Evolutionary Perspective on Learning Energy Metabolism

Over many years of teaching Intro Biology, I have found that the unit on energy metabolism, comprising cellular respiration and photosynthesis, has been the most difficult for students to master. The pathways are complex, they occur in different cellular compartments, and vary depending on the availability of oxygen. The standard freshman biology textbook presentation focuses on glucose metabolism, and does not even begin to address metabolic diversity and barely touches on catabolism of fatty acids and amino acids. Moreover, the standard textbook version of how this elaborate metabolic network evolved beginning with glycolysis is probably wrong, accordingly to the newly published essay by Lane et al. (2010). What I would like to do, instead, is present an evolutionary approach that begins with concepts and processes fundamental to all living cells, that must have been present in the last universal common ancestor (LUCA).

How do cells get the energy to perform work?

ATP synthesis and hydrolysis

We find that all cells – Bacteria, Archaea, Eukarya – use the energy released via ATP hydrolysis to ADP and inorganic phosphate to perform most of the cellular work. How do cells make ATP? Cells can regenerate ATP from ADP in either of two ways: either by substrate-level phosphorylation, or by oxidative phosphorylation.

Substrate-level phosphorylation means that a phosphate is transferred to ADP from a phosphorylated organic compound.  A couple of the enzymes in glycolysis make ATP through substrate-level phosphorylation, as well as an enzyme in the citric acid cycle.  However, these reactions tap only a small fraction of the potential energy in glucose, so that only a small amount of ATP is made this way in cells undergoing respiration. Substrate-level phosphorylation by glycolysis enzymes is the major source of ATP only in cells undergoing fermentation (fermentative cells perform glycolysis, but no respiration).

Oxidative phosphorylation is an apparently more complex process where a proton-motive force across a membrane powers an ATP synthase enzyme complex (a molecular machine) to make ATP from ADP and inorganic phosphate.  Oxidative phosphorylation is coupled to oxidative pathways that release large amounts of free energy, and makes the vast majority of the ATP in respiring cells.  Surprisingly, oxidative phosphorylation appears to be at least as ancient as glycolysis and fermentation, and operates in both anaerobic and aerobic environments. Oxidative phosphorylation may have played a key role in the origin of life in reducing environments created by alkaline hydrothermal vents (Lane et al. 2010), such as the Lost City, pictured below.

Lost City carbonate chimneys

Cellular Metabolic Pathways

The energy for ATP synthesis via either substrate-level phosphorylation or oxidative phosphorylation comes from organic molecules (such as carbohydrates), or from sunlight, or from inorganic electron donors. We can classify organisms according to their source of energy and organic carbon:

  • heterotrophs – get energy and organic carbon from metabolism of pre-existing organic compounds (food)
  • photoautotrophs – use energy from sunlight to make their own organic carbon compounds from carbon dioxide
  • chemoautotrophs – use energy from inorganic chemicals to make their own organic carbon compounds from carbon dioxide

Metabolic pathways carry out reactions that capture energy from these various sources (organic compounds, sunlight or chemicals) and couple them to synthesis of ATP from ADP.

Update July 2010:  in light of the biggest news event of this summer, the BP oil spill in the gulf, here are links to articles on cold-seep communities in the Gulf of Mexico, where the energy source for primary production by chemosynthetic bacteria is from hydrocarbons and hydrogen sulfide:

NY Times:  http://www.nytimes.com/2010/06/22/science/22cool.html

Science News Daily: http://bit.ly/asIzSV

Wikipedia: http://en.wikipedia.org/wiki/Cold_seep

Redox Reactions

In these metabolic pathways, we find that the most free energy is released by oxidation-reduction reactions, also known as redox reactions. Redox reactions are electron transfer reactions.  A molecule that loses electrons is oxidized; a molecule that gains electrons is reduced. Different molecules have different tendencies to gain electrons, called the redox potential. A redox reaction between a pair of molecules with a large difference in redox potential results in a large release of free energy. In cells and aqueous environments, the electrons are accompanied by protons. The result is that hydrogen atoms are being transferred, and many enzymes that carry out redox reactions are called dehydrogenases. Living cells are the original hydrogen fuel cells!

Cellular energy metabolism features a series of redox reactions. Heterotrophs oxidize (take electrons from) organic molecules (food) and give them to an electron carrier molecule, called NAD+ (in the oxidized form)  that accepts electrons from food to become NADH (the reduced form). NADH then cycles back to NAD+ by giving electrons to (reducing) an electron acceptor protein in a membrane, thus becoming oxidized to NAD+ again. In the membrane, the electrons are transferred down an electron transport chain, consisting of a series of membrane proteins and molecules with increasing redox potential. Components of the electron transport chain use the sequential releases of free energy to pump protons across the membrane against their electrochemical gradient.  The resulting H+ concentration (pH) gradient across the membrane is a form of stored energy, analogous to an electric battery. At the end of the electron transport chain is the  terminal electron acceptorThe terminal electron acceptor is molecular oxygen (O2) in aerobic respiration, and other molecules such as nitrate, iron, or sulfate in anaerobic respiration.


The cascade of electrons transfers (redox reactions), that culminates in the reduction of the terminal electron acceptor, is called respiration. The amount of energy released by these redox reactions, and thus the amount of energy available for ATP synthesis, depends on the redox potential of the terminal electron acceptor. Oxygen (O2) has the greatest redox potential, and thus aerobic respiration results in the most ATP synthesized. Bacteria and Archaea can use other terminal electron acceptors with lower redox potential when oxygen is not available. This anaerobic respiration produces less ATP.

Bacteria can modify their electron transport chains to use a variety of electron donors and electron acceptors, and will switch to the best available electron sources and sinks available in their environment.  In marine sediments, microbial communities stratify according to redox potential.  The deeper, more anoxic layers use electron acceptors with progressively lower reducing potential.


All prokaryotic cells (bacteria and archaea) maintain a proton gradient (pH gradient) across their plasma membranes. The interior of the cell is relatively alkaline, whereas the exterior is relatively acidic. A 1000-fold difference in proton concentrations across the membrane results in a proton motive force, consisting of both the chemical concentration gradient of protons and a voltage gradient across the membrane.  Free energy is released by the return of protons across the membrane down their concentration and voltage gradients.  The lipid bilayer membrane is relatively impermeable to protons, so energy released by diffusion of protons via transport proteins and proton channels can be used by the cell to accomplish work, such as active transport of substances across the membrane and  synthesis of ATP from ADP and inorganic phosphate.  The proton diffusion-powered synthesis of ATP is called chemiosmosis.

In eukaryotes, mitochondria maintain a proton gradient across the inner mitochondrial membrane and chloroplasts maintain a proton gradient across the thylakoid membrane.  Since both these organelles are thought to have originated as prokaryotic endosymbionts, the mitochondrial inner membrane and the thylakoid membrane correspond to the original plasma membranes of the ancestral endosymbionts. Both mitochondria and chloroplasts use the proton gradient for chemiosmotic ATP synthesis and active transport of metabolites into and out of the organelles.

F1ATP Synthase

Oxidative phosphorylation is the process of chemiosmotic ATP synthesis, using energy from a membrane proton gradient. The F1ATP synthase enzyme complex that performs this task is located in the membrane, and is a remarkable rotor-stator molecular machine (Stock et al. 1999).

The proton motive force drives protons through a channel in the ATP synthase, and turns the rotor at approx 100 rpm.  The turning rotor changes the shape of the cytoplasmic subunits, which bind ADP and inorganic phosphate and bond them together to form ATP. Each 360 degree turn of the rotor results in synthesis of 3 ATP molecules. This method of ATP synthesis is called oxidative phosphorylation, because the proton gradient is generated, and maintained, by redox reactions that actively transport protons across the membrane.

The ATP synthases in mitochondria, chloroplasts, and bacteria are all structurally similar, and highly homologous at the molecular sequence level (Watt et al. 2010). A lesser degree of similarity, and more distant homology, exists with archaeal ATP synthases and vacuolar membrane ATPases that function in active transport of protons across the membrane, using the energy from ATP hydrolysis. Indeed, ATP synthases can work in reverse to hydrolyze ATP and replenish the membrane proton gradient.

The generation of a proton gradient across a membrane and chemiosmosis are universal to life on earth, and are  fundamental ways for cells to make a living. Lane and colleagues speculate that “proton power” may have been the earliest form of energy metabolism, essential to, and pre-dating, the last universal common ancestor, LUCA (Lane, 2009; Lane et al. 2010).


Lane, N 2009 Was our oldest ancestor a proton-powered rock? New Scientist 19 October 2009 http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html?page=1

Lane, N, JF Allen, W Martin 2010 How did LUCA make a living? Chemiosmosis in the origin of life. BioEssays DOI 10.1002/bies.200900131

Stock D, Leslie AGW, Walker JE 1999 Molecular architecture of the rotary motor in ATP synthase. Science 286:1700–1705. Abstract/FREE Full Text

Watt, IN, MG Montgomery, MJ Runswick, AGW Leslie, JE Walker 2010 Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria PNAS 107 : 16823-16827 doi:10.1073/pnas.1012260107


About jchoigt

I'm an Associate Professor in the School of Biology at Georgia Tech, and Faculty Coordinator of the Professional MS Bioinformatics degree program.
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9 Responses to Evolutionary Perspective on Learning Energy Metabolism

  1. Biology 1510 Student says:

    Is the “rotor-stator molecular machine” in cellular respiration the same as whatever powers the flagella for locomotion?

    Since it is like a “machine”, is there a way to continually force ATP production even if concentrations are higher on the inside than the out? (What about a “prosthetic” synthase?) What would happen if ATP synthesis occurs only in one direction within that cell?

    • jchoigt says:

      There are some similarities between the flagellar motor and the ATP synthase. As long as there is sufficient proton motive force, and ADP to be phosphorylated, ATP synthase will continually synthesize ATP. Not sure what you mean by a “prosthetic” synthase or ATP synthesis occurring in only one direction.

  2. Biology 1510 Student says:

    Oh, I just forgot to realize that ATP production in the synthase of course wouldn’t continue to try and produce more ATP without proton concentration on the outside…

    Why does the ATP synthase need to work in reverse? A high concentration of ATP would be a good thing, why would it need to hydrolyze ATP instead of just storing the ATP?

    • jchoigt says:

      The ATP synthase does not usually work in reverse. In bacteria, the proton gradient is used for flagellar locomotion and active transport of some substances, so if the cell has plenty of ATP, and the proton gradient has been depleted, the bacterial cell can replenish the proton gradient by running ATP synthase in reverse. I’m not sure if ATP synthase ever runs in reverse in mitochondria – I can’t think of how the mitochondria would have high levels of ATP if the proton gradient is depleted.

  3. Bio 1510 says:

    Can you help me understand cellular respiration and fermentation?
    I get glycolysis, but what are the sub-parts of cellular respiration and fermentation. Is citric acid cycle in the cellular respiration category? Is there a specific diagram of cellar respiration or fermentation that we should really focus on?

    • Bio 1510 says:

      And also, is not glycolysis part of cellular respiration? and oxidative phospohorylation these are all components of cellular respiration?
      Because lecture you wanted us to diagram for

      And fermentation consists of glycolysis also. And is the purpose for fermentation the replenishing of NAD+ or electron acceptors or something that it regenerates?

      • jchoigt says:

        Respiration is the oxidation of organic compounds to carbon dioxide. Cells can oxidize sugars such as glucose, fats, and proteins to provide energy to make ATP. Which pathways are needed depends on the compound that is being oxidized. Glucose oxidation involves glycolysis, pyruvate oxidation, and the citric acid cycle. Oxidation of fatty acids involves mainly the citric acid cycle.
        Respiration pathways all require a functional electron transport chain. Notice that they all require NAD+ (and FAD for the citric acid cycle) as electron acceptors, and generate reduced electron carriers, NADH (and FADH2 in the case of the citric acid cycle). NADH and FADH2 give their electrons to the electron transport chain and thereby return to their oxidized forms, NAD+ and FAD to keep the respiratory pathways running. The electron transport chain generates a proton gradient across the membrane for chemiosmotic ATP synthesis (oxidative phosphorylation)

        Fermentation reactions convert higher energy organic compounds to lower energy organic compounds, with no net oxidation (no net reduction of electron carriers). Fermentation reactions produce a much smaller deltaG than oxidation reactions, and therefore produce much less ATP (via substrate-level phosphorylation). Therefore, given a choice, cells will run respiration reactions rather than fermentation reactions.

        If cells cannot respire, because there is no suitable terminal electron acceptor available for their electron transport chain, they have to run fermentation. Fermentation regenerates NAD+ by using the NADH generated during glycolysis to reoxidize pyruvate to lactate or ethanol. So you can think of fermentation as an alternative way to regenerate NAD+, in the absence of the electron transport chain, in order to keep glycolysis going.

  4. Another Bio 1510 Student says:

    Our textbook goes into ten steps of detail about the process of glycolysis; will we need to learn all of those or should we instead learn the evolutionary approach described here?

    • I don’t see the point in students at this stage trying to memorize the detailed steps of glycolysis or the citric acid cycle. You can always look that up on Wikipedia or other places. I’m more concerned that you should realize that all life on earth makes ATP in fundamentally the same way, and what that means about how cells respired before there was oxygen, and how cells respire or ferment today in anaerobic environments. I think this is highly relevant for students of environmental engineering, bioenergy, as well as biology and biochemistry.

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