The chemical logic behind... Fermentation and Respiration

Prof. Doutor Pedro Silva

Associate Professor, Universidade Fernando Pessoa


Other metabolic pathways:

Enzymes relay the electrons released by substrate oxidation to special molecules we call electron acceptors. Electron acceptors may be organic or inorganic, and the most common examples thereof are NAD+ and FAD. Each of these molecules ca accept two electrons, yielding NADH+H+ and FADH2, respectively. Since cellular amounts of NAD+ and FAD are very small, special mechanisms are needed in order to convert NADH+H+ and FADH2 back into NAD+ and FAD. This is performed through electron transfer from NADH+H+ and FADH2 to other molecules, which may occur through either fermentation or respiration. Contrary to general belief, the distinction between these two processes does not lie on a requirement for O2!


In fermentation, NADH (or FADH2) donates its electrons to a molecule produced by the same metabolic pathway that produced the electrons carried by NADH (or FADH2). For instance, during intense physical exercise by muscles, NADH generated through glycolysis transfers its electrons to pyruvate (an organic molecule produced by glycolysis), yielding lactate.

(The relationship between the pH drop in muscles during lactate production and the occurrence of cramps is discussed in detail in these two papers). This process is called lactic fermentation . Many other kinds of fermentation have been found in microorganisms, and the most well-known among these is alcoholic fermentation:


In respiration, the final acceptor of NADH (or FADH2) electrons is not a product of the metabolic pathway that released the electrons carried by NADH (or FADH2). Many microorganisms use SO42-, SeO42- ,NO3-, NO2-, NO, U6+ (uranium), Fe3+, H+, etc. as final electron acceptors. Mammals use O2, and their respiration is therefore called aerobic respiration. Aerobic respiration happens in the inner mitochondrial membrane, which contains the relevant electron-transfering protein complexes. each of these complexes accepts electrons from a molecule and transfers them to a different compound, and the full assembly is therefore termed theelectron transport chain:

In complexes I, III and IV , electron transfer releases enough energy to transfer H+ from the mitochondrial matrix to the intermembrane space. This causes an increase of H+ concentration (and electric potential) in the intermembrane s+ace, i.e. a larger chemical potential of H+ in the intermembrane space relative to the matrix. However, when we have two solutions with different concentrations on both sides of a membrane, solute tend to diffuse from the regions of higher chemical potential to areas of lower potential (for a neutral species, this is equivalent to moving from areas of higher concentration to areas of lower concentration).

The inner mitochondrial membrane is not permeable to H+. Under normal conditions, the only way for protons to flow back to the matrix is through a special protein: ATP synthetase. This complex protein contains two major portions: an intermembrane proton channel (F0) coupled to a catalytic protein complex (F1) facing the mitochondrial matrix. The F1 portion contains several subunits with different functions, and converts the energy released by the return of protons to the matrix into chemical energy used to synthesize ATP from ADP and Pi.

NADH is unable to cross the mitochondrial membrane. There are therefore mechanisms to transfer electrons from NADH molecules produced in the cytoplasm during glycolisis to the electron transport chain. These are:

  • the malate-aspartate shuttle (which also works in gluconeogenesis): NADH transfers its electrons to oxaloacetate, converting it to malate. Malate can enter the mitochondrion, where it is dehidrogenated to oxaloacetate and transfer is electrons to NAD+. This NADH then transfers its electrons to teh electron transport chain through complex I. Through this shuttle, approxiamtely 3 ATP are produced from each cytoplasmic NADH.

  • the glycerol-3-P shuttle. In this shuttle, which is very active in brown adipose tissue, cytoplasmic NADH transfer its electrons to the glycolytic intermediate DHAP (dihydroxyacetone phosphate). DHAP is converted to glycerol-3-P, which donates its electrons to ubiquinone through a FAD-linked glycerol-3-P dehydrogenase located in the outer face of the inner mitochondrial membrane. Through this shuttle, approxiamtely 2 ATP are produced from each cytoplasmic NADH.

    The amount of ATP produced by ATP synthase is therefore related to the difference in H+ concentration across the membrane. Since NADH oxidation causes prroton efflux from the matrix in three protein complexes (I, III e IV), whereas FADH2 oxidation to FAD is only accompanied by such an efflux in two complexes (III e IV), more ATP can be produced from NADH than from FADH2. Oxidation of a NADH molecule produces almost 3 ATP, and FADH2 oxidation yields almost 2 ATP.

    Mitochondrial respiration may occur without ATP production, as long as the released protons are able to return to the matrix without passing through the ATP synthetase. This can happen e.g. if ionophores (lipid-soluble molecules with the ability to transport ions) are added to the mitochondria. In brown adipose tissue, a special protein (thermogenin) forms a proton channel in the mitochondion inner membrane. The flow of protons back into the matrix through this protein instead of ATP synthetase is responsible for the heat generation characteristic of this tissue.

    Further reading

    cover Biochemistry, by Donald Voet & Judith Voet

    An excellent text. It presents Biochemistry with frequent references to organic chemistry and biochemical logic. Highly reccommended for students of Biochemistry, Chemistry and Pharmaceutical Sciences.

    cover Biochemistry, Stryer

    A widely used classical text, frequently updated and re-issued.

    cover Textbook of Biochemistry with Clinical Correlations, Thomas Devlin

    Strongly advised to students in Nursing, Medicine, Dentistry, etc. Plenty of examples of application of biochemical knowledge to clinical cases.

    cover Principles of Biochemistry, Lehninger

    A widely used classical text, frequently updated and re-issued.