A cell is the smallest independently functioning unit of a living organism. Even bacteria, which are extremely small, independently-living organisms, have a cellular structure. All living structures of human anatomy contain cells, and almost all functions of human physiology are performed in cells or are initiated by cells. Thus, cells are the basic building blocks of all organisms. Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being).
In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term “cell” for the box-like structures he observed when viewing cork tissue through a lens. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory.
There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells.
Eukaryote (eukaryotic cells)
A eukaryote is any organism whose cells have a nucleus enclosed within membranes, unlike prokaryotes (bacteria and archaea), which have no membrane-bound organelles. They constitute the most complex domain and include five kingdoms: plants, mushrooms, animals, protists and chromista.
Prokaryote (prokaryotic cells)
A prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. They include two kingdoms, Archaea and Bacteria, and are characterized by being devoid of an intracellular membrane system; in particular, they lack a structured nucleus, unlike eukaryotic cells, which represent the other domain.
Cell biology history
At the end of the 20th century, knowledge in the field of cell biology increased exponentially. On the one hand, the accurate knowledge and the related fields of application increased so much that single research can only master a limited section of cell biology, on the other hand, a new paradigm established itself and it was called Network Biology (Barabàsi, Oltavai 2004). This paradigm tries to give a clear framework in order to understand the cell functional organization and to master its complexity. Therefore, this aspect of the cell theory’s evolution is going to be sketched out, reporting only some progress in particular fields and referring to more specific voices the treatment of other themes of great scientific and applicable interest (e.g. bioinformatics, biotechnology, cytokine, cloning, DNA, a human embryo, growth factors, genome, plasmids, proteome, RNA, molecular probes, transplants, tumors, and cancers).
The focal point of the cell biology (that is the clear and documented statement that the cell represents not only the basic anatomical element but the basis of every physiological activity) is still valid after more than a century and a half from its formulation (Schleiden in 1838; Schwann in 1839). With the revision of M. Schleiden’s cytogenetic theory by R. Virchow, E. Strasburger, and W. Flemming, at the end of the 19th century, the foundation of the theory was consolidated.
Thanks to the improvement of microscopes and the introduction of more improved preparation techniques, up to the 1920s a large number of researchers created the body of knowledge that was summarised in the “bible” of cytologists, “The cell in development and heredity” (1925) by E.B. Wilson. Researches continued until the second post-war period, but the absence of real technological signs of progress and the missed formulation of new concepts took to a standstill. Until the end of the 1940s, cell biologists were in the frustrating situation of “look and don’t touch”, as wrote A. Claude, one of the pioneers of modern cell biology, in his Noble lecture of 1974. For this reason, Claude reports: “I remember vividly my student days, spending hours at the light microscope, turning endlessly the micrometric screw, and gazing at the blurred boundary which concealed the mysterious ground substance where the secret mechanisms of cell life might be found.”
The subcellular structures shaded off into the invisible world of molecules and there were not any experimental techniques that could allow analyzing the chemical composition, to inspect the physiological activities. Around 1950, in the biological sciences, there was a great turning point, that was determined by the confluence of research fields, knowledge, theoretical interpretations, whose premises were created in the ‘30s and ‘40s, but until then they were not linked.
This general observation is worth also the modern cell biology, which was created in the 1950s by an ever closer twist of three separate lines of research, that is biochemistry, genetics, and cytology, a discipline that studies the cell structure. The framework of cell biology became wider and more complex even for the use of more and more powerful and innovative techniques: the electron microscopy, the separation of cellular constituents through techniques of fractional centrifugation or in intensity gradient, the use of radioactive precursors, the development of histochemistry, the techniques that use antibodies and fluorescent dye and the techniques of genetic manipulation.
In the last decade of the 20th century and in the first years of the 21st century, important progress in knowledge was observed, especially in some specific fields and some of these new acquisitions will be analyzed in detail in order to introduce the problem of cellular complexity, to show how the framework becomes clearer and how we are going to master the complexity through new formalized descriptions.
Sequencing of the human genome, completed in 2003, and of other organisms, that were used as models in the experimentation in genetic and development biology, allowed to overcome the characterization of single genes and to obtain an integrated vision of the total functioning of the genome organization. This knowledge added a deeper comprehension of several mechanisms of gene expression regulation.
Topics of the cell biology concern the functioning and the functional connections between the cellular organelles. On the end, it is discussed the theme of “molecular machines” that intervene during the protein synthesis, the strange turning mechanism with which mitochondria transform the energy of sugar into usable form by cell, of control mechanisms of correct protein transformation, of a new model for the functioning of Golgi apparatus, of the complete description of mechanisms of the control of the cell cycle.
The term “mechanisms” recurs several times, so much that we could talk about a new mechanism at the cellular level, but there is a difference: on the one hand, eighteenth-century mechanists looked for mechanical components of their time (levers, springs, bellows, filters, wheels) in the organs and in the tissues, on the other hand for the modern cell biologist the “speckles” are molecules that compose the living “matter”. This is an improper term from the chemical point of view, but it is used as the survival of the 19th-century scientific language: a myriad of molecules, of every dimension and structure, from the huge proteic macromolecules to the small molecules of simple sugar or of microRNA.
Protein synthesis: enzymes are not only proteins
During the ‘60s the protein synthesis mechanism was explained, at any rate in its main lines and it was demonstrated that the “assembly bench” of proteins was made up small granular particles, already described by electronic microscopists, and the insulation techniques of cellular fractions allowed to analyze the molecular composition. Overall every particle had about 82 proteins and 4 molecules of RNA and they were called ribosomes.
Actually, we have to consider the ribosome as something more than an assembly bench on the surface of which the big protein molecules are put together: it appears like an automatic control machine, where the band with the information (mRNA) governs the behavior of the machine itself, that inserts every single amino acid in the right position so that the predetermined amino acid sequence defines the characteristics and the biological activities of the protein. In the early years of the 21st century, the molecular architecture of the ribosome was revealed in every detail thanks to the application of techniques, such as the X-ray crystallography and the nuclear magnetic resonance (Yusupov, Yusupova, Baucom, et al. 2001; Noller 2005).
However, one of the data had provoked astonishment in biologists years before and it was the observation that the activity of peptide transferase (the enzyme that catalyzes the fundamental reaction of protein synthesis, that is the sequence of amino acids for the formation of the so-called peptide bond) was not a protein, but one of the fundamental RNA of the ribosome. For those who do not know these problems, a simple chemical detail could sound not very important, but for biologists, it was a real conceptual revolution.
In 1926 J. Sumner obtained the crystallization of the enzyme urease and he isolated the enzyme in a chemically pure form; in this way, he demonstrated that it was a protein and biologists believed that the equation enzyme = protein had universal value. It was born the concept of a division of work between the macromolecules: nucleic acids, DNA, and RNA would be depositories and mediators of genetic information, whereas proteins would be executors of those biochemical processes that make work the cell.
At the beginning of the ‘80s, it was found that RNA molecules were able to work as enzymes; this observation contradicted the entirety of a principle accepted by everyone and it suggested that in the depth of geological times, about three billion years ago, life could have had a very different origin from what they have thought up to that time.
An RNA world
On 28th February 1935, two months before the publication of the note where the molecular model for DNA was proposed, at the Eagle Pub of Cambridge, F. Crick announced triumphantly that with J.Watson he had discovered “the secret of life” (Watson, Berry 2004).
For fifty years DNA has reigned undisturbed. From the molecular processes point of view, life had had from its origin the same fundamental characteristics: DNA as an archive of information, proteins as catalysts that sent biochemical processes and RNA as a useful intermediary between these two categories of molecules. When it was clear that RNA molecules had catalytic properties, that is they were able to store information and catalyze chemical reactions, a new theory of an RNA primordial world was created.
There are lots of data in favor of this idea and among these the greater ease of RNA molecules spontaneous formation, compared to the DNA molecules, in the conditions of the primeval Earth. In the “present” cells, with their extraordinary variety of structures and the versatility of their activity, proteins are efficient catalysts of biochemical processes.
DNA molecules are able to replicate without any mistakes and they represent the perfect archive for genetic information. However, proteins are not able to replicate, whereas DNA can’t be a catalyst because of its double-helical form. Only RNA can carry out both functions, even if in a not very efficient manner and on this data is based the hypothesis of an RNA primeval world, that is a world populated be very simple organisms, that contained an RNA molecule in a little bladder. At some point in this first phase of evolution, of this passage from chemistry to life, DNA appeared, and with it also proteins, RNA lost most of its original functions and what is left today is only a residue and a trace of a disappeared world.
Chemical energy through a molecular turbine
Cell biology and molecular biology manuals are full of mechanic models that want to explain the behavior and the functions of molecular structures, proposing well-known machinery. Nevertheless, a new acquisition is particularly amazing because modeled reality and its explicative model are superimposable.
This model concerns the final phase of energy transfers in mitochondria, those cellular organs defined as power station of the cell and that are able to make the cellular respiration so that to use the energy contained in the chemical bonds of sugar and fat molecules in order to synthesize a compound that represents a form of chemical energy available for the cell, the adenosine triphosphate (ATP). The first phase does not require the presence of oxygen and in this period only a small part of ATP is created.
The second phase of the energy metabolism produces most of ATP and it requires the presence of oxygen because on the atmospheric oxygen molecules converge hydrogen ions, or protons, and electrons originated by the previous phase, assembling molecules of water, a by-product of the cellular respiration.
Biochemists described these processes under the name of oxidative phosphorylation, meaning that the energy, resulting from the complete oxidation of sugar and fat to carbon dioxide and water, was used to phosphorylate, that inserts another phosphoric residue on the precursor of ATP, charging it of easy expendable energy. However for many years remained the question about how the two phenomena could be connected: the potential drop of electrons carried to oxygen by proteic complexes present in the innermost membrane of mitochondria and the binding of the oxygen in protons, produced water, a molecule with low energy content, releasing the energy used to produce ATP. What bound the two processes?
In the ‘70s a biochemist of the University of Edinburgh, P. Mitchell, who won the Nobel Prize for chemistry in 1978, had proposed a model that was called chemiosmotic, according to which the electrons potential drop’s energy was used by some proteic processes of the mitochondria’s inner membrane in order to transfer protons from the innermost compartment to the space between the two mitochondrial membranes.
The depletion of protons of the inner compartment, called mitochondrial, would have produced between the two sides of the inner membrane a concentration difference, that is an osmotic gradient, and an electric charge difference, since protons, or hydrogen ions, were electrically charged and it would have represented an accumulation of potential energy, available for the ATP synthesis.
Mitchell’s model was confirmed by lots of experiments, so a step forward had been taken in the comprehension of the process, but a part of the connection between electrons transport and the ATP phosphorylation was still missing. We need to take a step back and to introduce in the mosaic of researches another piece, that will be fully meaningful at the end of the ‘90s.
At the beginning of the ‘60s, an electronic microscopist was able to use this instrument at the limit of its technical possibilities and he described spherical particles connected by a slender stem to the inner mitochondrial membrane. A few years later, the biochemist E. Racker succeeded in isolating these particles that he named F1, demonstrating that they behaved like an enzyme that divided ATP, so as an ATPase. We will ask how it is possible that in mitochondria there is the enzyme that destroys the substance that they have to produce. We have to remember that enzymes have the function of biological catalysts, so they accelerate the speed of a reaction, they do not determine its way, which depends on the starting conditions.
According to the situation, an ATPase can both divide and produce ATP and in this last case, it is called ATPase, which is the enzyme that synthesizes ATP. The following experiments confirmed that particles, discovered by Fernandez-Moran and biochemically characterized by Racker, were really indispensable to connect the electrons transport to the ATP phosphorylation.
In cell biology manuals a mechanical model is often represented in order to explain the functioning of this ATPase/synthesis and precisely that of a rotary pump, whose rotating blades can push fluid into an exhaust pipe, but if the fluid flow would have been reversed and it would push the blades in the opposite direction, this machine would become a turbine. The enzyme would have worked as ATP synthase if there was sufficient protons flow to rotate the hypothetical turbine in order to transform the energy of this flow into the rotary motion of its axis and in the model it would have taken to the ATP synthase.
The model is not only metaphorical, but it has got also a certain biological substance because it is known that it is possible to make work in reverse those “pumps” that provide for maintaining the ionic concentration gradients between the two sides of the membrane, consuming ATP. Pumps can work also inverting the ionic gradients, as turbines and producing ATP instead of consuming it. In 1997 P. Boyer published an innovative hypothesis.
According to this idea the three catalytic sites for the ATP synthase, which were present in the globular portion of the particle observed by Fernandez-Moran and were characterized by Racked, would pass alternately through three phases of the ATP synthesis process. It could suggest that the particle rotated on itself, as a turbine moved by the falls of protons, that flowed from the external compartment of mitochondria into the internal one.
In the same year, J.Walker and his partners published a very detailed anatomic model of the F1 particle, confirming Boyer’s hypothesis. Shortly after, observations at the microscope were led attacking to the particles some fluorescent molecules, like signal flags, and they permitted to see directly the fast rotation of the particle’s head (Wada, Sambongi, Futai 2000).
The analogical model of the rotating turbine was imagined at the beginning as a useful educational device, but then it revealed itself more relevant to the reality than expected.
News about the Golgi apparatus
In 1898 the histologist and pathologist of the University of Pavia, C. Golgi, applied a new method of coloring, the black reaction, that allowed him to describe the histology of the nervous system. For this discovery, he received the Nobel Prise in 1906 and he observed randomly a new cell structure that he called internal reticular apparatus. The methodical application of this technique to many different cell types allowed Golgi and his students to demonstrate that this organelle was in every type of cell and that one of its functions was connected to the secretion process in the glandular cells.
After this first time of successful research followed a period of confusion because of technical reasons (e.g. the low resolution of the light microscope, the lack of methods to reveal and follow molecules in their movements) but also because of the creation of a hypertrophic and confusing terminology, so much that the organelle’s existence was questioned. Doubts about the real existence of the Golgi apparatus were dispelled by electronic microscopic observations between the end of the ‘50s and the beginning of the ‘60s of the 20th century.
During these observations, Golgi’s black reaction was applied at the ultrastructural level. Trust of biologists in the “reality” of electronic imagines took away any doubts and it allowed a new cycle of studies about this fundamental cellular organelle. From the ultrastructural point of view, the Golgi apparatus consists of a stack of cisterns, or “flattened bags”, surrounded by a cloud of vesicles that seem to melt or to bud from the edge of those bags.
The new ideas about the Golgi apparatus originate from researches of the ‘60s, led by L. Caro, G. Palade, and J. Jamieson, who showed with the use of radioactive amino acids the directional passage of proteins from the rough endoplasmic reticulum through the apparatus. M. Peterson and P.C. Loblond’s researches demonstrated that in the Golgi apparatus takes place the synthesis of the complex carbohydrate and then in the ‘80s W.G. Dunphy and J.E. Rothman’s studies pointed out enzymatic heterogeneity of cisterns and the parallelism between the passage of proteins through the stacked cisterns and their following biochemical transformations.
In a eukaryotic cell, thousands of proteins are synthesized, they have to be distributed precisely, taking their place between the fundamental cytoplasm’s proteins or between the cytoskeleton proteins and then they have to be segregated in this or that compartment, this or that organelle, fitting in a determined area of membranes or finally being secreted in a pole of the cell.
The Golgi apparatus is the business center of this macromolecular traffic and this is the fundamental role that M.G. Farquhar and G.E. Palade give to the organelle in 1981. Route choices are based on complex and sensitive processes of recognition of segments of the same protein amino acid sequence (signal sequence), as between the end of the ‘70s and the beginning of the ‘80s G. Blobel, B. Dobberstein and P. Walter underlined, and on the next “labeling” of proteins trough the addition of oligosaccharides, that is structures as sapling made up short chains of simple sugars.
Passing through the pile of cisterns in the Golgi apparatus, different proteins are modified, some tracts at the extremities are cut and carbohydrates are modified by different enzymes of the following cisterns. How can proteins pass from a cistern to the following one and so on, so that completely cross the Golgi apparatus, arriving at the complete maturation? Until the middle of the ‘80s, it was believed that cisterns were transitional structures, that came from vesicles that detached themselves from the rough endoplasmic reticulum, place of proteins synthesis, and then they flew trough the pile and they became again vesicles, that melted with other compartments of the cell.
This model was named the model of cisterns maturation. Between the middle of the ‘80s and the beginning of the ‘90s, cell biologists preference turned to a different model, called of vesicular transport, according to which cisterns were fixed structures and proteins were transported from a cistern to the following one by vesicles that have been budded by the edge of a cistern in order to meet with the following cistern.
In every cistern, proteins would have found a different enzymatic environment that produces the following maturation step. Each of the two models had explanatory difficulties and contradictions. Proteins are gradually modified by different enzymatic environments, passing from a cistern to another. If every cistern moves through the pile with its own proteins, then also its enzymatic complement moves, keeping unvaried for that determined cistern. In this way, it is difficult to explain the sequence of different enzymatic interventions for the maturation of the protein. For this reason, the vesicular transport model was preferred to the cistern maturation model, even if some observations contradicted it. Some big molecular complexes (e.g. precursors of collagen fibrils, secreted by fibroblasts) are too bulky to enter in the transport vesicles, so they always stay in the single cistern, whereas this last one moves towards the pile. This observation shows that cisterns move from a facet to another of the apparatus, crossing the entire pile.
Even if both models have their supporters, overtime was preferred a model that combines the characteristics of those ones described. In this “combined” model, cisterns flow to form a facet to another of the apparatus, transporting within them big molecular complexes, that could not enter in the vesicles of transport. Whereas transport vesicles detach from a cistern and melt with the following one, carrying protein molecules, other vesicles continue in a retrograde motion, carrying backward the enzymatic complement of the cistern that moves forward to the farthest cistern.
In this way, even if cisterns flow through the pile, the enzymatic contents of every level of the pile are unvaried, whereas it is modified the contents of the moving cistern. We could try to propose an analogical model, comparing Golgi apparatus to the factory, cisterns to different productions departments, proteins to semi-finished products that pass from a department to the following one, the transport vesicles shuttle among lorries that carry towards semi-finished products and backward machine tools from a department to the following one in the assembly line.
Cells were not designed by chemical engineers, they formed through causal and contorted paths of evolution. Our mind tries to apply our way of thinking to natural processes. Many processes could appear unnecessary complicated and, according to our point of view, they could be simplified and optimized, but this is the result that nature produced in the past three billion years.
Many new data are accumulating about vesicular transport systems among different cellular compartments. To the traditional techniques (electron microscopy, radiolabelling or fluorescent labeling) a new, ingenious method of labeling added: the use of green fluorescent protein or GRP (Green Fluorescent Protein), a little protein of some jellyfishes, that emits a green light when the fluorescence is excited by the ultraviolet light. The gene of this protein, isolated and cloned, can be tied to the protein’s gene of which we want to study the movements. The produced chimerical protein will be fluorescent and we can follow its movements in the living cell. The vesicular transport needs a series of delicate molecular devices, that have to be partly discovered.
The description of these subtle mechanisms is another example of the complexity of cellular processes. From the endoplasmic reticulum’s membranes take shape vesicles with specific contents. It is realized with the cooperation between endoplasmic reticulum’s membranes proteins and proteins of cytoplasm, called coat proteins or COP (Coat Proteins) that shape a floccose covering, that can be easily recognized under the microscope. Integral proteins act as receivers for the vesicle’s charge. With their far end pointed towards the light of cisterns, they recognize and establish a homogeneous whole of molecules that will become the charge of the vesicle itself and they tie COP, sticking out with the tail to its cytosolic side.
In cooperation with other cytoplasmic proteins, the covering closes, detaches, and stabilizes the transport vesicle. The transport can be retrograde because some proteins of the reticulum’s cisterns can be accidentally carried with the proteins to export. However the mistake can be corrected: resident proteins have got a tail of specific amino acids that represents a sort of label that is recognized by membrane receptors, which in turn recruit a COP; in this way is created a new vesicle that brings back to the origin the wrong charge. Over COP, there is another protein, clathrin (from the Greek clathron, “cage”) that shapes delicate and precious cages both around vesicles that transport molecules or particles from the plasmatic membrane to the cell’s inside, and around vesicles that moves among the compartments of the so-called digestive system of the cell.
The transport vesicle’s anchorage and the fusion to the specific compartment are made with the mechanism of the stereochemical mutual recognition, which is one of the fundamental characteristics of proteins. Vesicles have got specific receptors, recognized by complementary receptors protruding from the destination compartment’s membrane and the vesicle’s docking to the target membrane causes the fusion of the two membranes and the “delivery” of the charge. Before the definitive docking, the vesicle is caught from afar, by long filamentous proteins that attract it towards the arrival membrane (Pfeffer 1999), as those thin ropes that are thrown from the boats to boatmen in order to pull the heavy mooring ropes towards the dock.
Problems for the correct protein folding
In 1956 C. Anfinsen proved that the three-dimensional structure of proteins is determined by their amino acid sequence. Since the biologic activity of a protein depends on its space configuration, it is clear that the correct folding of the polypeptide sequence is essential so that a protein can function properly. Even though the folding is ruled by simple physical-chemical aspects, some molecules can assume a wrong configuration, becoming useless or even harmful, but the cell is able to fix these mistakes through the intervention of particular proteins, that are called chaperones.
The story of these proteins begins in 1962, when an Italian biologist, F. Ritossa, observed that in some Drosophila larva, raised above the optimum temperature, there was the activation of some particular genes. Ten years later it was clear that the activation of these genes was correlated to the appearance of particular proteins, that were defined Heat Shock Proteins (HSP). These proteins appeared in very different organisms, from bacteria to plants, to mammals and they were present also in normal conditions, even if in a lower concentration. Following studies clarified that these proteins work to co-operate the right folding of proteins or to correct it. The delicate architecture of proteins can be damaged in some cases also by moderate rises in temperature that cause an initial extraction of the polypeptide chain.
The protein can have hydrophobic groups above ground, that are first isolated compared to the cytoplasm’s aqueous environment because they are enclosed in the winding of the membrane. As fat droplets meet in order to shape “eyes” on its surface, then the hydrophobic groups of proteins can aggregate them in plural molecular complexes, with grave damages for the functionality of the cell. The name of these proteins, chaperones, comes from the French word chaperon, which refers to that old relative who went with the young lady of a good family to the Mass or shopping, monitoring that she would not give glances or messages with hasty and cheeky young men. In the same way, chaperones prevent that a protein is in the left-field, wrapping itself in a wrong way or shaping detrimental aggregates with other molecules. Beyond the metaphor of costume, it was proposed a physical-chemical model that explains the functioning of one of these chaperones and precisely of the couple GroEL/GroES, studied with high-definition electronic microscopy techniques (Chen, Singler 1999) and X-ray diffraction (Xu, Horwich, Singler 1997). GroEL is made up of four overlapping rings and each is assembled of seven identical subunits. Every couple of rings constitutes an open cylindrical chamber, ready to welcome the malformed protein, that ties to hydrophobic groups on the surface of the internal chamber. The capture of the malformed protein and the bond with the ATP molecule, which provides energy for the process, allows the joint of GroES, which constitutes a sort of cover that closes one of the two GroEL chambers. The bond with GroES produces a conformational change of the walls of the chamber, that expand and from which internal surface disappear the hydrophobic groups.
The wrong wrapped protein has the chance to re-wrap in a protected environment. After about fifteen seconds the chamber opens again and the protein is expelled, but if it is not right wrapped, it can be captured again for a new cycle of correction. The two chambers of GroEL function alternately in a continuous cycle. The problem of reaching the correct three-dimensional shape arises again for the organelles that are delimited by a membrane, like mitochondria and chloroplasts; most of these proteins are encoded by nuclear genes and they are synthesized in the cytosol. Here arises the problem of the import of these proteins through the membrane that surrounds organelles.
The problem comes because membranes have got special proteic canals that transfer proteins through the membrane, but proteins can cross them only in the totally extended shape; so after having passed the border of the organelle, they have to be right re-wrapped in the biological functional shape. Also, in this case, different chaperones have been found and they take actin sequence (Hsp60, Hsp70), unrolling, and rewinding proteins that are imported into organelles (Bauer, Hofmann, Neupert, et al. 2000; Chen, Schnell 1999). If a protein does not succeed in reaching the correct form or if it finishes its useful life in the cell, it is destroyed.
The lacking degradation of proteins, that are not properly shaped or that are losing their functional conformation and can shape dangerous aggregates, can damage the cell and in some cases, the cell can be directed towards the tumor transformation. For the proteins, degradation provides a process named ubiquitination, a word that derives from the name of a little protein that is tied in more pairs with proteins that have to be destroyed, the ubiquitin. The real destruction is made by a big proteic complex named proteasome, whose structure was revealed by observations of the high-resolution electronic microscope (Holzl, Kapelari, Kellermann, et al. 2000). In the electronic images, the proteasome appears as a real molecular spot, an empty cylinder, whose two breaks have got a mobile cover.
The protein marked by ubiquitin is recognized by the proteasome, gradually unrolled when it is introduced in its cavity, and digested in its constituent amino acids by proteolytic enzymes that form its side. Proteolysis determined by the ubiquitin-proteasome system (UPS) has not got only the task to clean the cell of malformed proteins, but also the most delicate regulative tasks. Proteins perform many different tasks in the cellular processes and controlled proteolysis can demobilize a no more useful cellular program, allowing the construction of a new one. It is very interesting the observation that proteolysis determined by the ubiquitin-proteasome system is under a space control in many functions or cellular types (Pines, Lindon 2005).
The control is made through a clear localization of UPS components in this or that part of the cell. Among many examples, there are some particularly evident. In the granular endoplasmic reticulum, which is the seat of synthesis of many proteins types, UPS components are localized in the cisterns, in order to delete the malformed proteins in the same place of production. In the neurons, the UPS is localized in the synaptic terminations and its task, connected to the transport of the protein through the axoplasmic flow, can explain the synaptic plasticity, that is the ability that has got the central nervous system to reshape contacts between neurons and therefore neuronal circuits, a phenomenon that is considered at the base of learning and memory processes.
Macromolecule and water
Water represents about 70-80% of the cell’s total mass. This notion and the electronic micrographs contribute to creating a mental image of a watery cytoplasm where macromolecule fluctuates in a diluted solution. For the electronic micrographs, we are trying to get the most contrast of a determined structure compared to an empty background and to the schematic pictures of manuals. This image is totally false (Mentré, Hui Bon Hoa 2001).
The surface of macromolecule basically consists of hydrophilic residues that lure water dipoles. Simple geometrical calculus and experimental data show that water is just enough to form two molecular layers around macromolecule. In other words, in a cell the distance between two macromolecules is on average 1,2 nanometres, which is little compared to the mean diameter of globular proteins, which is the most plentiful macromolecule in a cell, that is 3,4 nanometres.
The overcrowding of macromolecule has got a fundamental task in the association of macromolecular processes and in their regulation. The macromolecular overcrowding produces also a speed in the development of the biochemical reactions that are unimaginable in our macroscopic world. Whereas enzymes or other macromolecules disperse very slowly in the cytoplasm, experiments with fluorescent dyes or little marked molecules show that they disperse very quickly.
A little organic molecule, e.g. an enzyme’s substratum, can disperse over a distance of 10 microns, that is for about half of the diameter of a typical animal cell, in a fifth of a second. In the cell, an abundant substratum can have a concentration of 0,5 mM and it means that 500.00 molecules of substratum collide with the active site of the enzyme per second.
With so high concentrations the enzyme’s active site will be saturated and the formation speed of products of the enzymatic reaction will be determined by how quickly the enzyme can operate. For many enzymes, this value called the number of turns over is on the order of 1000 molecules per second. So, in the cell little molecules are pushed in a frenetic dance by the thermal agitation and metabolic chains unroll at very fast rates that are difficult to imagine.
The regulation of the cell cycle
The cell cycle is a process by which a cell creates two daughter cells and through this process life preserved, in an interrupted chain of generations, from the farthest ancestor communal to all organisms. The cell system’s study is very important for biology and the comprehension of its delicate mechanisms can lead to important signs of progress in the therapy of cancers. The cell cycle consists of four phases: the phase of DNA duplication, the S phase, the phase where the mitosis occurs (that is the division of the mother cell in two daughter cells), the M phase and between them there are the two intermission phases G1 and G2, before and after the S phase.
The passage through the sequence G1, S, G2, M is regulated by a number of “border controls”, or checkpoints, that stop the cycle when they recognize mistakes or defects in the duplication or in the distribution of the hereditary material. If mistakes cannot be corrected, the cell is directed towards a cellular organized death. Passages from a phase to another are regulated by the enzymes called MPF (Maturation Promoting Factors, that is those factors that promote maturation) that are made up two elements, a protein, named cyclin, and the real enzyme, a kinase, that is an enzyme that ties phosphate groups and other proteins, named Cdk (Cyclin-dependent kinase).
The cell’s progression towards different phases of the cycle depends on the production of cyclins, specific for every phase, that activates the particular Cdk, and then they are degraded after having carried out their activity. In their turn, Cdk phosphorylates other proteins, whose activity is required for the progression in the cycle, and their activity is controlled by some factors: cyclins concentration, their phosphorylation state, Cdk ‘s inhibitors, the synthesis and the protein degradation of cyclins and of other factors and finally the shift of the cycle regulators among different cellular compartments in different phases. Many laboratories dedicated to the study of the dependent kinase, but one of the most interesting was achieved by M. Bettencourt-Dias and by his colleagues (2004).
These scientists analyzed the functions of the entire completion of protein kinase of Drosophilia, 228 enzymes, with techniques of silencing, that is an arrest of the expression, of the corresponding genes. Of these kinases, 80 resulted involved in the regulation of the cell cycle: some were already known, others were new. Some of them were part of the kinase families that phosphorylate the tubulin, the actin, or the associated proteins; others were components of the intracellular signal chains and their lack led to defects in the cellular reproduction, suggesting new roles for the already known enzymes.
The complete knowledge of kinase allowed to reveal the tight twist among systems that control the cell physiology, the cell dimensions, stressful situations, reporting processes, and regulatory mechanisms of the cell cycle. So a tight integration among functional systems was demonstrated in the cell vital activity. The fundamental functional mechanisms of the cell are very conservative, they keep happening identical in the farthest organisms and it convinces scientists to conclude that, on the basis of data got in Drosophila, “[…] the high level of conservation of cell cycle regulators suggests that the study of their human components is useful to understand and to treat proliferative diseases.” (Bettencourt-Dias, Giet, Sinka, et al. 2004).
Reductionism and systematic view: signaling pathways
In order to give some examples of complexity at the cellular level, we are going to summarize the so-called signaling pathways, a very active and of great interest field of research, even if from the applicative point of view, for its clear links with the drug therapy and the control of the tumor growth.
Also, a schematic and summary treatment, like that of the cell biology manuals, requires many tens of pages and in the scientific magazines, there are new data about this subject. Cells receive continuous signals from the surrounding areas, both they are unicellular organisms, and they are part of a multicellular organization.
In this context, a very used expression is “signal transduction”, that shows that a stimulus collected by a receptor at the cellular surface is different from the signal that is released in the cell. The second intracellular signal provokes a chain of molecular interactions, that usually forks in one or more points and that finishes with an answer that can consist of an expression modification of one or more genes, a modification of the activity of some enzymes, a transformation of the cytoskeletal structure, a change of the permeability with specific ion, the activation or the repression of the DNA synthesis and finally the keeping in life or rather the cell death induction.
Every cell has got more than a type of receptors and each of them can provoke more than a type of answers because between a receptor and a protein, named effector (from which starts the intracellular signal), exists a class of mediatic proteins, named G proteins from their bond with GTP; these proteins can activate more than a type of effectors, provoking multiple answers. Vice versa, more receptors can activate the same G protein, so that the same answer is activated after different signals. Finally, we have to notice that for all protein components exist many isoforms, that is slightly different molecular forms, codified by the same genes, but then modified at the level of synthesis, as a result of alternative splicing, that is differences in the maturation of the RNA corresponding messengers, or even after the synthesis.
The different isoforms can be present in different cells and they show various behaviors and biochemical affinities. The number of components in the signaling pathways is already very high if we consider the codified genes, but in this way it becomes countless. From this brief description, we obtain a mental picture of a great variety of signaling branched chains, but actually, these chains interact, so we should imagine a model as a very complicate net, through which travel signals, that produce or regulate or stop other signals.