Origin and evolution of cells

The timescale of life on Earth; the prebiotic synthesis of organic compounds; the RNA world and ribozymes; why the Earth in particular can support life; how nature constructed the first cells, acquired a membrane and moved to a DNA genome; the structure, genetics and metabolism of the prokaryotic cell; the last universal common ancestor; the three superkingdoms; the eukaryotic cell and the prokaryote-to-eukaryote transition; the endosymbiotic origin of mitochondria and chloroplasts; and horizontal gene transfer.

If we equate the whole existence of the Universe to a single year, the events fall out like this. BYA means billion years ago, MYA million years ago.

The striking thing about this table is how late everything is. Life appears only in the last quarter of the year, and everything we would recognise as an animal happens in the final fortnight.

The first mass extinction, 2.45 BYA, is known as the Great Oxygenation Event (GOE). The lecture also gives "the Cambrian explosion" as an alternative name for it.

It was caused by cyanobacteria doing photosynthesis, and the sequence is worth following because it explains why oxygen took so long to appear in the air.

Before the GOE, organic matter and dissolved iron captured any free oxygen. The dissolved iron became iron oxide and made huge deposits as banded iron rock. Only when not enough iron remained to capture more oxygen did free oxygen accumulate in the atmosphere.

Oxygen is toxic for anaerobic cells, and that is the reason the GOE was an extinction.

This is the primordial soup that cooks itself.

The prerequisites for the synthesis and accumulation of organic compounds were two:

• the absence of molecular oxygen;
• the supply of energy by lightning.

Stanley Miller and Harold Urey modelled the process in 1953, in the experiment that gave the field its founding demonstration.

Among known compounds, only RNA can both replicate and catalyse reactions. That single property is the whole argument.

In the RNA world, RNA was the only biopolymer. Later on, living systems acquired first proteins and then DNA.

A ribozyme is an RNA with catalytic function.

RNA is responsible for protein synthesis to this day: peptide bond formation is catalysed by the largest ribosomal RNA, which is 23S in prokaryotes and 28S in eukaryotes, located in the large ribosomal subunit. The official name of that ribozyme is the peptidyl transferase (PTC).

The chemical heart of protein synthesis is therefore still RNA, which is a living fossil of the RNA world inside every cell in your body.

Stromatolites - the Greek word for "layered rock" - are microbial reefs created by cyanobacteria.

They are among the oldest direct evidence of life. Fossilised stromatolite in the Strelley Pool chert of Western Australia is about 3.4 billion years old, and living stromatolites can still be seen today in Hamelin Pool, Shark Bay, Western Australia.

Volvox, a simple colonial green alga, is the living illustration of the colonial stage. Brasilodon is the 225-million-year-old mammal described in 2022, and a candidate for the world's first bird has been found in China. The plesiadapiforms, reconstructed from associated skeletal material, are the early radiation of the primates, and Paranthropus is an early hominin.

Ordovician-Silurian, 450 to 440 MYA. The most probable cause was a gamma-ray burst originating from a hypernova in a nearby arm of the Milky Way, within 6,000 light years of Earth. The ozone layer was damaged, exposing organisms to high levels of extreme ultraviolet radiation. A gamma-ray burst could also explain the rapid onset of glaciation, since ozone and nitrogen would react to form nitrogen dioxide, a darkly coloured aerosol which cools the Earth. The planet needed 0.5 million years to recover.

Permian-Triassic, 250 MYA, the "Great Dying". The reason was massive eruptive events, the largest known volcanic activity, and the eruptions continued for two million years. This is the largest extinction: about 96% of all marine species and 70% of land species were killed. The recovery of vertebrates took 30 million years, and the vacant niches created the opportunity for the archosaurs to become ascendant.

Cretaceous-Paleogene (K-Pg). Three quarters of organisms died. It was caused by an asteroid 10 km in diameter slamming into Earth, provoking volcanoes, fires and tsunami, and filling the atmosphere with gas, dust and debris that drastically altered the climate. Ectothermic species up to 25 kg were the best survivors, which was good for mammals and birds.

In the Solar System, the Earth is the only planet capable of supporting life. There are several main reasons.

• The right distance from the Sun, where the planet receives enough energy to allow water to exist as a liquid on its surface.
• The right size and mass. A rocky planet of that size has gravity that can hold an atmosphere. Planets without a thick atmosphere lack the matter necessary for primal biochemistry, have little insulation, and have poor heat transfer across their surfaces.
• A magnetic field, which protects the planet from radiation, whether from solar flares or other origins. The magnetosphere is a natural shield against space weather, and it is required if a planet is to sustain surface water for prolonged periods.
• A big moon to stabilise the Earth's axis, which makes the rhythm of the seasons stable.
• A huge amount of water. Water is an excellent solvent for many substances, which means an excellent medium for chemical reactions.

The habitable zone is also temporary. The Sun's current age is 4.6 billion years; as it becomes an old red giant at about 12.5 billion years, a planet in the habitable zone can stay warm for only a limited span.

The whole sequence, in order.

• The primitive atmosphere was devoid of molecular oxygen (O₂). This allowed carbon and hydrogen to interact with each other and with other atoms, resulting in the formation of various organic molecules. This is prebiotic, or abiogenic, synthesis of organic compounds.
• Chemical reactions became more diverse, and a primordial organic soup was formed in the ocean.
• Molecules able to influence reactions in the environment and to construct their own copies appeared, initially by chance. In other words, a class of molecules controlled both the biochemical reactions and their own replication.
• Multiple data indicate that these molecules were RNA, that is, at some stage of its earliest evolution life was an RNA world in which RNA molecules catalysed their own replication.
• Some RNA started to catalyse protein synthesis.
• The biochemical reactions and the genome were enclosed in a lipid bilayer, a membrane, and the genome was transferred to DNA.

Around the RNA and proteins, lipids self-organised into bilayers, producing a protocell.

These earliest membranes were fairly permeable, and so allowed the import and export of substances without today's elaborate membrane transport systems. That permeability is not a defect in the story; it is what made the first cells possible before any transport protein existed.

Liposomes, vesicles with lipid bilayer walls obtained in the laboratory, are a good model of biomembranes and can be seen under phase-contrast microscopy.

At some stage, one of the early living systems based on RNA and proteins started using the more stable DNA to store its genetic information.

Stability is the whole reason for the change. RNA can do two jobs badly; DNA does one job well, and by then proteins had taken over the catalysis.

• The main distinction in the living world is prokaryote versus eukaryote.
• The distinguishing trait is the absence or presence of a nucleus, but there are many other differences.
• Prokaryotes are simpler than eukaryotes and evolved earlier. For a long time, life on Earth was prokaryotic only.
• To know the basic life functions and the minimum equipment of life structures, you must study the prokaryotic cell. In many respects it is "the cell".
• Prokaryotes are unicellular, so organism equals cell. Some are colonial.
• Prokaryotes have all the types of metabolism seen in eukaryotes, and more.

• Typically 1 to 10 μm, shaped as a sphere, a rod, or a bent rod.
• The cell's central region, called the nucleoid, is occupied by a large circular DNA molecule, the bacterial chromosome.
• Between the nucleoid and the cell membrane there is cytoplasm full of ribosomes. It can contain small DNA molecules called plasmids.
• Above the membrane there is a polysaccharide cell wall.
• Above the cell wall, many prokaryotes - the Gram negative bacteria - have a second, outer lipid membrane.
• Some have a polysaccharide capsule as the outermost layer.
• The wall often has appendages with an attachment function, called pili and fimbriae. In some bacteria it has flagella.
• Some bacteria, under harsh conditions, turn into a metabolically inactive, highly resistant form called a spore.
• Cyanobacteria are photoautotrophs and have intracellular pigment-containing membranes, which is an exception among prokaryotes.

The biological model. The species most often used as research objects are called biological models, and the most important prokaryotic model is Escherichia coli. E. coli is a member of our normal gut flora, living in our intestines without causing harm, though some strains are pathogenic. Some E. coli strains that synthesise enterotoxins or cause diarrhoea have pili, and most of them have flagella.

Fimbriae and pili are thin protein structures originating from the cytoplasmic membrane of many bacteria. Both are able to stick bacteria to surfaces, but pili are typically longer and fewer in number than fimbriae.

The usage of the words is worth getting right:

• Pilus/pili usually refers to the sex or conjugation pilus, a fine tube which mediates attachment between bacterial cells and is used for the exchange of genetic material. There are usually only one or a few sex pili per cell.
• Fimbriae usually refers to structures that attach bacteria to other surfaces, and there are many per cell.

Flagella are long structures present on the cell wall of most bacteria. They help in detecting nearby molecules and also in locomotion. They are made of a protein called flagellin, and the base of the flagellum is embedded in the upper layer of the cell wall.

Remember: the structure of prokaryotic and eukaryotic flagella is quite different. They share a name and nothing else.

The lack of a nuclear envelope and of mRNA processing allows translation to start while the mRNA is still being synthesised.

Transcription and translation therefore happen on the same molecule at the same time, which is impossible in a eukaryote.

Prokaryotes have no sexual processes. The closest thing they have is bacterial conjugation.

It is the transfer of a plasmid, or a part of the chromosome, through a protein "tunnel" from one cell to another. The tunnel is formed by an unusually long pilus, called the sex or F pilus, which is different from the other types of pili.

The bacterial chromosome is attached to the cell membrane by proteins, and replication starts at that point.

After replication, proteins bring one of the daughter chromosomes to the opposite pole of the cell. When the middle of the cell is cleared of DNA, partition starts and a new wall is formed in the middle.

If conditions are good, bacteria divide every 30 minutes.

The bacterial nucleoid is organised as multiple loops compacted by nucleoid-associated proteins.

Nucleoid-associated proteins are typically small, abundant, DNA-binding proteins that control nucleoid architecture and gene activity.

Bacterial condensin complexes, the structural maintenance of chromosome (SMC) proteins, function in chromosome structure and segregation - the same family that shapes our own chromosomes.

Most nutrients are in the form of polymers and cannot pass through the cell membrane. Heterotrophic prokaryotes therefore secrete enzymes that hydrolyse polymers to monomers, and only then take the monomers across the membrane.

Because of this mechanism of feeding, bacteria can make available much more food than they actually eat, and the surplus is what other organisms live on.

There are three mechanisms of substrate utilisation:

• Selfish. Cells use surface-associated enzymes to bind and partially degrade polysaccharides, which are taken directly into the periplasm for further degradation, with little or no production of extracellular hydrolysis products.
• Sharing. Cells use surface-associated or free extracellular enzymes to degrade polysaccharide to sizes suitable for uptake. This causes the production of extracellular hydrolysis products, which are public goods.
• Scavenging. Cells do not or cannot produce enzymes for the hydrolysis of polysaccharides, but take up the hydrolysis products produced by other organisms.

Photosynthetic prokaryotes appeared quite early in evolution.

At first they used H₂S as the electron donor, converting it to S, as some bacteria still do to this day. Then cyanobacteria started to use H₂O, converting it to O₂.

This caused the accumulation of O₂ in the atmosphere, called the Great Oxygenation (Oxidation) Event, or the Oxygen Catastrophe.

The culprits are still with us: fossil cyanobacteria 850 million years old look much like living cyanobacteria today.

As O₂ accumulated, many prokaryotes became aerobic. Their electron transport (respiratory) chains and ATP synthase are in the cell membrane - not in an organelle, because there is none.

In some anaerobes the respiratory chain ends not with O₂ but with NO₃⁻, SO₄²⁻ or S. This is anaerobic respiration, and it is not to be confused with fermentation.

The proton gradient. Protons are pumped out across the membrane by the electron transport system, similarly to the case in mitochondria, using NADH as the energy source derived from glycolysis and the Krebs cycle. The resulting proton gradient is used for:

• ion and metabolite transport, for example of proline and lactose;
• ATP synthesis by ATP synthase;
• flagellar rotation, which costs roughly 1,040 H⁺ per revolution.

Almost all early organisms died out without leaving descendants. One of them, however, gave rise to all extant organisms, and it is called the last universal common ancestor (LUCA).

The only way to study it is by comparing the genomes of modern organisms which are as unrelated as possible - whatever they all share, LUCA must have had.

According to present data, LUCA lived almost 4 billion years ago. It was an anaerobic chemoautotroph which used energy from the anaerobic oxidation of H₂ and fixed CO₂ by chemosynthesis. It lived in hydrothermal vents, sources of heated water on the ocean bottom. With regard to its structure, it was a prokaryote.

Our closest known prokaryotic relations are a group of archaeans found in hydrothermal vents as hot as 300 °C, at a depth of over 2,300 m, in the zone between Greenland and Norway.

The vent field resembles the presumed habitat of LUCA. The archaeans discovered there are genetically close to eukaryotes, and they are anaerobic heterotrophs and chemoautotrophs.

There are two groups of prokaryotes: bacteria (eubacteria) and archaea (archaebacteria).

Bacteria are numerous and prosperous. Archaea include a few species living in hot springs and other extreme habitats - but, crucially, archaea also include the ancestor of the eukaryotes.

This is why the living world is subdivided into three large groups, or superkingdoms:

• Relatively large, typically 10 to 100 μm.
• Endomembranes, compartmentation and cytosis.
• Nucleus with linear chromosomes.
• Mitochondria.
• Cytoskeleton.
• Flagella, different from the prokaryotic ones.
• Mostly aerobic heterotrophs.
• Some are photoautotrophs with chloroplasts.
• Cells divide by mitosis.
• Sexual processes.
• Multicellularity has evolved several times.

• The ancestor was an anaerobic, heterotrophic archaeon.
• It developed a cytoskeleton as internal support and disposed of its outer support, the cell wall.
• The cytoskeleton gave full control over membranes, allowing endocytosis, an endomembrane system, and true predation.
• The genome was surrounded by membranes, pulled inside from the cell membrane, to be protected from the mechanical forces in the cytoplasm. This meant a nucleus and mitosis.
• The proto-eukaryote fed on bacteria, engulfing and digesting them. One, however, was not digested. Its progeny remained in the host cytoplasm as endosymbionts, became mitochondria, and made the host aerobic.

The order is not certain. The changes may have appeared in another order. The ancestor may have acquired mitochondria before the nucleus, because all known eukaryotes have or have had mitochondria. It is also possible that the proto-mitochondrion entered the host voluntarily as a parasite and only later became an endosymbiont.

To have a suitable surface-to-volume ratio, the eukaryotic cell has to increase its membrane surface by means of intracellular membranes. These enclose spaces called compartments.

This is the point that makes the eukaryotic cell make sense as a whole: it is not that compartments were a good idea, it is that a cell of that size cannot work without them.

Compartmentation in turn requires a cytoskeleton. The cytoskeleton is a network of filaments responsible for the cell's architecture and choreography. It has two main systems, microtubules and microfilaments, and animals have a third type, the intermediate filaments. The cytoskeleton provides support for organelles, gives animal cells their shapes, and is indispensable for mitosis.

The endosymbiotic theory of the origin of mitochondria was first proposed in the 1920s by Ivan Wallin, but was accepted only after a landmark 1966 article by Lynn Margulis.

The evidence:

• Mitochondria have their own DNA and ribosomes, which are of prokaryotic rather than eukaryotic type.
• Protein synthesis in mitochondria is sensitive to inhibitors of prokaryotic translation.

The mitochondrial precursor is thought to have belonged to the alpha-proteobacteria, a group of Gram negative bacteria which includes the pathogenic Rickettsia and other species that live inside eukaryotic host cells.

Most mitochondrial genes have been lost or taken over by the nucleus. Human mitochondrial DNA encodes only 13 proteins, while that of the freshwater protozoan Reclinomonas encodes 62.

Chloroplasts. Later, some eukaryotes became photoautotrophs by ingesting cyanobacteria and turning them into chloroplasts. Chloroplasts also have their own genome and ribosomes of prokaryotic type.

Vertical gene transfer is the process by which genes are transferred from parent to offspring.

Horizontal gene transfer is not related to reproduction: it can occur between unrelated individuals.

Horizontal gene transfer between eukaryotes and prokaryotes was a very important event in evolution, and it means that the tree of life is not purely a tree - branches exchange material.

In the syntrophic models of eukaryogenesis, this is explicit: an endosymbiosis is stabilised by horizontal gene transfer, which then becomes endosymbiotic gene transfer (EGT) as the symbiont's genes migrate to the host nucleus.

One published reconstruction runs through the following steps, and it is worth reading once for the logic rather than memorising.

• Facultative symbioses occur as a function of conditions, between an Asgard archaeon and a sulfate-reducing bacterium, in anoxic environments.
• The periplasmic space, where complex organics are hydrolysed to simpler molecules, starts to develop in the vicinity of the archaeon, to facilitate the transfer of amino acids and other simple organics. This is the first eukaryotic common ancestor, FECA (1).
• There follows extensive development of an internal periplasmic membrane in contact with the archaeon: the future nuclear membrane. The incipient endomembrane system has secretory purposes, the direct export of hydrolytic enzymes to the periplasm without damaging the cytoplasm. FECA (2).
• Transport channels traversing the archaeal membrane and the protonuclear membrane evolve, to facilitate protein transport to the future eukaryotic cytoplasm. Translation locates preferentially close to the membrane, near the membrane pores.
• The archaeal membrane is lost, and ribosomes progressively migrate along the endomembrane system, the future endoplasmic reticulum.
• Transcription, occurring in the archaeon which is the future nucleus, and translation, associated with the ER, become uncoupled.
• Introns start invading the future eukaryotic genome, with rapid genome evolution and an increase in size.
• The periplasm becomes fully internalised, keeping its original digestive functions as specialised vacuoles and organelles, and its secretory functions as ER, exocytosis and endocytosis.
• The proto-nuclear membrane is retained to maintain uncoupled transcription and translation and to prevent aberrant protein synthesis after the intron invasion. The nuclear pore regulates traffic across the compartments, and ribosomal particles are still assembled in the nucleus.
• Along the way there is loss of bacterial sulfate reduction and loss of archaeal energy metabolism.

• Only RNA can both replicate and catalyse, which is why the RNA world is the accepted first stage. The peptidyl transferase in your own ribosomes is a surviving ribozyme.
• The order was: prebiotic soup, self-replicating RNA, RNA catalysing protein synthesis, enclosure in a lipid bilayer, then transfer of the genome to DNA for stability.
• The Great Oxygenation Event at 2.45 BYA was the first mass extinction. Cyanobacteria caused it by switching their electron donor from H₂S to H₂O, and free oxygen only appeared once the dissolved iron ran out.
• LUCA lived nearly 4 BYA, was a prokaryote, and was an anaerobic chemoautotroph in hydrothermal vents.
• Three superkingdoms: Bacteria, Archaea, Eukaryota - and the eukaryotes came out of the archaea.
• The prokaryotic cell is "the cell": nucleoid with a circular chromosome, ribosomes, plasmids, cell wall, and in Gram negatives an outer membrane. Respiratory chain and ATP synthase sit in the cell membrane.
• Pili are few and long and used for conjugation; fimbriae are many and short and used for attachment.
• The eukaryotic cell needs endomembranes because of its surface-to-volume ratio, and needs a cytoskeleton because of the endomembranes.
• Mitochondria came from alpha-proteobacteria, chloroplasts from cyanobacteria. The evidence is their own prokaryotic-type DNA and ribosomes and their sensitivity to prokaryotic translation inhibitors.