The earth was formed about 4,500,000,000 years ago. The original atmosphere was a reducing one, containing (among other constituents) nitrogen, methane, carbon dioxide, hydrogen sulphide and water vapour. There was no free oxygen, so oxidative phosphorylation was not an option for the earliest organisms, which relied instead on a fermentative metabolism. Pre-biotic synthesis in thunderstorms and volcanic vents is believed to have left a rich legacy of the most common stable metabolites, which were scavenged by our distant ancestors.
The earliest living organisms were subject from the start to a relentless selection pressure for better substrate uptake systems. It is conceivable that trans-membrane proton gradients were originally used to drive substrate uptake. The F1ATPase may at first have fulfilled this important function, as the sodium gradient and the Na/K-ATPase still do today. Selection pressures would favour efficient ion pumping, leakproof membranes and steadily increasing gradients in order to scour the remaining metabolites from a depleted environment.
The importance of substrate uptake is that even marginal improvements yield an immediate selective advantage. In this situation the evolution of the earliest "photosynthesis" does not appear an unduly difficult step, serving initially to supplement pre-existing ion gradients from a widely available free power supply.
The earliest photosynthetic organisms were unable to produce oxygen from water, and relied instead on a variety of easier electron donors such as hydrogen sulfide and ferrous iron. They titrated the earth's crust, exhausting one reductant after another, subject always to the constant pressure to handle stronger oxidants and bigger gradients. It is likely that photosynthetic electron transport and oxidative electron transport systems evolved together, starting in each case from the most highly reducing end of their respective electron transport chains.
The transhydrogenase may be the most ancient part of the respiratory chain, capable of energising the outer membrane in a primitive fermentative bacterium long before any oxygen was present in the earth's atmosphere. The other respiratory chain components were probably added sequentially, as more effective oxidants slowly became available over hundreds of millions of years through the photosynthetic activities of the cyanobacteria and, very much later, the green plants. Meanwhile the selection pressure continued for larger and larger ion gradients. Eventually the trans-membrane pH gradient was sufficient to force the F1ATPase backwards (in its modern physiological direction) and modern photosynthesis and oxidative phosphorylation became possible.
All the gaseous oxygen in the present atmosphere is believed to have had a biological origin, and was mostly formed sometime between 3,000,000,000 and 1,000,000,000 years ago, as a result of photosynthesis by cyanobacteria and the earliest green plants. Electron transport was a prokaryotic invention, and its practitioners must have enjoyed a tremendous selective advantage from efficient ATP synthesis. Moreover, the rising atmospheric concentration of highly toxic and reactive oxygen was a serious threat to our eukaryotic ancestors. Even today, despite the evolution of effective anti-oxidants, most of our tissues maintain their intracellular oxygen concentration in the micromolar range,1000 times below the bloodstream value.
Primitive eukaryotes, however, had evolved one technique which no prokaryote could perform: they were sufficiently large and flexible to swallow other organisms whole, probably digesting them for food. How much more efficient, though, to keep a few aerobic bacteria as guests, supplying them with substrates in return for an endless supply of ATP? The original bacterial ion porters could continue to operate, and a single host cell mutation might be sufficient to insert an adenine nucleotide carrier through the bacterial cell wall.
Mitochondria are thought to have evolved at least 2000 million years ago from primitive bacteria which enjoyed such a symbiotic relationship with early eukaryotic cells.
It must have been difficult initially to synchronise the activities of the two genomes, and there followed a gradual transfer of mitochondrial genetic functions to the eukaryotic cell nucleus, where they were better integrated with the other cellular controls. This process has progressed to varying extents in different species, so that yeast and mammalian mitochondria differ slightly in the functions which they have retained.
Mitochondria still show some signs of their ancient origin. Mitochondrial ribosomes are the 70S (bacterial) type, in contrast to the 80S ribosomes found elsewhere in the cell. As in prokaryotes there is a very high proportion of coding DNA, and an absence of repeats. Mitochondrial genes are transcribed as multigenic transcripts which are cleaved and polyadenylated to yield mature mRNAs. Unlike their nuclear cousins, mitochondrial genes are small, generally lacking introns, and the chromosomes are circular, conforming to the bacterial pattern.
In addition to the mitochondrial ribosomes and transfer RNA, the small amount of mitochondrial DNA codes for only 13 polypeptides in humans. These are mainly the hydrophobic cores of the major trans-membrane proton pumps, which are sticky and insoluble and difficult to move around the cell. All the remaining mitochondrial genes have migrated to the nucleus, and the hundreds of other mitochondrial proteins are now imported from the cytosol.
Maternal inheritance: The vast majority of mitochondria in a fertilised egg derive from the hundreds of thousands of mitochondria in the large maternal egg rather than the small number in the tiny sperm. As a result most mitochondrial traits appear to be transmitted exclusively through the maternal line.
Nevertheless, there are obvious difficulties with this hypothesis. If maternal transmission were the only mechanism, and there were no device within each cell to eliminate defects and synchronise the multiple copies of the mitochondrial DNA, within a relatively short period there would be thousands of mitochondrial variants. These are not observed in practice, despite the fact that mitochondrial DNA is less well protected than nuclear DNA and mitochondrial DNA replication lacks some of the error detection systems employed in the cell nucleus. Single-parent inheritance also denies to a species the evolutionary advantages of recombination and sexual reproduction.
Electron micrographs show that sperm contain two types of mitochondria: the large spiral structure which provides the power for flagellar movements, and two smaller, less specialised mitochondria packaged next to the male pronucleus with the paternal DNA. Whatever the function of this curious arrangement, its effects are not apparently manifest in the immediately succeeding generation.
Mitochondrial Eve: Assuming a largely maternal inheritance, analysis of human mitochondrial DNA is consistent with the hypothesis that the entire modern human race is descended from a single female or a group of closely related sisters, who lived in Africa about 200,000 years ago.
There are numerous objectors to this hypothesis, nevertheless the limited variability of our nuclear DNA also suggests that our ancestors recently went through an "evolutionary bottleneck" with a very small number of survivors. Our presence on the planet appears to have been a close run thing.