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The cell. 1. Introduction.

The ORIGIN of the CELL

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1. Living organism
2. Where?
3. When?
4. How?

The discovery of the origin of life is the discovery of the origin of the cell. It is unknown how the first cell appeared on Earth, but it is widely accepted that it was by physicochemical processes. In the twenties of the 20th century, A.I. Oparin and J.B.S. Haldane proposed the first physicochemical theories on the origin of life (also suggested by C. Darwin in one of his personal letters).

The origin of life as a physicochemical process has consequences in the field of biology. a) We can create life. A cell could be made from scratch by using molecules that exist in current cells and placing them together into a membrane bound compartment. b) Extra-terrestrial life. Physicochemical conditions, similar to those present on Earth during the origin of life, may have occurred elsewhere in the Universe. Extraterrestrial life may have emerged.

1. What is a living organism?

When searching for the origin of life, it is first necessary to know what a living organism is. It could be said that life is one of the properties that a living organism must have. However, there is a new problem: what is life? There is no one definition of life that is widely accepted by the scientific community. Nowadays, scientists often define life as a set of properties that an organism should fulfill to be considered as a living organism. Some of the most popular ones are the following:

a) Reproduction and transmission of information encoded by deoxyribonucleic acid (DNA).
 b) Maintaining homeostasis by using external energy (metabolism).
 c) Ability to respond to external and internal stimuli.
 d) Ability to evolve by Darwinian evolution (variation and natural selection).
 e) Some others.

2. Where did the first cells appear?

Scientists agree that the first cells emerged from organic molecules in the early Earth. These molecules may have been generated in different terrestrial environments and accumulated in the water. However, it is not excluded that many of these early organic molecules were synthesized in other planets and in the outer space, and came to the Earth as rains of asteroids and comets. Organic molecules were concentrated in some places where it is supposed that the first cells emerged. It has been suggested that these place were near to hydrothermal vents in the ocean or hot springs in the sweet water, with a rich mineral content. Hydrothermal vents show temperature and ions gradients that favor mineral catalysis to form complex molecular systems that evolved into the first cells.

3. When did the first cells appear?

The Earth is about 4500 x 106 years old. The fossils indicate that the first cells were already on Earth between 3500 x 106 and 3800 x 106 years ago (Figure 1). It means that the physicochemical processes leading to the first living organisms should have started earlier, in a period called the prebiotic era.

Clock
Figure 1. Temporal sequence of some relevant events since the beginning of life on Earth.

4. How did the first cell appear?

We can imagine the steps, starting from simple molecules until the appearance of the first cells, as follows:

Organic molecules

Organic molecules, plus water and some ions, are the building blocks of living organisms. The most relevant are proteins, nucleic acids, sugars and fat. How were they synthesized in the early Earth? There are several plausible scenarios. a) Terrestrial origin under extreme environmental conditions. If a flask containing CO2, ammonia, methane and hydrogen, is heated to high temperature and exposed to electric discharges, some complex organic molecules are obtained, such as hydrogen cyanide, formaldehyde, some amino acids, some sugars, purines and pyrimidines (necessary for nucleotide synthesis). This was the experiment carried out by Miller and Urey when they were trying to replicate the earliest environment on Earth (Figure 2). It does not prove that the origin of life was like this. However, it shows that complex organic molecules can be formed by physicochemical reactions. Furthermore, different places on early Earth could have had distinct environmental features that yielded different sets of complex organic molecules. Plausible sites for prebiotic synthesis are hot sea vents, fumaroles and hot springs, where strong temperature gradients and high water pressure can be found, in addition to minerals. b) Extraterrestrial origin. It has been shown that more or less complex organic molecules can be synthesized in the outer space, and they can be found in comets and meteorites. It is possible that a huge amount of extraterrestrial organic compounds reached the Earth surface, which could have then started the chemical reactions for the origin of life.

Miller-Urey experiment
Figure 2. Drawing of the device of Miller and Urey. This device were used to demonstrate the formation of complex organic molecules from simple organic ones. The chemical reactions were developed in an environment that was supposed to be similar to that present in the early Earth. Experiments were done in the fifties of the twentieth century.

Polymers

So, we already have organic molecules. However, the most relevant molecules for the cell are present as organic polymers: amino acid chains for proteins, nucleotides strands for DNA and RNA, sugar chains for starch and glycogen.However, several hypotheses have been proposed.

a) Heating and drying. In the laboratory, heating semi-dry compounds have been shown to produce chains of organic molecules.

b) Mineral surface catalysis. Minerals could have been key players during the origin of life for several reasons. They concentrate, select, work as template, and perform catalysis of organic chemical reactions. In an adverse environment, minerals may also have been sheltered places for the first complex organic molecule systems.

c) Fumaroles and hot springs. Sea vents, fumaroles, hot springs, hydrothermal vents, provide strong gradients of temperature and water pressure that, with the help of minerals, facilitate chemical reactions. Currently, organic molecules are produced in fumaroles. Although fumaroles are likely places to produce organic compounds, fresh water hydrothermal vents are also places of interest, since they are near volcanoes where hydration and drying cycles can concentrate organic compounds and facilitate chemical reactions at high temperatures. Furthermore, freshwater environments are more suitable for spontaneous membrane assembly than the sea, and there are low concentrations of calcium and magnesium, ions that inhibit the formation and integrity of membranes.

e) Lipid membranes. Several laboratory experiments have demonstrated that the surface of lipid membranes, such as cell membranes, can recruit, select and concentrate simple organic molecules. This scenario is interesting because it addresses two questions: why only a few specific types of organic molecules were included in membrane bags or vesicles, and how the protocells were first formed.

Cell membrane

One of the major leaps during the birth of the first cells was the development of a barrier to separate the intracellular and extracellular environments. Membranes provide many advantages: a) molecules for metabolic reactions are held together and are not lost by diffusion; therefore, the chance of chemical reactions is higher and more efficient; b) internal molecules are not shared with neighbors, so that new advantageous molecules for new chemical pathways are not used by competitors, that is, "selfish evolution"; c) a proper internal environment can be set to enhance chemical reactions and to counteract or buffer external environmental changes as well. Maintaining optimal inner parameters is known as homeostasis. Lipid membranes can spontaneously assemble from amphipathic lipids, which have hydrophilic and hydrophobic domains.

Protocell
Protocells

Two ways for the association between organic molecules, such as nucleotides and amino acids, and membranes have been suggested (Figure 3). a) It is plausible that water shaking could have led membranes sheets to form vesicles or small bags that enclosed groups of molecules. By chemical reactions, these molecules increased in number and the vesicle became larger. At one point, the vesicles gained the ability to divide by strangulation, giving rise to two new vesicles with the same types of molecules as the mother vesicle. The growth of the vesicles could have happened thanks to the properties of the membrane: allowing the extracellular supply of small molecules that could freely cross the membrane, but hampering the exit of larger molecules (such as polymers). b) Another scenario suggests that there was an association between simple organic molecules and lipid membrane surfaces. At one point, these macromolecules became trapped into vesicles or, if synthesized onto vesicles membranes, they acquired the ability to cross the membrane and remain within the vesicle. If one of these mechanism actually occurred, it is convenient to reconsider the order of events during the cell birth, because membranes were then the most important elements during the formation of the first protocells.

Cellularity
Figure 3. Models of cellularization: life inside the vesicle (top) and life outside the vesicle (bottom). The membrane is a key element to select, concentrate and favor chemical reactions (modified from Black y Blosser, 2016).

Autoreplication

Another major step during the origin of life was to change from a system of molecules formed randomly by external agents to a system with molecules generated by the system itself. It was then possible to produce copies of the molecules of the system, and therefore to achieve self-replication. It led to a main property of life: the transmission of information. Within vesicles, more or less accurate copies of some polymer systems were made. However, the self-replication process could make mistakes leading to variations of the monomer sequences. Some polymers or polymers system with slightly different sequences could have performed better during their own replication and yield more copies. Then, membrane vesicles with more productive molecules could grow faster, get more external resources and leave more offspring. Thus, we have a competition for external resources by populations of vesicles having different sets of polymers. They had discovered another property of life: variability and natural selection, i.e.,Darwinian evolution. Some authors think that one type of molecule could have initiated the autoreplication and evolution process, but others suggest that a system of molecules connected by chemical reactions could have been the starting point, with a self-replication of the entire molecular network.

RNA world
RNA world

Two main model have emerged to explain the prebiotic process that led to the first cell: the ARN world and the metabolic world.

ARN World. If a single type of molecule is assumed to be the first self-replicator, which one was it? The eyes turn to the RNA. Some RNA molecules have the ability to carry out enzymatic reactions (that is why they are known as ribozymes). For example, ribonucleoproteins can cut messenger RNA molecules and join them (mRNA splicing), and protein synthesis on ribosomes is accomplished by ribosomal RNA. Therefore, it is plausible, although unlikely, that RNA molecules could have made copies of themselves in the early Earth, by synthesizing a sequence complementary to their own nucleotide sequence. The nucleotide sequence is known to determine the 3D form of RNA, influencing stability and activity (Figure 4). In this scenario, some errors may have occurred during the copying process ("mutations") that gave more or less stable molecules. Darwinian competition could have then started. All these steps have been proposed to occur during the prebiotic period on early Earth, and are the base of the RNA world model.

tRNA
Figure 4. 3D form of a transfer RNA molecule present in the current cells. Complementary nucleotides from different parts of the molecule establish electrical interactions (green lines), and fold the polymer into a specific 3D conformation.

Metabolic world. An early world with networks of chemical reactions that gave rise to complex molecular systems also has some experimental support. In this model, replication was not achieved by a single type of molecule, but by a group of molecules connected by chemical reactions. At some point, a membrane was also needed for creating a protected environment, got the ability of growing and division of the system, and the ability to evolve.

Molecular interactions

No matter the molecule, or molecules, that got the capacity of self-replication and evolution, interactions between different types of molecules (polypeptides, DNA, RNA, lipids, sugars) should have occurred, leading to complex chemical systems. Over the time, the entire molecular mix evolved and faced environmental selection by modifying interactions between each other. This introduces a new concept: coevolution of molecular forms.

Genetic code

At some point in this story, RNA must have been involved in the synthesis of proteins (polypeptides). This was a critical step because a code was invented: 3 nucleotides in a particular order meaning a particular amino acid. This code is known as the genetic code, and it is present in all living organisms. The universality of the genetic code suggests that it was invented only once, and was inherited by all living organisms. This reasoning leads to think that all living organisms descend from only one type of cell, known as LUCA (last universal common ancestor). However, some authors suggest that the genetic code was invented before the cellularization process, and although bacteria and archaea inherited the genetic code, they went to independent cellularization processes.

DNA

In current cells, the information inherited is encoded in DNA, not in RNA, neither in proteins. Compared to RNA, DNA is a more stable molecule because it is a double strand, which makes easier replication and repairing. At some point before LUCA, genetic information was trasferred from RNA to DNA, which became the container for storing, transcribing and transmitting the information necessary to form a new protocell.

Cell theory
Origin of eukaryotes
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