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       Bioenergetics is the study of energy flow through living systems. It encompasses the chemical reactions in cellular pathways that harness energy for biological functions. Much like the typical internal combustion engine, cells derive energy from hydrocarbons. On the cellular level, this begins with the breakdown of sugars into glucose and the subsequent breakdown of glucose itself, termed glycolysis, in the cytosol. In some cases, lipids are also used for this purpose in a process called lipolysis. The products enter into the Krebs cycle, also known as the tricarboxylic acid cycle (TCA) or the citric acid cycle, in the mitochondria. Following this, the electron transport chain (ETC) utilizes the proton motive force to generate ATP through ATP synthase. This article will provide a short summary of each of these steps.


       Of the sugars, glucose (C6H12O6) is the chief monosaccharide that cells use, although other sugars are used as well.  Glycolysis occurs in two major phases, the preparatory phase and the pay-off phase, and releases 2 molecules of pyruvate (CH3COCOO- + H+) and 2 molecules of reduced nicotinamide adenine dinucleotide (NADH) as the net products. A brief treatment of the reactions that occur is presented below. Additional links are also provided.

Glycolysis Table.jpg


For more information, please see here and here.


       Lipids are typically stored as triglycerides after absorption. Hormone-sensitive lipase catalyzes triglyceride release from fat stores, as well as the release of free fatty acids from glycerol. Transport through the outer mitochondrial membrane is performed by carnitine acyl-transferases while transport through the inner membrane into the matrix is carried out by carnitine. Once inside, the fatty acid-carnitine reacts with coenzyme A to produce acetyl coenzyme A (acetyl-CoA).



* Figure adapted from Lipid Library AOCS

β-oxidation occurs in four major steps:

  • Dehydrogenation by acyl-CoA dehydrogenase, producing 1 molecule of FADH2
  • Hydration by enoyl-CoA hydratase
  • Dehydrogenation by 3-hydroxyacyl-CoA dehydrogenase, producing 1 molecule of NADH
  • Cleavage by thiolase results in acetyl-CoA and a fatty acid shortened by 2 carbons

It is worthy to note that, within a physiological context, the thermodynamics governing lipid consumption actually yields more energy than that of glucose. This is mostly due to hydrophobic interactions excluding water from the lipid molecule during storage, while glucose has many groups on it that allow for hydration. Stored as a triglyceride, a gram of fatty acids equates to an estimated 9kcal while a gram of carbohydrate yields 4kcal.


       Fermentation occurs through two routes, alcoholic fermentation and lactic acid fermentation, so named for their products. Alcoholic fermentation, catalyzed by zymase, creates two molecules of ethanol and two molecules of carbon dioxide. Lactic acid fermentation, catalyzed by lactate dehydrogenase, generates two molecules of lactic acid. Both systems regenerate NAD+.



Fermentation has become particularly important in most recent times for its applicability in bioreactor construction for production of biomaterials. Because a number of microorganisms that produce commercially desirable products preferentially undergo fermentation, understanding how to manipulate these biochemical pathways in order to optimize yield of those products has become a chief priority for many researchers.

For additional information about fermentation, see here.

 Krebs Cycle

       The Krebs cycle, or the Citric Acid Cycle, follows after glycolysis and produces 2 more molecules of ATP (or GTP), 6 NAD+, two molecules of coenzyme Q (QH2), and two molecules of CO2 per glucose molecule. This process takes place in the mitochondria and sits at the crux of many major pathways. In addition to the products of glycolysis, the metabolism of amino acids and fatty acids also converge into the TCA. Additionally, citrate created by this cycle is an important part of fatty acid synthesis. Succinate, another product of the cycle, is an entrance point into the electron transport chain, described later.

Decarboxylation of pyruvate results in acetyl-CoA, a starting material for TCA cycle. A carbon receptor, oxaloacetate, is also necessary to begin the cycle.

Krebs Cycle.png

This table summarizes the reactants, products, enzymes involved in each process depicted above.






cis-Aconitate + Water

Cis-Aconite + Water



Isocitrate + NAD+

Isocitrate dehydrogenase

Oxalosuccinate + NADH + H+


Isocitrate dehydrogenase


α-Ketoglutarate + NAD++ CoA-SH

α-Ketoglutarate dehydrogrenase

Succinyl-CoA + NADH + H+ + CO2

Succinyl CoA + GDP/ADP + Pi

Succinyl-CoA synthetase

Succinate + CoA-SH + GTP/ATP

Succinate + ubiquinone

Succinate dehydrogenase

Fumarate + ubiquinol

Fumarate + Water



L-Malate + NAD+

Malate dehydrogenase 

Oxaloacetate + NADH + H+

Oxaloacetate + acetyl CoA + Water

Citrate Synthase

Citrate + CoA-SH

Note that the products of the Krebs cycle are the same as the starting materials. Regulation of this cycle occurs through the consumption of products and the ensuing balance between products and reactants.

For a more in-depth treatment, please see here.

 Electron Transport Chain

       In mitochondria, electrons progress along the ETC by transferring through several increasingly electronegative groups known as complexes.

Mito ETC3.png


  • Complex I (NADH dehydrogenase) transfers two electrons from NADH to ubiquinone (Q), creating ubiquinol (QH2). Four protons are transferred from the matrix to the intermembrane space, forming the proton gradient.
  • Complex II (succinate dehydrogenase) operates in parallel to complex I. FAD+ electron carriers from succinate aid in further electron transfer to ubiquinone. This process does not transfer any protons across the membrane.
  • Complex III (cytochome bc1) is a water soluble electron carrier in the intermembrane space consisting of Q0 and Qi sites. At the Q0 site, two cytochome C carriers receive two electrons from QH2 while two other electrons re-enter the quinone pool after reduction at the Qi site. At this, 4 protons are translocated from the reduction of quinone to quinol and the release of protons from two ubiquinol molecules.  
  • Complex IV (cytochrome C oxidase) catalyzes the last electron transfer from cytochrome C to molecular oxygen, creating two molecules of water. This complex also contributes to the proton gradient, translocating 2 protons across the membrane.

Occasionally, electron transfer will create free radicals that are damaging to the cell. The formation of free radicals and oxidative stress are thought to have roles in aging. Complex I is a main contributor to superoxide formation, due to electron leakage to the final electron acceptor oxygen. At higher membrane potentials, Complex III also contributes to this process.

In chloroplasts, a parallel system operates across the thylakoid membrane with its own very specialized players.

Chloro ETC2.png


  • Photosystem II (PSII) is comprised of the stromal facing light harvesting complex (LHC), and the lumenal facing oxygen evolving complex (OEC). The OEC splits molecules of water and deposits protons in the lumen. The antenna complex, built from light-sensitive pigments like carotenoids and chlorophyll a/b, is the site of electron excitation by a photon of 680nm.
  • Plastoquinone (PQ) accepts the electrons from PSII and binds two H+ from the stroma, becoming plastohydroquinone (PQH2).
  • Cytochrome b6f receives the electrons by oxidizing PQH2, releasing more protons into the lumen. The electrons are then passed onto photosystem I.
  • Photosystem I (PSI) is the second site of electron excitation, this time at a wavelength of 700nm. This passes the electrons to the next agents, ferrodoxin and ferrodoxin-NAD+ reductase.
  • Ferrodoxin (Fd) and ferrodoxin-NAD+ reductase (FNR) transfer the electrons to NAD+, allowing it to enter into further metabolic processes.

ATP synthase is the last component of the electron transport chain and the last component of the energy production arm of aerobic metabolism. The protein is a molecular generator comprised of two portions, the intermembrane F0 portion that functions as a channel and the intermembrane facing F1 portion that catalyzes the phosphorylation of ADP to ATP. It is the diffusion of protons down their gradient through this protein and turning the F1 crank that generates ATP. It is worthy to note that this process is regulated by the release of ADP from the F1 machinery. Without proton flow, ADP cannot be released and ATP cannot be generated.

The ETC has been extensively studied as a biophysical phenomenon for decades. Beginning with Peter Mitchell's chemiosmotic coupling hypothesis, the field has evolved to include intramembrane protein movement and membrane dynamics. 

For more information, visit The Electron Transport Chain.


       Biofuels take advantage of the products that living systems produce and repurpose them for fuel. Bioethanol is created via fermentation, and can be used as an additive to fuel for vehicles to improve emissions. Currently, corn has become a popular crop for this reason. Biodiesel is produced from hydrocarbons through transesterification and is generally composed of fatty acid methyl esterases (FAMEs). However, in order for new fuels to replace our current ones, they must be prepared relatively easily and yield at least as much energy. As such, development of new techniques for growing batch-culture microorganisms, like bacteria and algae, have made biodiesel production a burgeoning field.



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