH and oxygen.

The energy created by the light-dependent pathways, in the form of ATP and NADPH, drives the fixation of carbon dioxide into glucose. The core of this process is the Calvin cycle (sometimes called the Calvin-Benson cycle). The Calvin cycle produces glyceraldehyde 3-phosphate (G3P). Like the citric acid cycle, the Calvin cycle regenerates its substrate, a five-carbon sugar called ribulose 1,5-bisphosphate (Rubisco). It can be summarized in three steps: CO2 fixation, reduction, and regeneration of the Rubisco substrate. In the reduction step, ATP from the light-dependent portion of photosynthesis is used to add energy by phosphorylation, while NADPH from PSII reduces the resulting molecules for a net result of six G3P molecules. However, some of this G3P is used to regenerate Rubisco in a series of enzymatic reactions. Only one G3P is created for every turn of the cycle, requiring three molecules of CO2. Once two molecules of G3P are available they can combine by reverse glycolysis to form glucose-6-phosphate and eventually one glucose molecule.

Light-Dependent and Light-Independent Reactions

In the chloroplast, light-independent reactions (Calvin cycle) use energy derived from light-dependent reactions and electron carriers to transform carbon dioxide into sugar.


Chemoautotrophic bacteria can oxidize inorganic compounds to liberate energy that is used to reduce carbon dioxide or methane.
Chemosynthetic pathways synthesize reduced, organic compounds from carbon dioxide or methane using energy extracted from inorganic compounds instead of sunlight as in photosynthesis. There are bacterial and archaeal chemoautotrophic organism, but none are eukaryotic. Common inorganic compounds used as energy sources are nitrate (NO3-), molecular hydrogen (H2), hydrogen sulfide (H2S), ammonia (NH4+), and ferrous iron (FeO). Chemoautotrophs oxidize one of these inorganic compounds and utilize the liberated electrons to reduce carbon dioxide. In general, chemoautotrophs are abundant in extreme environments with chemistry not typically associated with life and where sunlight is nonexistent. In extreme environments, chemoautotrophs often serve as the base of the ecosystem that provides energy to all other organisms. The greatest abundance of chemoautotrophs exist in the deep ocean where hydrothermal vents release large quantities of hydrogen sulfide. The biomass produced by chemoautotrophs around hydrothermal vents can support large and diverse ecosystems. Not all chemoautotrophs are restricted to extreme environments though. The iron bacteria, Thiobacillus ferrooxidans, is found in freshwater systems with high iron concentrations. T. ferrooxidans oxidizes ferrous iron to iron oxide, commonly called rust, often in the human built environment where it stains sinks, toilets, and bathtubs.

Fatty Acid Synthesis

Fatty acids can be formed from acetyl-CoA and NADPH.
Fatty acids are hydrocarbons with a carboxylic acids at one end that can be further classified as straight-chain or branching and as saturated or unsaturated depending on the conformation of the aliphatic tail. Lipids are assigned a "lipid number" according to the form C:D in which C represents the number of carbons and D the number of double bonds. Palmitic acid, a common, representative straight-chain saturated fatty acid, is described by the lipid number 16:0. Lipids, including fatty acids, are useful as long-term stores of energy and cellular components. Mycobacterium tuberculosis, for instance, derives some of its pathogenicity, or disease-causing ability, from a waxy lipid called mycolic acid. Mycolic acid is incorporated in the cell wall and makes it highly robust against disruption, such as antibiotic treatment. Fatty acids combine with glycerol and a phosphate ion to form phospholipids, which are the backbone of the phospholipid bilayer that forms the cell membrane.


A triglyceride consists of three fatty acids and one glycerol. The fatty acids may be saturated (no double bonds) or unsaturated (one or more double bonds).
Microbial fatty acid synthesis can occur through several pathways that all utilize acetyl-CoA. Enzymes (most notably microbial fatty acid synthase) add carbons to the chain. NADPH serves as the reducing agent at multiple steps to convert acetyl-CoA into lipids. Acetyl-CoA is available as a product from some of the metabolic pathways discussed above, notably glycolysis. NADPH is formed during the decarboxylation of malate to form pyruvate and by the pentose phosphate pathway. NADPH is consumed in synthesis, in contrast to NADH, which is produced in catabolism of lipids. The reverse of straight-chain synthesis is beta oxidation. Beta oxidation (β-oxidation) is a catabolic process that breaks down fatty acids to produce acetyl-CoA, NADH, and FADH2.