Electron transport chain

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Electron_transport_chain 

An electron transport chain (ETC) is a series of protein complexes and other molecules which transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples this electron transfer with the transfer of protons (H⁺ ions) across a membrane. Many of the enzymes in the electron transport chain are embedded within the membrane.

The flow of electrons through the electron transport chain is an exergonic process. The energy from the redox reactions creates an electrochemical proton gradient that drives the synthesis of adenosine triphosphate (ATP). In aerobic respiration, the flow of electrons terminates with molecular oxygen as the final electron acceptor. In anaerobic respiration, other electron acceptors are used, such as sulfate.

In an electron transport chain, the redox reactions are driven by the difference in the Gibbs free energy of reactants and products. The free energy released when a higher-energy electron donor and acceptor convert to lower-energy products, while electrons are transferred from a lower to a higher redox potential, is used by the complexes in the electron transport chain to create an electrochemical gradient of ions. It is this electrochemical gradient that drives the synthesis of ATP via coupling with oxidative phosphorylation through ATP synthase.

In eukaryotic organisms, the electron transport chain, and site of oxidative phosphorylation, is found on the inner mitochondrial membrane. The energy released by reactions of oxygen and reduced compounds such as cytochrome c and (indirectly) NADH and FADH₂ is used by the electron transport chain to pump protons into the intermembrane space, generating the electrochemical gradient over the inner mitochondrial membrane. In photosynthetic eukaryotes, the electron transport chain is found on the thylakoid membrane. Here, light energy drives electron transport through a proton pump and the resulting proton gradient causes subsequent synthesis of ATP. In bacteria, the electron transport chain can vary between species but it always constitutes a set of redox reactions that are coupled to the synthesis of ATP through the generation of an electrochemical gradient and oxidative phosphorylation through ATP synthase.

Mitochondrial electron transport chains

The electron transport chain in the mitochondrion is the site of oxidative phosphorylation in eukaryotes. It mediates the reaction between NADH or succinate generated in the citric acid cycle and oxygen to power ATP synthase.

Most eukaryotic cells have mitochondria, which produce ATP from reactions of oxygen with products of the citric acid cycle, fatty acid metabolism, and amino acid metabolism. At the inner mitochondrial membrane, electrons from NADH and FADH₂ pass through the electron transport chain to oxygen, which provides the energy driving the process as it is reduced to water. The electron transport chain comprises an enzymatic series of electron donors and acceptors. Each electron donor will pass electrons to an acceptor of higher redox potential, which in turn donates these electrons to another acceptor, a process that continues down the series until electrons are passed to oxygen, the terminal electron acceptor in the chain. Each reaction releases energy because a higher-energy donor and acceptor convert to lower-energy products. Via the transferred electrons, this energy is used to generate a proton gradient across the mitochondrial membrane by "pumping" protons into the intermembrane space, producing a state of higher free energy that has the potential to do work. This entire process is called oxidative phosphorylation since ADP is phosphorylated to ATP by using the electrochemical gradient that the redox reactions of the electron transport chain have established driven by energy-releasing reactions of oxygen.

Mitochondrial redox carriers

Energy associated with the transfer of electrons down the electron transport chain is used to pump protons from the mitochondrial matrix into the intermembrane space, creating an electrochemical proton gradient (ΔpH) across the inner mitochondrial membrane. This proton gradient is largely but not exclusively responsible for the mitochondrial membrane potential (ΔΨ_M). It allows ATP synthase to use the flow of H⁺ through the enzyme back into the matrix to generate ATP from adenosine diphosphate (ADP) and inorganic phosphate. Complex I (NADH coenzyme Q reductase; labeled I) accepts electrons from the Krebs cycle electron carrier nicotinamide adenine dinucleotide (NADH), and passes them to coenzyme Q (ubiquinone; labeled Q), which also receives electrons from Complex II (succinate dehydrogenase; labeled II). Q passes electrons to Complex III (cytochrome bc₁ complex; labeled III), which passes them to cytochrome c (cyt c). Cyt c passes electrons to Complex IV (cytochrome c oxidase; labeled IV).

Four membrane-bound complexes have been identified in mitochondria. Each is an extremely complex transmembrane structure that is embedded in the inner membrane. Three of them are proton pumps. The structures are electrically connected by lipid-soluble electron carriers and water-soluble electron carriers. The overall electron transport chain can be summarized as follows:

Complex I

Further information: Respiratory complex I

In Complex I (NADH ubiquinone oxidoreductase, Type I NADH dehydrogenase, or mitochondrial complex I; EC 7.1.1.2), two electrons are removed from NADH and transferred to a lipid-soluble carrier, ubiquinone (Q). The reduced product, ubiquinol (QH₂), freely diffuses within the membrane, and Complex I translocates four protons (H⁺) across the membrane, thus producing a proton gradient. Complex I is one of the main sites at which premature electron leakage to oxygen occurs, thus being one of the main sites of production of superoxide.

The pathway of electrons is as follows:

NADH is oxidized to NAD⁺, by reducing flavin mononucleotide to FMNH₂ in one two-electron step. FMNH₂ is then oxidized in two one-electron steps, through a semiquinone intermediate. Each electron thus transfers from the FMNH₂ to an Fe–S cluster, from the Fe-S cluster to ubiquinone (Q). Transfer of the first electron results in the free-radical (semiquinone) form of Q, and transfer of the second electron reduces the semiquinone form to the ubiquinol form, QH₂. During this process, four protons are translocated from the mitochondrial matrix to the intermembrane space. As the electrons move through the complex an electron current is produced along the 180 Angstrom width of the complex within the membrane. This current powers the active transport of four protons to the intermembrane space per two electrons from NADH.

Complex II

In Complex II (succinate dehydrogenase or succinate-CoQ reductase; EC 1.3.5.1) additional electrons are delivered into the quinone pool (Q) originating from succinate and transferred (via flavin adenine dinucleotide (FAD)) to Q. Complex II consists of four protein subunits: succinate dehydrogenase (SDHA); succinate dehydrogenase [ubiquinone] iron–sulfur subunit mitochondrial (SDHB); succinate dehydrogenase complex subunit C (SDHC); and succinate dehydrogenase complex subunit D (SDHD). Other electron donors (e.g., fatty acids and glycerol 3-phosphate) also direct electrons into Q (via FAD). Complex II is a parallel electron transport pathway to Complex I, but unlike Complex I, no protons are transported to the intermembrane space in this pathway. Therefore, the pathway through Complex II contributes less energy to the overall electron transport chain process.

Complex III

In Complex III (cytochrome bc₁ complex or CoQH₂-cytochrome c reductase; EC 7.1.1.8), the Q-cycle contributes to the proton gradient by an asymmetric absorption/release of protons. Two electrons are removed from QH₂ at the Q_O site and sequentially transferred to two molecules of cytochrome c, a water-soluble electron carrier located within the intermembrane space. The two other electrons sequentially pass across the protein to the Q_i site where the quinone part of ubiquinone is reduced to quinol. A proton gradient is formed by one quinol (${\displaystyle 2{\text{H}}_2^{+}{\text{e}}^{-}}$) oxidations at the Q_o site to form one quinone (${\displaystyle 2{\text{H}}_2^{+}{\text{e}}^{-}}$) at the Q_i site. (In total, four protons are translocated: two protons reduce quinone to quinol and two protons are released from two ubiquinol molecules.)

${\displaystyle {\text{QH}}_2^{}+2}$${\displaystyle \text{ cytochrome }c}$${\displaystyle ({\text{Fe}}^{\text{III}})+2\text{H}}$${\displaystyle {}_{\text{in}}^{+}}$${\displaystyle ⟶\text{Q}+2}$${\displaystyle \text{ cytochrome }c}$${\displaystyle ({\text{Fe}}^{\text{II}})+4\text{H}}$${\displaystyle {}_{\text{out}}^{+}}$

When electron transfer is reduced (by a high membrane potential or respiratory inhibitors such as antimycin A), Complex III may leak electrons to molecular oxygen, resulting in superoxide formation.

This complex is inhibited by dimercaprol (British Anti-Lewisite, BAL), naphthoquinone and antimycin.

Complex IV

In Complex IV (cytochrome c oxidase; EC 7.1.1.9), sometimes called cytochrome AA3, four electrons are removed from four molecules of cytochrome c and transferred to molecular oxygen (O₂) and four protons, producing two molecules of water. The complex contains coordinated copper ions and several heme groups. At the same time, eight protons are removed from the mitochondrial matrix (although only four are translocated across the membrane), contributing to the proton gradient. The exact details of proton pumping in Complex IV are still under study. Cyanide is an inhibitor of Complex IV.

Coupling with oxidative phosphorylation

Depiction of ATP synthase, the site of oxidative phosphorylation to generate ATP.

According to the chemiosmotic coupling hypothesis, proposed by Nobel Prize in Chemistry winner Peter D. Mitchell, the electron transport chain and oxidative phosphorylation are coupled by a proton gradient across the inner mitochondrial membrane. The efflux of protons from the mitochondrial matrix creates an electrochemical gradient (proton gradient). This gradient is used by the F_OF₁ ATP-synthase complex to make ATP via oxidative phosphorylation. ATP-synthase is sometimes described as Complex V of the electron transport chain.

The F_O component acts as a channel that harnesses the proton flow to drive rotation. It is composed of a, b and c subunits. Protons in the inter-membrane space of mitochondria first enter the ATP-synthase complex through an a subunit channel. Then protons bind to the c subunits, which are oriented in a ring (the c-ring), where the number of c subunits determines how many protons are required to make the c-ring and the attached γ-rotor turn one full revolution. There are 8 c subunits in humans, thus 8 protons are required. Protons are released as a result of the rotation of the c-ring, being directed into the mitochondrial matrix along the a subunit channels. This proton reflux drives the mechanical rotation of the c-ring and the γ-axle. The rotation of the γ-rotor causes the sequential alternation of conformational states in the catalytic β-subunits in F₁.

There are three different conformational states, which are:

• Open, in this state the β-subunit has low affinity to ligands, releasing the previously synthesized ATP molecule.
• Loose, Binds ADP and P_i together loosely.
• Tight, Binds ADP and P_i so tightly that it catalyzes the condensation reaction to form ATP.

This cycle is known as the binding change mechanism (coined by Paul D. Boyer), explaining the conversion of mechanical rotation to chemical energy.

Coupling with oxidative phosphorylation is a key step for ATP production. However, in specific cases, uncoupling the two processes may be biologically useful. The uncoupling protein, thermogenin—present in the inner mitochondrial membrane of brown adipose tissue—provides for an alternative flow of protons back to the inner mitochondrial matrix. Thyroxine is also a natural uncoupler. This alternative flow results in thermogenesis rather than ATP production.

Reverse electron flow

Reverse electron flow is the transfer of electrons through the electron transport chain through the reverse redox reactions. Usually requiring a significant amount of energy to be used, this can reduce the oxidized forms of electron donors. For example, NAD⁺ can be reduced to NADH by Complex I. There are several factors that have been shown to induce reverse electron flow. However, more work needs to be done to confirm this. One example is blockage of ATP synthase, resulting in a build-up of protons and therefore a higher proton-motive force, inducing reverse electron flow.

Prokaryotic electron transport chains

In eukaryotes, NADH is the most important electron donor. The associated electron transport chain is NADH → Complex I → Q → Complex III → cytochrome c → Complex IV → O₂ where Complexes I, III and IV are proton pumps, while Q and cytochrome c are mobile electron carriers. The electron acceptor for this process is molecular oxygen.

In prokaryotes (bacteria and archaea) the situation is more complicated, because there are several different electron donors and several different electron acceptors. The generalized electron transport chain in bacteria is:

Electrons can enter the chain at three levels: at the level of a dehydrogenase, at the level of the quinone pool, or at the level of a mobile cytochrome electron carrier. These levels correspond to successively more positive redox potentials, or to successively decreased potential differences relative to the terminal electron acceptor. In other words, they correspond to successively smaller Gibbs free energy changes for the overall redox reaction.

Individual bacteria use multiple electron transport chains, often simultaneously. Bacteria can use a number of different electron donors, a number of different dehydrogenases, a number of different oxidases and reductases, and a number of different electron acceptors. For example, E. coli (when growing aerobically using glucose and oxygen as an energy source) uses two different NADH dehydrogenases and two different quinol oxidases, for a total of four different electron transport chains operating simultaneously.

A common feature of all electron transport chains is the presence of a proton pump to create an electrochemical gradient over a membrane. Bacterial electron transport chains may contain as many as three proton pumps, like mitochondria, or they may contain two or at least one.

Electron donors

In the current biosphere, the most common electron donors are organic molecules. Organisms that use organic molecules as an electron source are called organotrophs. Chemoorganotrophs (animals, fungi, protists) and photolithotrophs (plants and algae) constitute the vast majority of all familiar life forms.

Some prokaryotes can use inorganic matter as an electron source. Such an organism is called a (chemo)lithotroph ("rock-eater"). Inorganic electron donors include hydrogen, carbon monoxide, ammonia, nitrite, sulfur, sulfide, manganese oxide, and ferrous iron. Lithotrophs have been found growing in rock formations thousands of meters below the surface of Earth. Because of their volume of distribution, lithotrophs may actually outnumber organotrophs and phototrophs in our biosphere.

The use of inorganic electron donors such as hydrogen as an energy source is of particular interest in the study of evolution. This type of metabolism must logically have preceded the use of organic molecules and oxygen as an energy source.

Dehydrogenases: equivalents to complexes I and II

Bacteria can use several different electron donors. When organic matter is the electron source, the donor may be NADH or succinate, in which case electrons enter the electron transport chain via NADH dehydrogenase (similar to Complex I in mitochondria) or succinate dehydrogenase (similar to Complex II). Other dehydrogenases may be used to process different energy sources: formate dehydrogenase, lactate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, H₂ dehydrogenase (hydrogenase),electron transport chain. Some dehydrogenases are also proton pumps, while others funnel electrons into the quinone pool. Most dehydrogenases show induced expression in the bacterial cell in response to metabolic needs triggered by the environment in which the cells grow. In the case of lactate dehydrogenase in E. coli, the enzyme is used aerobically and in combination with other dehydrogenases. It is inducible and is expressed when the concentration of DL-lactate in the cell is high.

Quinone carriers

Quinones are mobile, lipid-soluble carriers that shuttle electrons (and protons) between large, relatively immobile macromolecular complexes embedded in the membrane. Bacteria use ubiquinone (Coenzyme Q, the same quinone that mitochondria use) and related quinones such as menaquinone (Vitamin K₂). Archaea in the genus Sulfolobus use caldariellaquinone. The use of different quinones is due to slight changes in redox potentials caused by changes in structure. The change in redox potentials of these quinones may be suited to changes in the electron acceptors or variations of redox potentials in bacterial complexes.

Proton pumps

A proton pump is any process that creates a proton gradient across a membrane. Protons can be physically moved across a membrane, as seen in mitochondrial Complexes I and IV. The same effect can be produced by moving electrons in the opposite direction. The result is the disappearance of a proton from the cytoplasm and the appearance of a proton in the periplasm. Mitochondrial Complex III is this second type of proton pump, which is mediated by a quinone (the Q cycle).

Some dehydrogenases are proton pumps, while others are not. Most oxidases and reductases are proton pumps, but some are not. Cytochrome bc₁ is a proton pump found in many, but not all, bacteria (not in E. coli). As the name implies, bacterial bc₁ is similar to mitochondrial bc₁ (Complex III).

Cytochrome electron carriers

Cytochromes are proteins that contain iron. They are found in two very different environments.

Some cytochromes are water-soluble carriers that shuttle electrons to and from large, immobile macromolecular structures imbedded in the membrane. The mobile cytochrome electron carrier in mitochondria is cytochrome c. Bacteria use a number of different mobile cytochrome electron carriers.

Other cytochromes are found within macromolecules such as Complex III and Complex IV. They also function as electron carriers, but in a very different, intramolecular, solid-state environment.

Electrons may enter an electron transport chain at the level of a mobile cytochrome or quinone carrier. For example, electrons from inorganic electron donors (nitrite, ferrous iron, electron transport chain) enter the electron transport chain at the cytochrome level. When electrons enter at a redox level greater than NADH, the electron transport chain must operate in reverse to produce this necessary, higher-energy molecule.

It has been observed that inter-protein electron transport between cytochromes c and c₁ (complex III) depends on pH and the presence of oxygen, suggesting that protons and superoxide may act as redox mediators in the long-distance electron transport process through the aqueous solution.

Electron acceptors and terminal oxidase/reductase

As there are a number of different electron donors (organic matter in organotrophs, inorganic matter in lithotrophs), there are a number of different electron acceptors, both organic and inorganic. As with other steps of the ETC, an enzyme is required to help with the process.

If oxygen is available, it is most often used as the terminal electron acceptor in aerobic bacteria and facultative anaerobes. An oxidase reduces the O₂ to water while oxidizing something else. In mitochondria, the terminal membrane complex (Complex IV) is cytochrome oxidase, which oxidizes the cytochrome. Aerobic bacteria use a number of different terminal oxidases. For example, E. coli (a facultative anaerobe) does not have a cytochrome oxidase or a bc₁ complex. Under aerobic conditions, it uses two different terminal quinol oxidases (both proton pumps) to reduce oxygen to water.

Bacterial terminal oxidases can be split into classes according to the molecules act as terminal electron acceptors. Class I oxidases are cytochrome oxidases and use oxygen as the terminal electron acceptor. Class II oxidases are quinol oxidases and can use a variety of terminal electron acceptors. Both of these classes can be subdivided into categories based on what redox-active components they contain. E.g. Heme aa3 Class 1 terminal oxidases are much more efficient than Class 2 terminal oxidases.

Mostly in anaerobic environments different electron acceptors are used, including nitrate, nitrite, ferric iron, sulfate, carbon dioxide, and small organic molecules such as fumarate. When bacteria grow in anaerobic environments, the terminal electron acceptor is reduced by an enzyme called a reductase. E. coli can use fumarate reductase, nitrate reductase, nitrite reductase, DMSO reductase, or trimethylamine-N-oxide reductase, depending on the availability of these acceptors in the environment.

Most terminal oxidases and reductases are inducible. They are synthesized by the organism as needed, in response to specific environmental conditions.

Photosynthesis

Further information: Light-dependent reaction and Photosynthetic reaction center

Photosynthetic electron transport chain of the thylakoid membrane.

In oxidative phosphorylation, electrons are transferred from an electron donor such as NADH to an acceptor such as O₂ through an electron transport chain, releasing energy. In photophosphorylation, the energy of sunlight is used to create a high-energy electron donor which can subsequently reduce oxidized components and couple to ATP synthesis via proton translocation by the electron transport chain.

Photosynthetic electron transport chains, like the mitochondrial chain, can be considered as a special case of the bacterial systems. They use mobile, lipid-soluble quinone carriers (phylloquinone and plastoquinone) and mobile, water-soluble carriers (cytochromes). They also contain a proton pump. The proton pump in all photosynthetic chains resembles mitochondrial Complex III. The commonly held theory of symbiogenesis proposes that both organelles descended from bacteria.

Fermentation

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Fermentation

Phylogenetic tree of bacteria and archaea, highlighting those that carry out fermentation. Their end products are also highlighted. Figure modified from Hackmann (2024).

Fermentation is a type of anaerobic metabolism that harnesses the redox potential of the reactants to make adenosine triphosphate (ATP) and organic end products. Organic molecules, such as glucose or other sugars, are catabolized and their electrons are transferred to other organic molecules (cofactors, coenzymes, etc.). Anaerobic glycolysis is a related term used to describe the occurrence of fermentation in organisms (usually multicellular organisms such as animals) when aerobic respiration cannot keep up with the ATP demand, due to insufficient oxygen supply or anaerobic conditions.

Fermentation is important in several areas of human society. Humans have used fermentation in the production and preservation of food for 13,000 years. It has been associated with health benefits, unique flavor profiles, and making products have better texture. Humans and their livestock also benefit from fermentation from the microbes in the gut that release end products that are subsequently used by the host for energy. Perhaps the most commonly known use for fermentation is at an industrial level to produce commodity chemicals, such as ethanol and lactate. Ethanol is used in a variety of alcoholic beverages (beers, wine, and spirits) while lactate can be neutralized to lactic acid and be used for food preservation, as a curing agent, or as a flavoring agent.

This complex metabolism utilizes a wide variety of substrates and can form nearly 300 different combinations of end products. Fermentation occurs in both prokaryotes and eukaryotes. The discovery of new end products and new fermentative organisms suggests that fermentation is more diverse than what has been studied.

Definition

A variety of definitions have been proposed throughout the years, but the simplest and most recent definition of fermentation proposed is "catabolism where organic compounds are both the electron donor and acceptor." This definition distinguishes fermentation from aerobic respiration (when oxygen is the acceptor) and types of anaerobic respiration (when an inorganic species is the acceptor). However, this definition does not encompass all forms of fermentation. For example, propionate fermentation which uses H₂ as an electron donor, or the second step of butyrate fermentation where CO₂ can act as an electron acceptor. Thus, it is simplest to use this definition while acknowledging that protons can also be used as electron donors and CO₂ as acceptors.

In 1876, before the discovery of anaerobic respiration, Louis Pasteur described it as "la vie sans air" (life without air). It was also common for fermentation to be defined based on how fermentation forms ATP which was catabolism that forms ATP through only substrate-level phosphorylation.

Industrial fermentation is another type of fermentation that is defined loosely as a large-scale biological manufacturing process; however, this definition focuses on the process of manufacturing rather than metabolic details.

Biological role and prevalence

Fermentation can be used by organisms to generate a net gain of ATP from exogenous sources of organic molecules, such as glucose. It was not a net source of energy in the earliest forms of life because they were mostly single cell organisms living in the ocean and the ocean does not contain significant concentrations of complex organic molecules.

Because fermentation does not need an exogenous electron acceptor, it is able to occur regardless of the environmental conditions. However, the primary disadvantage of fermentation is that fermentation is relatively inefficient and produces between 2 and 5 ATP molecules per glucose versus 32 ATP molecules during aerobic respiration.

Over 25% of bacteria and archaea carry out fermentation. Fermentation is especially prevalent in prokaryotes of the phylum Bacillota, but is most rare in Actinomycetota, according to phylogenetic analysis. The fermenting microbes are most frequently found in host-associated habitats such as the gastrointestinal tract, but also sediments, food, and other habitats. Both bacteria and archaea share the capacity for fermentation, leading to a wide variety of organic end products. The most common fermentation products include lactate, acetate, ethanol, carbon dioxide (CO₂), succinate, hydrogen (H₂), propionate, and butyrate.

In humans, fermentation pathways occur in health, as in exercising, and in disease, as in sepsis and hemorrhagic shock, providing energy for a period ranging from 10 seconds to 2 minutes. During this time, it can augment the energy produced by aerobic metabolism, but is limited by the buildup of lactate. Rest eventually becomes necessary.

Substrates and products of fermentation

The most common substrates and products of fermentation. Figure modified from Hackmann (2024).

Like many biochemical reactions, fermentation is an enzyme catalyzed reaction with the goal of either changing the initial substrate or forming a useful byproduct. When naturally occurring fermentation is carried out by microbes, the goal is usually to obtain useful metabolic products such as ATP, pyruvate, or lactic acid. The substrates used in this type of fermentation are often simple sugars (carbohydrates) that serve as a carbon source and this type of fermentation can be carried out by microbes and humans.

Food as a substrate for fermentation is the most common and oldest anthropogenic use of fermentation as it was a method to preserve food. This includes cereal, dairy products, rice, honey, bread, and beers. This type of naturally occurring fermentation continues to be harnessed by humans for preservative effects, flavor profiles, and texture profiles. Advances in fermentation has led to the engineering and industrialization of specific microbes and substrates in order to obtain certain flavor and texture profiles – this is most obvious when observing beer fermentation.

Biochemical overview

Overview of the biochemical pathways for fermentation of glucose. Figure modified from Hackmann (2024).

When an organic compound is fermented, it is broken down to a simpler molecule and releases electrons. The electrons are transferred to a redox cofactor, which, in turn, transfers them to an organic compound. ATP is generated in the process, and it can be formed via substrate-level phosphorylation or by ATP synthase.

When glucose is fermented, it enters glycolysis or the pentose phosphate pathway and is converted to pyruvate. From pyruvate, pathways branch out to form a number of end products (e.g. lactate). At several points, electrons are released and accepted by redox cofactors (NAD and ferredoxin). At later points, these cofactors donate electrons to their final acceptor and become oxidized. ATP is also formed at several points in the pathway.

The biochemical pathways of fermentation of glucose in poster format. Figure modified from Hackmann (2024).

Biochemistry of individual products

Ethanol

Main article: Ethanol fermentation

Yeast and other anaerobic microorganisms can convert the pyruvate produced from the oxidation of glucose by a glycolysis pathway to ethanol and CO₂. In ethanol fermentation, one glucose molecule is converted into two ethanol molecules and two carbon dioxide (CO₂) molecules. It is used to make bread dough rise: the carbon dioxide forms bubbles, expanding the dough into a foam. The ethanol is the intoxicating agent in alcoholic beverages such as wine, beer and liquor. Fermentation of feedstocks, including sugarcane, maize, and sugar beets, produces ethanol that is added to gasoline. In some species of fish, such as carp, it provides energy when oxygen is scarce (along with lactic acid fermentation).

Before fermentation, a glucose molecule breaks down into two pyruvate molecules (glycolysis). The energy from this exothermic reaction is used to bind inorganic phosphates to ADP, which converts it to ATP, and convert NAD⁺ to NADH. The pyruvates break down into two acetaldehyde molecules and give off two carbon dioxide molecules as waste products. The acetaldehyde is reduced into ethanol using the energy and hydrogen from NADH, and the NADH is oxidized into NAD⁺ so that the cycle may repeat. The reaction is catalyzed by the enzymes pyruvate decarboxylase and alcohol dehydrogenase.

History of bioethanol fermentation

The history of ethanol as a fuel spans several centuries and is marked by a series of significant milestones. Samuel Morey, an American inventor, was the first to produce ethanol by fermenting corn in 1826. However, it was not until the California Gold Rush in the 1850s that ethanol was first used as a fuel in the United States. Rudolf Diesel demonstrated his engine, which could run on vegetable oils and ethanol, in 1895, but the widespread use of petroleum-based diesel engines made ethanol less popular as a fuel. In the 1970s, the oil crisis reignited interest in ethanol, and Brazil became a leader in ethanol production and use. The United States began producing ethanol on a large scale in the 1980s and 1990s as a fuel additive to gasoline, due to government regulations. Today, ethanol continues to be explored as a sustainable and renewable fuel source, with researchers developing new technologies and biomass sources for its production.

• 1826: Samuel Morey, an American inventor, was the first to produce ethanol by fermenting corn. However, ethanol was not widely used as a fuel until many years later. (1)
• 1850s: Ethanol was first used as a fuel in the United States during the California gold rush. Miners used ethanol as a fuel for lamps and stoves because it was cheaper than whale oil. (2)
• 1895: German engineer Rudolf Diesel demonstrated his engine, which was designed to run on vegetable oils, including ethanol. However, the widespread use of diesel engines fueled by petroleum made ethanol less popular as a fuel. (3)
• 1970s: The oil crisis of the 1970s led to renewed interest in ethanol as a fuel. Brazil became a leader in ethanol production and use, due in part to government policies that encouraged the use of biofuels. (4)
• 1980s–1990s: The United States began to produce ethanol on a large scale as a fuel additive to gasoline. This was due to the passage of the Clean Air Act in 1990, which required the use of oxygenates, such as ethanol, to reduce emissions. (5)
• 2000s–present: There has been continued interest in ethanol as a renewable and sustainable fuel. Researchers are exploring new sources of biomass for ethanol production, such as switchgrass and algae, and developing new technologies to improve the efficiency of the fermentation process. (6)

Lactate

Main article: Lactic acid fermentation See also: Mixed acid fermentation, Lactate shuttle hypothesis, and Lactic acidosis

Pyruvate is the terminal electron acceptor in lactic acid fermentation, and homolactic fermentation (producing only lactic acid) is the simplest type of fermentation. Pyruvate from glycolysis undergoes a simple redox reaction, forming lactic acid. Overall, one molecule of glucose (or any six-carbon sugar) is converted to two molecules of lactic acid:

C₆H₁₂O₆ → 2 CH₃CHOHCOOH

It occurs in the muscles of animals when they need energy faster than the blood can supply oxygen. (In mammals, lactate can be transformed by the liver back into glucose using the Cori cycle.) It also occurs in some kinds of bacteria (such as lactobacilli) and some fungi. It is the type of bacteria that convert lactose into lactic acid in yogurt, giving it its sour taste. These lactic acid bacteria can carry out either homolactic fermentation, where the end-product is mostly lactic acid, or heterolactic fermentation, where some lactate is further metabolized to ethanol and carbon dioxide (via the phosphoketolase pathway), acetate, or other metabolic products, e.g.:

C₆H₁₂O₆ → CH₃CHOHCOOH + C₂H₅OH + CO₂

If lactose is fermented (as in yogurts and cheeses), it is first converted into glucose and galactose (both six-carbon sugars with the same atomic formula):

C₁₂H₂₂O₁₁ + H₂O → 2 C₆H₁₂O₆

Heterolactic fermentation is in a sense intermediate between lactic acid fermentation and other types, e.g. alcoholic fermentation. Reasons to go further and convert lactic acid into something else include:

• The acidity of lactic acid impedes biological processes. This can be beneficial to the fermenting organism as it drives out competitors that are unadapted to the acidity. As a result, the food will have a longer shelf life (one reason foods are purposely fermented in the first place); however, beyond a certain point, the acidity starts affecting the organism that produces it.
• The high concentration of lactic acid (the final product of fermentation) drives the equilibrium backwards (Le Chatelier's principle), decreasing the rate at which fermentation can occur and slowing down growth.
• Ethanol, into which lactic acid can be easily converted, is volatile and will readily escape, allowing the reaction to proceed easily. CO₂ is also produced, but it is only weakly acidic and even more volatile than ethanol.
• Acetic acid (another conversion product) is acidic and not as volatile as ethanol; however, in the presence of limited oxygen, its creation from lactic acid releases additional energy. It is a lighter molecule than lactic acid, forming fewer hydrogen bonds with its surroundings (due to having fewer groups that can form such bonds), thus is more volatile and will also allow the reaction to proceed more quickly.
• If propionic acid, butyric acid, and longer monocarboxylic acids are produced, the amount of acidity produced per glucose consumed will decrease, as with ethanol, allowing faster growth.

Hydrogen gas

Main article: Fermentative hydrogen production

Hydrogen gas is produced in many types of fermentation as a way to regenerate NAD⁺ from NADH. Electrons are transferred to ferredoxin, which in turn is oxidized by hydrogenase, producing H₂. Hydrogen gas is a substrate for methanogens and sulfate reducers, which keep the concentration of hydrogen low and favor the production of such an energy-rich compound, but hydrogen gas at a fairly high concentration can nevertheless be formed, as in flatus.

For example, Clostridium pasteurianum ferments glucose to butyrate, acetate, carbon dioxide, and hydrogen gas. The reaction leading to acetate is:

C₆H₁₂O₆ + 4 H₂O → 2 CH₃COO⁻ + 2 HCO₃⁻ + 4 H⁺ + 4 H₂

Glyoxylate

Glyoxylate fermentation is a type of fermentation used by microbes that are able to utilize glyoxylate as a nitrogen source.

Other

Other types of fermentation include mixed acid fermentation, butanediol fermentation, butyrate fermentation, caproate fermentation, and acetone–butanol–ethanol fermentation.

In the broader sense

In food and industrial contexts, any chemical modification performed by a living being in a controlled container can be termed "fermentation". The following do not fall into the biochemical sense, but are called fermentation in the larger sense:

Alternative protein

Further information: List of fermented foods

Fermentation is used to produce the heme protein found in the Impossible Burger.

Fermentation can be used to make alternative protein sources. It is commonly used to modify existing protein foods, including plant-based ones such as soy, into more flavorful forms such as tempeh and fermented tofu.

More modern "fermentation" makes recombinant protein to help produce meat analogue, milk substitute, cheese analogues, and egg substitutes. Some examples are:

• Recombinant myoglobin for faux meat (Motif Foodworks)
• Recombinant leghemoglobin for faux meat (Impossible Foods)
• Recombinant whey protein for dairy replacement (Perfect Day)
• Recombinant casein protein for dairy replacements (Those Vegan Cowboys)
• Recombinant egg white (EVERY)

Heme proteins such as myoglobin and hemoglobin give meat its characteristic texture, flavor, color, and aroma. The myoglobin and leghemoglobin ingredients can be used to replicate this property, despite them coming from a vat instead of meat.

Enzymes

Industrial fermentation can be used for enzyme production, where proteins with catalytic activity are produced and secreted by microorganisms. The development of fermentation processes, microbial strain engineering and recombinant gene technologies has enabled the commercialization of a wide range of enzymes. Enzymes are used in all kinds of industrial segments, such as food (lactose removal, cheese flavor), beverage (juice treatment), baking (bread softness, dough conditioning), animal feed, detergents (protein, starch and lipid stain removal), textile, personal care and pulp and paper industries.

Modes of industrial operation

Most industrial fermentation uses batch or fed-batch procedures, although continuous fermentation can be more economical if various challenges, particularly the difficulty of maintaining sterility, can be met.

Batch

In a batch process, all the ingredients are combined and the reactions proceed without any further input. Batch fermentation has been used for millennia to make bread and alcoholic beverages, and it is still a common method, especially when the process is not well understood. However, it can be expensive because the fermentor must be sterilized using high pressure steam between batches. Strictly speaking, there is often addition of small quantities of chemicals to control the pH or suppress foaming.

Batch fermentation goes through a series of phases. There is a lag phase in which cells adjust to their environment; then a phase in which exponential growth occurs. Once many of the nutrients have been consumed, the growth slows and becomes non-exponential, but production of secondary metabolites (including commercially important antibiotics and enzymes) accelerates. This continues through a stationary phase after most of the nutrients have been consumed, and then the cells die.

Fed-batch

See also: Fed-batch culture

Fed-batch fermentation is a variation of batch fermentation where some of the ingredients are added during the fermentation. This allows greater control over the stages of the process. In particular, production of secondary metabolites can be increased by adding a limited quantity of nutrients during the non-exponential growth phase. Fed-batch operations are often sandwiched between batch operations.

Open

The high cost of sterilizing the fermentor between batches can be avoided using various open fermentation approaches that are able to resist contamination. One is to use a naturally evolved mixed culture. This is particularly favored in wastewater treatment, since mixed populations can adapt to a wide variety of wastes. Thermophilic bacteria can produce lactic acid at temperatures of around 50 °Celsius, sufficient to discourage microbial contamination; and ethanol has been produced at a temperature of 70 °C. This is just below its boiling point (78 °C), making it easy to extract. Halophilic bacteria can produce bioplastics in hypersaline conditions. Solid-state fermentation adds a small amount of water to a solid substrate; it is widely used in the food industry to produce flavors, enzymes and organic acids.

Continuous

In continuous fermentation, substrates are added and final products removed continuously. There are three varieties: chemostats, which hold nutrient levels constant; turbidostats, which keep cell mass constant; and plug flow reactors in which the culture medium flows steadily through a tube while the cells are recycled from the outlet to the inlet. If the process works well, there is a steady flow of feed and effluent and the costs of repeatedly setting up a batch are avoided. Also, it can prolong the exponential growth phase and avoid byproducts that inhibit the reactions by continuously removing them. However, it is difficult to maintain a steady state and avoid contamination, and the design tends to be complex. Typically the fermentor must run for over 500 hours to be more economical than batch processors.

History of the use of fermentation

Main article: Fermentation in food processing

The use of fermentation, particularly for beverages, has existed since the Neolithic and has been documented dating from 7000 to 6600 BCE in Jiahu, China, 5000 BCE in India, Ayurveda mentions many Medicated Wines, 6000 BCE in Georgia, 3150 BCE in ancient Egypt, 3000 BCE in Babylon, 2000 BCE in pre-Hispanic Mexico, and 1500 BC in Sudan. Fermented foods have a religious significance in Judaism and Christianity. The Baltic god Rugutis was worshiped as the agent of fermentation.

Louis Pasteur in his laboratory

The 'father of modern chemistry', Antoine Lavoisier, had viewed fermentation as a simple chemical reaction and rejected the notion that living organisms could be involved. By the 19th century, this was seen as vitalism, which was lampooned in an anonymous 1839 publication by Justus von Liebig and Friedrich Wöhler.

In 1837, Charles Cagniard de la Tour, Theodor Schwann and Friedrich Traugott Kützing independently published papers concluding, as a result of microscopic investigations, that yeast is a living organism that reproduces by budding. Schwann boiled grape juice to kill the yeast and found that no fermentation would occur until new yeast was added. The turning point came when Louis Pasteur (1822–1895), during the 1850s and 1860s, repeated Schwann's experiments and showed fermentation is initiated by living organisms in a series of investigations. In 1857, Pasteur showed lactic acid fermentation is caused by living organisms. In 1860, he demonstrated how bacteria cause souring in milk, a process formerly thought to be merely a chemical change. His work in identifying the role of microorganisms in food spoilage led to the process of pasteurization.

In 1877, working to improve the French brewing industry, Pasteur published his famous paper on fermentation, "Etudes sur la Bière", which was translated into English in 1879 as "Studies on fermentation". He defined fermentation (incorrectly) as "Life without air".

Although showing fermentation resulted from the action of living microorganisms was a breakthrough, it did not explain the basic nature of fermentation; nor did it prove it is caused by microorganisms which appear to be always present. Many scientists, including Pasteur, had unsuccessfully attempted to extract the fermentation enzyme from yeast.

Success came in 1897 when the German chemist Eduard Buechner ground up yeast, extracted a juice from them, then found to his amazement this "dead" liquid would ferment a sugar solution, forming carbon dioxide and alcohol much like living yeasts.

Buechner's results are considered to mark the birth of biochemistry. The "unorganized ferments" behaved just like the organized ones. From that time on, the term enzyme came to be applied to all ferments. It was then understood fermentation is caused by enzymes produced by microorganisms. In 1907, Buechner won the Nobel Prize in chemistry for his work.

Advances in microbiology and fermentation technology have continued steadily up until the present. For example, in the 1930s, it was discovered microorganisms could be mutated with physical and chemical treatments to be higher-yielding, faster-growing, tolerant of less oxygen, and able to use a more concentrated medium.

Post 1930s

The field of fermentation has been critical to producing a wide range of consumer goods, from food and drink to industrial chemicals and pharmaceuticals. Since its early beginnings in ancient civilizations, fermentation has continued to evolve and expand, with new techniques and technologies driving advances in product quality, yield, and efficiency. The period from the 1930s onward saw a number of significant advancements in fermentation technology, including the development of new processes for producing high-value products like antibiotics and enzymes, the increasing importance of fermentation in the production of bulk chemicals, and a growing interest in the use of fermentation for the production of functional foods and nutraceuticals.

In the 1970s and 1980s, fermentation became increasingly important in producing bulk chemicals like ethanol, lactic acid, and citric acid. This led to developing new fermentation techniques and genetically engineered microorganisms to improve yields and reduce production costs. In the 1990s and 2000s, there was a growing interest in fermentation to produce functional foods and nutraceuticals, which have potential health benefits beyond basic nutrition. This led to new fermentation processes, probiotics, and other functional ingredients.

Circular economy

Recent research has begun to investigate the relationship between fermentation and creating a circular economy in effort to address the current climate crisis and the increasing demands for resources as the population grows. The production of fuels, materials, and other chemicals has led to a notable increase in greenhouse gasses and a subsequent increase in global temperatures. The current, linear economy relies heavily on fossil fuels and nonrenewable energy to produce chemicals and materials. In a circular economy, the use of renewable resources would be employed to produce chemicals; moreover, this type of economy focuses on reusing end-of-life chemicals and materials. Investigation into alternative biofuels and biomaterials has become increasingly popular with fermentation as a notable method.

The primary source of biomass for fermentation is using biomass feedstocks which contain a mix of carbohydrates, proteins, oils and fats, and lignin. Carbohydrates such as sucrose and starch (sources include sugarcane, corn, and cassava) are the most commonly used substrate for fermentation; however, in the discussion of biofuels, there are concerns regarding land competition between food and fuel biomass. Attention has been turned towards second-generation biomass feedstock such as silvergrass or wood chips.  

Anaerobic digestion

Anerobic digestion is found in all facets of biomass fermentation to create biofuels, biobased materials, and biochemicals. One of the most popular and established anaerobic fermentation process is the transformation of organic waste into biogas. Further research has explored the possibility and reusing residual solids left over from fermentative processes and converting them into "char-based materials". If successful, this would promote increased efficiency and a decreased environmental impact in the biomanufacturing industry. Additionally, homogenous gas streams of CO_2, and CH_4, can be formed from anaerobic digestion by some bacteria, while other bacteria are able to fixate CO₂ or CO and convert them into alcohols or fatty acids.

Biofuel production

One the most widely known biobased chemicals produced through fermentation, the process of fermenting sugars from plants into ethanol and CO₂ uses Saccharomyces cerevisiae. Biobased ethanol is used as a popular renewable transportation fuel and also holds value in the chemical industry as the precursor for ethylene, which can be converted into polyethylene. Commercial bioethanol production via fermentation is dominant in Brazil and the USA and employs sugarcane and starch from corn as feedstocks. The process involves starch enzymatic hydrolysis to glucose, followed by fermentation and distillation. There were around 200 ethanol plants operating in the U.S. as of 2021, with capacities of production varying from 6 kilotonnes to over one million tonnes annually.

Biochemical production

Succinic acid is an important biobased chemical utilized for the production of biodegradable polymers including polybutylene succinate (PBS) and as feedstock to other biobased chemicals like 1,4-butanediol. Succinic acid can be produced via the fermentation of sugar and carbon dioxide using native strains of bacteria; however, yields depend upon strain and conditions. Neutral or acidic fermentations are feasible, with low-pH fermentations facilitated by acid-resistant yeast strains simplifying downstream recovery through avoiding neutralization and reacidification.

Throughout the 2010s, several companies ordered commercial-scale production facilities, e.g., BioAmber, Myriant, Reverdia, and Succinity, on different host organisms and feedstocks like corn syrup and sorghum starch. While having proven the technical feasibility of succinic acid large-scale biobased production, most of them failed to compete economically with petrochemical products on a commercial scale. Several of the plants were spun off or shut down to new proprietors, demonstrating the financial challenges of scaling up bio-based platforms within current markets. However, these projects are evidence that under right market conditions, succinic acid biobased has promise for greater industrial use.

Product production

Fermentation plays a significant role in producing precursor polymers to products and food additives such as amino acids, organic acids, triglycerides and fatty acids.

Amino acids are industrially produced through fermentation by microorganisms such as Corynebacterium glutamicum and Escherichia coli. The global market application for amino acids is primarily food and feed additive. L-glutamic acid and L-lysine are the most commonly found amino acids in this market with L-glutamic acid being mainly used as a food flavoring in the form of monosodium glutamate (MSG) and L-lysine being mainly used as an animal feed supplement. Other amino acids like L-threonine and L-phenylalanine are also produced on large scales for different applications.

Organic acids such as citric acid, lactic acid, and acetic acid are procured by microbial fermentation. Citric acid finds widespread use in the food industry as a preservative and flavoring agent. Lactic acid is used in food preservation and as a precursor for biodegradable plastics. Acetic acid is used in food as vinegar and as a chemical reagent in industries. These organic acids are produced using microorganisms like Aspergillus niger and Lactobacillus species under controlled fermentation conditions.

Fatty acids and triglycerides are produced by fermentation on oleaginous microorganisms such as Yarrowia lipolytica and certain fungi. These microorganisms can accumulate lipids under specific culture conditions and therefore are suitable for industrial-scale production of lipids. The fatty acids produced can be used in the manufacture of soaps, detergents, and as starting compounds for various chemicals. Triglycerides are energy storage compounds with applications in the food industry and biofuel sector. The fermentation processes involve the optimization of environmental conditions and nutrient composition for maximum lipid accumulation.