Mitochondria: The Bacteria That Never Left

Every cell you have is running on a partnership that began about 1.5 billion years ago, when one cell swallowed another and the smaller one never left. What it became is the mitochondrion, and it is still carrying its own set of instructions.

This article looks at how that relationship shows up in the evidence. It covers how the energy is made, and why the ATP figure in most textbooks has been wrong for decades.

How Many, and Where

Mitochondria are usually drawn as bean-shaped, but they are not fixed like that. They fuse and divide continuously, and they move along the cytoskeleton. Boguszewska and colleagues describe them as a dynamic network rather than a bag of separate organelles.

The number per cell varies enormously. It runs from a handful to several thousand, and it tracks demand. Liver and heart muscle carry large numbers because they work continuously. A cell that mostly sits still needs fewer.

Mitochondria in a cell. Their number tracks how much energy the cell spends, which is why liver and heart muscle carry so many. Ryan Kissinger for NIAID, public domain, via Wikimedia Commons

Structurally there are two membranes. The outer one is porous, and porin channels may account for more than a third of its surface area. The inner one is the opposite. It is close to impermeable, and that is the point: it holds the gradient that the energy comes from.

The parts of a mitochondrion. The inner membrane folds inward into cristae, and the matrix between them is where the citric acid cycle runs. OpenStax, CC BY 4.0, via Wikimedia Commons

Folding is not decoration. Every fold increases the membrane area available to hold respiratory chain complexes and ATP synthases. That is why the inner membrane looks like a set of shelves rather than a smooth bag.

How We Know It Was a Bacterium

The strongest support for the endosymbiotic story is not a diagram. It is that mitochondria arrived carrying their own genome, and that the genome still works.

A tomogram of a single mitochondrion. The folded inner membrane, the cristae, is where the respiratory chain sits. Terrence G. Frey, CC BY 3.0, via Wikimedia Commons

A Genome, and a Very Small One

Boguszewska and colleagues report that human mitochondrial DNA carries 37 genes. Thirteen of them encode protein. The rest are ribosomal RNA and transfer RNA, which the mitochondrion needs to read those thirteen.

Now set that against the proteins a mitochondrion actually needs. Boguszewska and colleagues put the figure at about 1,100, and all but thirteen of them are encoded in the nucleus, made in the cytosol, then imported. The cell and the organelle have been sharing the work for so long that only a sliver of the original bacterial genome is left.

That sharing happened by a named process: endosymbiotic gene transfer. Genes for biosynthesis and other core functions moved to the host over time. That is why the bacterial ancestor and the nucleus are hard to separate from each other.

The Ancestor, More Precisely

The symbiont was not a generic bacterium. Boguszewska and colleagues place it among the alpha-proteobacteria, related to the Rickettsiales lineage. The host, they add, was most probably an archaeon, of the Asgard superphylum.

Martin and colleagues reach the same conclusion from a different direction. They argue that current versions of the theory have the host as an archaeon rather than another eukaryote.

That is a real correction to the older textbook version, in which one cell simply engulfed another. The host was not a fully formed eukaryotic cell. It was something simpler that ended up with more complexity afterwards.

The Argument That Held Up

The clean version says an aerobic bacterium was swallowed because oxygen was available and breathing was useful. Martin and colleagues note that more than 20 different versions of endosymbiotic theory have been published. The classical ones struggled with a specific problem.

If the organelle was always an oxygen breather, then the anaerobic versions of it are awkward. Those exist. They are called hydrogenosomes, and they make hydrogen instead of using oxygen. Classic accounts tended to explain them away as not being mitochondria at all.

Giardia intestinalis. It lives without oxygen and has no ordinary mitochondria, which is the strongest evidence that the organelle began as a free-living bacterium. Servier Medical Art, CC BY 2.0, via Wikimedia Commons

A Prediction That Held

The hydrogen hypothesis, as Martin and colleagues set it out, predicts three things. Every eukaryote has mitochondria or has secondarily lost them. The host was an archaeon. And aerobic and anaerobic forms should interleave across the eukaryotic tree, rather than sitting in separate groups.

They report that all three predictions have since been borne out. That is unusual here, and it is worth stating plainly. This is a case where a sharp prediction turned out to be right, not a story that kept being adjusted.

The energetic reason follows the same way. Martin and colleagues argue that only cells that had mitochondria had the bioenergetic means to reach eukaryotic complexity. They note there are no true intermediates between prokaryote and eukaryote, which is what you would expect if the transition was fast and once.

One historical correction is worth making, because it is often told wrongly. Martin and colleagues point out that Altmann is not credited with proposing the symbiotic origin of mitochondria. In his 1890 book he did not mention mitochondria, or their older name chondriosomes, and did not propose endosymbiosis.

How the Energy Is Made

Cellular respiration is usually taught as three stages. Keeping to three is fine, but the labels hide where each one actually happens and what it costs.

Glycolysis, in the Cytosol

One glucose molecule is split into two pyruvate, with a small amount of ATP made along the way. This happens outside the mitochondrion, in the cytosol, and it does not need oxygen.

That last point matters more than it looks. Glycolysis is the reason a cell can keep working when oxygen runs short, which is exactly what happens in exercising muscle.

The Citric Acid Cycle, in the Matrix

Pyruvate is broken down further, releasing carbon dioxide and loading electrons onto carriers. This runs in the matrix, the fluid inside the inner membrane.

Most of the energy is not stored as ATP at this stage. It goes onto carrier molecules, which is why the cycle is often described as producing very little ATP directly.

It is also wrong to say this cycle requires oxygen. It consumes no oxygen itself. It depends on oxygen only indirectly. The electron transport chain has to keep regenerating the oxidised carrier the cycle hands electrons to. Cut off the chain, and the cycle stalls on its own backlog.

The Chain, in the Inner Membrane

The carriers deliver their electrons to the respiratory chain, a series of complexes set into the inner membrane. As electrons move along it, protons get pumped out of the matrix into the intermembrane space.

Water forms at the end, as oxygen takes up the electrons and the protons that have come back through the motor. That is the only step in the whole pathway where molecular oxygen is consumed.

So the sequence is not "oxygen lets the cell make energy". It is "the chain moves electrons, and pumping protons needs somewhere to put them, and oxygen is what lets the used-up carriers start again."

The Motor That Does the Work

The protons now fall back through the inner membrane, and the thing they fall through is a rotary machine.

An ATP synthase. It is a rotary motor: protons flow through it down their gradient and the shaft turns, like a water wheel. Atpsynthesizer, CC BY-SA 3.0, via Wikimedia Commons

One Residue Does the Work

Klusch and colleagues solved the structure of an intact mitochondrial ATP synthase and found something surprisingly simple at the center of it.

The membrane part, called Fo, contains a ring of identical subunits. Each one has a single glutamate residue, and that residue is the proton-binding site. The lumen-facing channel protonates it. As the ring turns, that glutamate reaches the matrix-facing channel and releases the proton.

Meanwhile an arginine sits between the two channels and prevents protons leaking straight through. Klusch and colleagues argue the steep potential across that sub-nanometre gap is what produces net directional rotation. The gradient does the turning, and ATP comes out the other end.

Why the Ring Size Matters

The c-ring is not the same size in everything. Klusch and colleagues report 8 subunits in mammalian mitochondria and 10 in yeasts and in the alga they worked on. Across organisms the range runs from 8 to 15.

Each subunit carries one proton across per turn. A bigger ring means more protons per turn, and that single structural fact is part of why one cell type gets more ATP out of the same glucose than another.

The Number in the Textbooks Is Outdated

Here is the part most likely to surprise you, because the figure has been printed for fifty years.

Amthor traces the history. By the 1970s, standard biochemistry textbooks gave 36, or sometimes 38, ATP per glucose as the total from aerobic respiration. That was already under downward revision before 1980, as the mechanism of oxidative phosphorylation became better understood.

Later estimates kept falling: 29.5 or 31, then 32, then 30 or 32 again. Refining the count for the real structure of ATP synthases moved it further.

Source and year	ATP per hexose
Lehninger and Stryer, 1970s	36 or 38
Hinkle et al., 1991	29.5 or 31
Taiz and Zeiger, 1991	32
Stryer, 1995	30 or 32
Amthor model, 2023, potential	about 27.5

Estimated potential yield of aerobic respiration, from the figures Amthor (2023) reviews.

Amthor's own model, built for plant respiration, comes out near 27.5 ATP per hexose when respiring sucrose. And he is careful to say that is the potential.

Real yields sit below it. Energy-conserving steps in the chain get bypassed even in healthy, unstressed cells. If a quarter of oxygen uptake goes through an alternative oxidase, which Amthor says is a typical fraction, the yield falls about 15 percent below potential.

So there is no single correct number, and Amthor says so directly. A potential ATP yield is unlikely to be a universal biological constant. The transport pathways differ, the shuttles that move molecules across the membrane differ, and so does the ATP synthase.

What you can say is bounded. Glycolysis yields 2 ATP directly, and the cycle yields a small amount more. The overwhelming majority comes from the chain, which is where the oxygen is needed.

Who Figured This Out

The Nobel Foundation records that Albert Szent-Gyorgyi had already identified several important reactions in metabolism. In 1937 Hans Krebs was able to present a complete picture of a cyclical part of it.

Krebs shared the 1953 Nobel Prize in Physiology or Medicine. Half of it went to Fritz Lipmann, recognised for discovering coenzyme A and its importance in intermediary metabolism.

That pairing is the useful part. The cycle that became metabolism's central loop was assembled in the same year, by the same kind of work, as the coenzyme that carries its products into the next step. Neither made sense on its own.

A single cell of Chlamydomonas under the electron microscope. Even in a green alga, most of the organelles doing the work are mitochondria. Dartmouth Electron Microscope Facility, public domain, via Wikimedia Commons

Key Terms in Plain English

These are the words in this article that would send you to a dictionary. Each one is given here the way it is actually used above.

Term	What it means here
ATP	Adenosine triphosphate, the molecule cells use to pay for work.
Matrix	The fluid inside a mitochondrion's inner membrane.
Cristae	Folds of the inner membrane that hold the respiratory chain.
Glycolysis	The splitting of glucose into pyruvate, done in the cytosol.
Citric acid cycle	The cyclic pathway that strips electrons off pyruvate in the matrix.
Electron transport chain	The membrane complexes that move electrons and pump protons.
Oxidative phosphorylation	Making ATP from a proton gradient across a membrane.
ATP synthase	The rotary motor that turns proton flow into ATP.
Proton gradient	The imbalance of hydrogen ions across a membrane that stores energy.
Endosymbiosis	One organism living permanently inside another, to both their benefit.
Hydrogenosome	An anaerobic form of the mitochondrion that produces hydrogen instead of using oxygen.

The words in this article that would otherwise send you to a dictionary.

Key Takeaways

• Mitochondria carry their own DNA: 37 human genes, 13 encoding protein, against roughly 1,100 mitochondrial proteins that have to be made from nuclear DNA.
• The ancestor was an alpha-proteobacterium and the host was an archaeon, not another eukaryote.
• Anaerobic forms exist, and the hydrogen hypothesis predicts them. That prediction has held up.
• The citric acid cycle does not consume oxygen directly. It stalls without oxygen only because the chain cannot regenerate its carriers.
• ATP synthase is a rotary motor. One glutamate residue per ring subunit picks up and releases each proton.
• The 36 ATP figure is obsolete. Current estimates are nearer 27 to 30, and lower still once real-world bypasses are counted.
• There is no universal ATP yield, because the machinery differs between organisms.

Frequently Asked Questions

Do mitochondria produce all of a cell's ATP?

No. Glycolysis happens in the cytosol and makes some. The mitochondrion handles the rest, including the large majority that comes from the chain.

Why are there so many in heart muscle?

Because cardiac muscle does not stop. Boguszewska and colleagues note that cells needing more energy carry more mitochondria, and liver and heart are the standard examples.

If Giardia has no mitochondria, does that disprove endosymbiosis?

No, and Martin and colleagues treat it as supporting evidence. The hydrogen hypothesis predicts that some lineages lost the organelle afterwards, which is what Giardia looks like.

Do all eukaryotes have mitochondria?

On the hydrogen hypothesis, all of them either have them or have lost them. Martin and colleagues report that prediction as borne out.

Where does the 36 ATP figure come from?

It was a reasonable estimate in the 1970s, based on assumptions about stoichiometry that later work revised. Amthor traces the corrections and finds the textbooks still citing the old figure.

Is heat a waste product?

In a plant cell, partly. Amthor notes that respiration can produce substantial useful heat, and that some plants do deliberately generate it.

Key references
• Martin, Garg and Zimorski 2015: endosymbiotic theories
• Amthor 2023: ATP yield of plant respiration
• Boguszewska et al. 2020: mitochondria and bacteria
• Nobel Prize: Hans Krebs, facts
• Klusch et al. 2017: the ATP synthase motor

Images: Wikimedia Commons, with the author and license named in each caption. Figures and dates follow the five sources above.

Scopes: The Trial That Turned on a School Textbook

A Tennessee statute went after a theory. A teacher went on trial. But the thing that actually sat in the middle of the case was a school textbook, and almost nobody remembers that.

George William Hunter's A Civic Biology was the book Tennessee had approved for high school use. Six of its pages covered evolution. John Scopes assigned those pages, and the state of Tennessee charged him with a crime for it.

This article looks at that trial through the book, and at what the book itself said. The story is stranger and less tidy than the version usually told.

What the Law Actually Said

The law was the Butler Act. Tennessee governor Austin Peay signed it into law on March 21, 1925. The text is narrower than the law's reputation, which matters for understanding the case.

It made it unlawful to teach any theory that denies the story of the Divine Creation of man as taught in the Bible. In its place you were forbidden to teach that man had descended from a lower order of animals. That is the whole prohibition, and it targets human origins.

Nothing in it banned teaching evolution from fossils, from geology, or from comparative anatomy of other animals. Those were not illegal in Tennessee that year, and they were the larger part of what Hunter's book taught.

A crowd gathered outside the Rhea County Courthouse in Dayton, Tennessee, during the trial in July 1925. Brown Brothers, public domain, via Wikimedia Commons

The Butler Act was not a southern outlier that sprang from nowhere. William Jennings Bryan had spent years campaigning against teaching evolution, and in 1918 he helped found the World's Christian Fundamentals Association.

The American Civil Liberties Union was organized in 1920 partly as a response to that body. When the Butler Act passed, the ACLU put a notice in Tennessee newspapers offering to pay the legal costs of anyone willing to test it.

Timing explains most of this. In 1900 only about one and a half percent of American teenagers attended a public high school. Twenty years later the number of students reading textbooks had grown twenty or thirty times over. Many of them went home with ideas their parents had never been raised on.

The Book That Made the Case

Several businessmen in Dayton read the ACLU notice and saw an opportunity. A trial would bring reporters and their money to a town whose population had fallen from about 3,000 in the 1890s to roughly 1,800 by 1925.

George Rappleyea, who managed a local coal company, argued the case at Fred Robinson's drugstore on May 5, 1925. John Scopes, then twenty-four and coaching football at the local high school, was called in and asked to stand trial.

John T. Scopes, the defendant, with his attorney John R. Neal during the 1925 trial. Bain News Service, public domain, via Wikimedia Commons

What Scopes had actually done was small. He was covering the biology timetable, and later said he could not recall whether he had taught evolution as a lesson at all.

The uncertainty mattered to nobody in the courtroom. What mattered was that the pages he assigned were the state's own. He held the book up in the drugstore and asked why it was illegal to teach from it.

The textbook is the reason the case is not quite what it sounds like. Scopes was prosecuted for using the book the state had prescribed. The statute and the textbook contradicted each other, and that contradiction is the trial.

What the book taught about evolution

On the science itself, Hunter was not writing fiction. The book explained that "evolution means change," that simple forms of life gave rise gradually to more complex ones, and that Darwin supplied the mechanism. Six pages carried that material.

The book gave no basis for understanding natural selection. It also took no side in the argument about where variation came from. It was a textbook of its moment, not a modern one.

What Else Was in the Book

Here the story stops being comfortable, and it is worth saying plainly rather than leaving out.

Hunter gave human evolution its own single page. On it he wrote of "races of men who were much lower in their mental organization than the present inhabitants."

Man, he added, had once been "little better than one of the lower animals." That is the whole of what Hunter offered for the origin of human beings.

He then set out five "races or varieties of men" and named four as lower types. The Caucasian went last, as "the highest type of all." That is what is printed on page 196 of the book.

Hunter was also an enthusiastic eugenist, which in 1925 was a respectable academic position held at Harvard, Columbia, Cornell and Brown. He defined eugenics as "the science of improving the human race through better heredity" and argued for separating the sexes among people he described as "defective."

Bryan read that material into the record in his closing argument, and quoted Darwin's own words on the weak being eliminated in uncivilized society. He called it proof that evolution dragged mankind down to the level of the brute.

So the most famous courtroom defeat of fundamentalism rested on a textbook with a chapter on sterilizing people the author thought inferior. That does not make Scopes wrong. It makes the story worth reading instead of retelling.

The seven scientists brought to Dayton to testify for the defense, outside the rented house they shared. Not one of them spoke to the jury. Watson Davis, public domain, via Wikimedia Commons

Eight Days in Dayton

The trial ran from July 10 to July 21, 1925, before Judge John T. Raulston. About a thousand people packed the courthouse on the first day, three hundred of them standing.

Roughly two hundred reporters came, and radio came with them. WGN in Chicago had been on the air for about a year. It spent $1,000 a day and rented an AT&T cable from Chicago to Dayton.

Four microphones went into the courtroom, and WGN rearranged the room so the microphones would work. Announcer Quinn Ryan narrated. It was the first live broadcast of any trial in American history.

The science never reached the jury

The defense called Maynard Metcalf, a zoologist from Johns Hopkins, to explain the science. Raulston let him begin, then ruled the whole of the defense's expert testimony inadmissible.

The jury was told nothing about the biology. The defense read prepared statements from eight scientists into the record instead, for the benefit of an appellate court.

Scopes himself never took the stand. The person on trial in the only trial ever held under the Butler Act did not testify in it.

The science news service did its best to make up for that. Watson Davis, managing editor of Science Service, telegraphed a list of scientists to Darrow's team from the train, then sent the invitations himself. He drafted their prepared statements once the trial was under way.

Davis and a colleague gave up their hotel rooms to stay with the witnesses at the rented house the press called the Defense Mansion. The New York Times sent Science Service a letter of thanks for the coverage.

That matters. The science which did reach the country came through reporters rather than through the court, because no expert witness was allowed to speak to the jury.

Bryan on the stand

On July 20 the defense called William Jennings Bryan as an expert on the Bible. The court moved outside under the trees, where a sign on the courthouse wall read "Read Your Bible."

Darrow's questions were designed to show that Bryan could not read the Bible literally. Asked whether the six days of creation were twenty-four hours each, Bryan answered: "My impression is that they were periods."

The next day Raulston struck Bryan's testimony from the record. Darrow then asked the jury to convict Scopes deliberately, so that the case could be appealed, which cost Bryan the closing argument he had spent weeks writing.

William Jennings Bryan, three-time presidential candidate, at the trial he came to Dayton to argue. United News Pictures, public domain, via Wikimedia Commons

What Happened Next

The jury deliberated for nine minutes and found Scopes guilty. Raulston fined him $100. It was the only prosecution ever brought under the Butler Act.

In January 1927 the Tennessee Supreme Court overturned the conviction on a technicality: the fine had been set by the judge rather than by the jury. The Butler Act itself stayed on the books.

Bryan died in his sleep in Dayton on July 26, 1925, five days after the verdict. He had been ill with diabetes for some time. The story that Darrow killed him with his cross-examination has been told for a century and is not what the record shows.

Scopes gave up teaching, took a master's degree at the University of Chicago and then worked as a petroleum engineer in Venezuela, where his notoriety would not follow him.

The statute itself did not last. Tennessee repealed the Butler Act in May 1967. Six months later the Supreme Court struck down an Arkansas law of the same kind in Epperson v. Arkansas.

The book kept going

The textbook is the last chapter of this story, and it is the one most often skipped. In 1926 Hunter substantially revised the book.

The entire six-page section on evolution was cut from the special edition made for school boards in the southern states. Only a vague reference to Darwin's "interpretation of the way in which all life changes" survived. The word evolution did not appear in the text or the index of the edition called New Civic Biology.

Textbook publishers across the country did the same thing on their own, dropping the subject from their books for the next three or four decades. No court ordered it. The law did not need to.

How the memory was rewritten

Bryan College opened in Dayton in 1930, in the old high school where Scopes had taught. It was named for the prosecutor who lost the public argument, and it still is.

The play Inherit the Wind, by Jerome Lawrence and Robert E. Lee, opened on Broadway in 1955 and used the trial to stand against McCarthyism rather than against the Butler Act. The 1960 film with Spencer Tracy and Fredric March reshaped the case into a contest between two dignified men.

What came out of that version is a courtroom story about reason against authority. The textbook goes missing, along with the scientific racism in it, the excluded experts, and the fact that both sides came out claiming victory while the law stood. Dayton itself now runs an annual festival that plays up the publicity stunt, which is closer to the truth.

The marker outside the Rhea County Courthouse, where Scopes was charged with a crime for assigning six pages of a state-approved textbook. Bneu2013, CC BY 4.0, via Wikimedia Commons

The Rhea County Courthouse in Dayton, Tennessee, where eight days of testimony in July 1925 made the Butler Act famous. Smithsonian Institution, no known restrictions, via Wikimedia Commons

Key Terms in Plain English

These are the words in this article that would send you to a dictionary. Each one is given here the way it is actually used above.

Term	What it means here
Butler Act	The 1925 Tennessee law that made teaching human origins a misdemeanor.
Eugenics	The now-discredited movement for improving humanity by selective breeding.
Fundamentalism	Reading the Bible as literally accurate, including its account of creation.
Misdemeanor	A criminal charge lighter than a felony, punishable by a fine.
Natural selection	Darwin's mechanism: better-adapted people leave more offspring.
Indictment	A formal charge that sends a person to trial.
ACLU	The American Civil Liberties Union, founded in 1920 to defend individual rights.
WCFA	The World's Christian Fundamentals Association, founded in 1918.
Appeal	Asking a higher court to review what a lower court decided.
Genetic	Relating to genes and inheritance.
Inadmissible	Ruled by the judge to be unusable as evidence.
Verdict	The jury's decision on guilt or innocence.

The words in this article that would otherwise send you to a dictionary.

Key Takeaways

• The Butler Act targeted human origins only, not evolution as a whole. Fossils, geology and animal anatomy stayed legal in Tennessee in 1925.
• Scopes was prosecuted for assigning pages from the textbook Tennessee had itself approved, which made the case a contradiction at its core.
• Hunter's book taught evolution, and it also ranked five "races of men" and praised eugenics. Bryan read that material into the record himself.
• The judge ruled the defense scientists inadmissible, so no biologist spoke to the jury. Scopes never testified either.
• Bryan died of diabetes five days after the verdict. The cross-examination theory is a century-old legend.
• The conviction fell on a technicality while the Butler Act stayed law, which Tennessee did not repeal until 1967.
• Publishers removed evolution from textbooks for 30 to 40 years without any court ordering them to.

Frequently Asked Questions

Did Scopes teach evolution?

The charge never rested on proving it. Prosecution called the assigned page the crime, and Scopes never disputed the reading. That is the whole point of the case: the statute turned a page assignment into a misdemeanor.

Why did the defense ask for a guilty verdict?

A guilty verdict could be appealed. An acquittal would have ended the matter, so Darrow asked the jury to convict deliberately so the case could reach a higher court.

Was the Butler Act really about banning evolution?

No. Its text covered teaching that man descended from a lower order of animals in place of divine creation. Evolution from other lines of evidence was not what it prohibited.

Did Clarence Darrow kill William Jennings Bryan?

There is no evidence for it. Bryan died on July 26, 1925, five days after the verdict, and had been ill with diabetes for some time.

Did the trial make teaching evolution legal?

No. Tennessee Supreme Court judges set the fine rather than the jury, so the conviction fell in 1927 and the law remained. Epperson v. Arkansas in 1968 was the ruling that struck down these laws.

Was "Monkey Trial" its original name?

No. H. L. Mencken coined it while covering the trial for the Baltimore Sun, and it stuck.

Key references
• PBS: Monkey Trial timeline
• PBS: the WGN broadcast
• HISTORY.com: the trial
• Smithsonian Magazine
• Linder, UMKC: the trial
• Linder, UMKC: eugenics
• Linda Hall Library

Images: Wikimedia Commons, with the author and license named in each caption. Figures and dates follow the seven sources above.