The second half of the twentieth century passed under the banner of biochemistry, molecular genetics and molecular biology. Humans have learned to observe molecules in artificial systems. Now we can study the same thing in a living cell, and this has radically changed the idea of how it works. Until now, a lot of unknown things remain, and this attracts researchers.
In recent years, several Nobel Prizes have been awarded for methods that have greatly contributed to the flourishing of cell biology: cryoelectron microscopy, high-resolution microscopy, fluorescent proteins, induced pluripotent cells. We’re in the midst of a revolution in cell biology, and it’s very exciting. New Nobel Prizes in this area are still awaiting their laureates.
The idea that a cell is something very stable and structured arises only on the basis of human perception. It is a mistake to compare a cell with a machine or mechanism. Any mechanism is necessarily designed, modeled, developed by someone; it always has a clearly verified scheme, where everything is in its place. A machine does not work without a person: someone has to assemble it, control its work, fix it if something goes wrong. Therefore, in nature, systems are not formed according to a predetermined plan, and the cell is no exception. Here, special stability is not needed, and it is rather harmful. And there can be no general building plan either.
It is often said that everything is written in DNA. Indeed, the genome indicates the composition of all proteins that can be synthesized by the cell. But that’s where it all ends. Nowhere is it described how much of this or that protein is needed, nowhere is it written in which cells these proteins will be synthesized, and in which they will not. Imagine that there is a document that states that it takes one hundred bricks, ten windows, and two batteries to build a house. Is this enough to build a house? Of course not. This is enough to collect a pile of rubbish, but nothing more. As soon as we are talking about a more or less complex system, a lot of additional information appears: where the bricks should be, and where are the windows, in what sequence the parts of the system should be assembled and much more. This is just not the case in the genome. Only bricks, but not a word about how to assemble a house.
Physicists and chemists have long been familiar with the phenomenon of self-organization. Under certain conditions, open systems – those into which matter and energy enters – are able to increase order within themselves. Isolated systems can only increase disorder (increase entropy), while the flow of energy into an open system can locally increase the order inside it, decrease entropy. A living cell is an open system that constantly absorbs the energy of the Sun or something else tasty that is on Earth, and due to this, it reduces its entropy. Thus, the principles by which houses are created and the principles by which living cells are created are completely different.
Self-organization is a process of ordering elements of one level in a system due to internal factors, without external specific influence. The hypothesis of ordering in the system due to its internal dynamics was expressed by the philosopher R. Descartes in the fifth part of “Discourse on the Method”.
At any level of life, we are faced with self-organization. A classic example of self-organization in wildlife is the soil amoeba Dictyostelium discoideum. They exist as free-living amoebas, but at some point they begin to creep down and form a fruiting body, so they were even considered to be relatives of mushrooms before. This process is very organized: waves of small amoebas crawl and merge with each other. And the slide begins with the fact that individual amoebas begin to produce and release special signaling molecules into the surrounding space.
How membranes work
Life is a cell, and it is separated from inanimate nature by the thinnest membranes. The basis of the membrane is a lipid bilayer, into which special proteins are embedded. A membrane cannot exist as a layer: its edges are thermodynamically absolutely unstable, and it must always be closed.
Membranes are very dynamic at different levels. Both lipid molecules and protein molecules in membranes move – this is called lateral mobility. Depending on the composition of the lipids, the fluidity of the membranes will be different. If lipids without double bonds in the tails predominate, the structure will be more rigid, roughly like soap. If there are double bonds, then the lipid will be more liquid, like oil. Depending on what kind of cell it is, in what conditions it is located, the structure of the membrane can change.
Membrane proteins can also float relatively freely. Around them, movable “coats” of lipids can be created, and if the movement must be stopped, special cellular components can do this. The movement of the membrane can be very easily observed under a microscope. If you paint live lymphocytes with antibodies to some membrane protein, then first the protein will be visible over the entire surface of the cell, then the mark will begin to slide into discrete specks, and then these specks can slide into one place. This is due to the fact that antibodies have two binding sites. When two membrane protein molecules collide, they can be cross-linked by an antibody that interacts with the two molecules. Then a third molecule can collide with them, and so on.
But it is not only the molecules in the membranes that are mobile. Inside the cell, the membranes themselves are constantly circulating. For example, enzymes are synthesized in the pancreas, which must be released into the intestines in order to digest food. They are synthesized in the endoplasmic reticulum, then they must enter the Golgi apparatus, in which many reactions will occur to them, and then they will fall into special bubbles, where they will be stored until we eat something. Then enzymes are thrown out of the cells and eventually enter the intestinal lumen. And enzymes cannot go all this way by themselves – they are carried only in vesicles. That is, the bubble must break away from the endoplasmic reticulum and transfer the substance to the Golgi apparatus.
There are many situations when the dynamics of membranes must be limited: sometimes the membranes behave differently from different sides on the same cell. This is characteristic of the intestinal epithelium: it has an outer surface and a lower (apical and basolateral surfaces). Absorption of substances occurs on the apical membrane. To deliver glucose into the body, you must first transfer it to the intestinal epithelium cell (this is an active process), and then release it from the cell into the body (this is already a passive process, glucose moves along the concentration gradient). The direction of this process should be only one, if we do not want to feed the bacteria living in the intestines. For this, the molecules that transport glucose on the apical and basolateral surfaces must be different. Accordingly, there is a mechanism that directs some proteins to the basolateral surface, while others to the apical surface. Also, proteins should not move between these membranes, or rather, between two sections of the same plasma membrane. For this, there is a special zone that limits the mobility of membrane components, and in this place proteins can no longer move.
Active transport is the transfer of a substance through the cell membrane or through a layer of cells, flowing from an area of low concentration to a high concentration, that is, with the expenditure of the body’s free energy. In most cases, but not always, the energy of ATP high-energy bonds serves as a source of energy for active transport.
Why are cells of different shapes
Since the early twentieth century, when biologists began to think more and more in terms of physics and chemistry, it was assumed that the cell should be a ball. It was already known that there is something dense on the surface of the cells, which means there must be surface tension, which means that a ball must turn out. This is not the case in living systems.
Then Nikolai Koltsov put forward a rather simple idea that there must be some kind of solid components that form a framework and allow cells to take different forms. Now it is clear that this is not entirely true. These components are there, but they are also insanely dynamic. Actin filaments are responsible for the formation of various outgrowths on the cell surface. Due to this dynamics, the cell can feel the space, fix itself, and stretch. Depending on what the cell interacted with, it takes one form or another. This is especially true for a multicellular organism: cells often grow in a complex, and it is very important which neighbors are around and how many there are. If the cells grow in one layer and there are a lot of them, they will become columns. If there are not very many cells, they will become cubes. Or, on the contrary, they can spread out into a flat layer. This is not recorded anywhere in the genome, and it is much more profitable to let everything go by itself, and the cells somehow self-organize. There are a lot of probabilistic phenomena in living nature.
Nikolai Konstantinovich Koltsov (1872-1940) – Russian biologist, founder of the Russian Soviet school of experimental biology, author of the fundamental idea of matrix synthesis of chromosomes
What does the genome consist of?
Although everyone knows that the human genome has been read and decoded, in reality this only applies to the part of it that encodes the genes. A significant part of the genome is formed by numerous repetitive sequences that do not encode any proteins. Some non-coding sequences live their own lives: they are able to move and reproduce within the genome. There was a perception that non-coding sequences are genetic garbage, but now it is clear that this is not the case. The regulation of gene expression is largely based on different noncoding RNAs. Other noncoding RNAs are needed to form nuclear structures – they are called architectural noncoding RNAs.
Non-coding regions can be useful on their own, as they help organize the three-dimensional space of the kernel. The spatial structure is especially important for DNA because it is very tightly packed in the nucleus. It happens that two genes distant from each other need to interact to ensure normal operation.
Genome size does not quite correlate with the complexity of the organism, although it is smaller in prokaryotes than in eukaryotes. An exon-intron structure appeared in the genes of eukaryotes. This complication was necessary in order to create a larger and more complex cell. But still it is not clear why some organisms need huge genomes, because it is very energy-intensive to maintain and replicate them. Such genomes are found in most agricultural plants, and for some reason the newt is the record holder among animals.
Most eukaryotic genes have a discontinuous structure, they contain coding sequences – exons and non-coding sequences – introns. In the mature mRNA molecule, only exons are present, and introns are excised from the primary transcript during splicing.
What was the driving force behind the emergence of the nucleus is not very clear. According to one hypothesis, the appearance of the nucleus made it possible to create greater complexity in the regulation of protein synthesis processes to control a more complex and large cell. In prokaryotes, RNA synthesis and protein synthesis occur in the same place almost simultaneously. In eukaryotes, RNA is synthesized in the nucleus, cut into pieces, then transported into the cytoplasm, and there is time to regulate some processes. There are RNAs that are held in specialized nuclear structures and are there until needed. When the time comes, they exit the nucleus, and protein is quickly synthesized on them.
In short, the complication of processes and regulatory pathways makes it possible to create a more complex cell. What is primary: the complication of the system or the emergence of new methods of regulation is not clear. If some changes were evolutionarily beneficial, they gradually accumulated and led to the formation of certain structures in the cell. Computer models suggest that even if the nucleus is not closed, it is still possible to create a gradient of proteins that bind to DNA. Gradient is beneficial and effective because then a lot of protein is there exactly where it is needed. It is inefficient to synthesize too much protein to fill the entire cell, so cells with structures similar to nuclei should have received an evolutionary advantage.
Each squirrel has its place
A significant proportion of proteins are constantly moving between the nucleus and the cytoplasm. An interesting example is troponin. It is a muscle protein required for contraction. Normally, it is predominantly located in the cytoplasm, but under certain conditions, for some reason, it moves into the nucleus. This is observed with aging or in tumors.
It happens that one and the same protein in the nucleus performs one function, and in the cytoplasm already another. Proteins with one function probably do not exist in nature. Obviously, no one has checked this, and it is impossible to check this, but, most likely, this is an assertion.
But in some cases, proteins still have small regions in which an address is recorded – a region of a protein that can interact with some structure in the cell, for example, with RNA in the nucleoli. The interaction is dynamic, and since there is a lot of RNA in the nucleolus, the protein interacts with it and accumulates.
There are nuclear localization signals for the transfer of protein to the nucleus. They interact with special adapters floating in the cytoplasm. The adapter-protein complex is recognized by the nuclear pores and is actively transported inside the nucleus, and the transport goes only in one direction. Such signals can be predicted, but the reliability of this is still very low. In half of the cytoplasmic proteins, nuclear localization signals are predicted. Most likely, most of this is a prediction error, but for some of these proteins there must be a mechanism for inactivating this signal. It can be turned off or hidden inside the molecule.
The cell is forced to develop mechanisms so that proteins do not end up where they do not need to be, especially if the protein can produce some unnecessary effect. For example, a protein can accidentally play the role of a transcription factor and break some well-oiled process. In the course of evolution, such processes are eliminated, but, unfortunately, there is no opportunity to make an absolutely effective system.
The mobility of proteins in the cell depends on their properties and what they interact with. Histones interact with DNA, this interaction is strong enough, so they sit there for hours. There are proteins of the nuclear envelope – lamins, which form a network and also very strongly interact, so they generally exchange for almost tens of hours. But these are exotic options for the cell. Any chemical reaction nevertheless passes very quickly, and proteins do not need to stay in one place for a long time. They move randomly around the cage and collide with their targets. Imagine how RNA polymerase synthesizes RNA from a gene. How can she return to the beginning of the gene? She will have to detach, and as soon as this happens, she begins to walk all over the cage.
In fact, high dynamics is normal, but we are not yet fully accustomed to it. When a process is very dynamic, it can be influenced, it can be easily regulated. And when the system is complex, regulation is necessary. All cells have the same genes, but they are different in meaning. In laboratories, they like to hang diagrams of some biochemical processes that take up half a wall. There are usually a lot of all sorts of arrows, interactions, and still this is only a tiny fraction of a percentage of what really happens in the cell.
Complex systems are much more stable than simple ones. Everything in a living organism is constantly changing, but only through dynamic processes can you create stable systems by self-organization. The main thing is that only this way of existence makes it possible to evolve, and evolution can proceed within the limits of even one organism. It is difficult to imagine the evolution of any crystal: under the same conditions, a crystal of table salt will form in the same way at any time – there is a rigid crystal lattice that does not change. And life can and should change. The crystal can be destroyed and then grown again. Life arose once, and if it is destroyed now, then there is almost no chance of re-emergence – at least on this planet.
To study a living cell, it is necessary to be able to observe the processes in it at the molecular level. Most modern methods of cell biology are based on fluorescent proteins. But two other things are also very important. First of all, these are attempts to create de novo structures in the cell. That is, you can move some cellular component to a local point and see how the assembly or disassembly of the complex will take place in a new place.
Lactose operon is a polycistronic operon of bacteria that encodes genes for lactose metabolism. The regulation of gene expression of lactose metabolism in E. coli was first described in 1961 by scientists François Jacob and Jacques Monod. A bacterial cell synthesizes enzymes involved in the metabolism of lactose only when lactose is present in the environment and the cell lacks glucose.
A local point can be set by inserting certain sequences into the genome with which something very specific interacts with. The simplest system was created on the basis of the bacterial regulator of the varnish operator. There is a lac operator with which the lac repressor protein interacts. Accordingly, if several lac-operators are inserted into the genome at a certain point, then the lac-repressor will be able to bring anything there.
If the structure depends on the work of a gene, for example, it is assembled on some RNA, you can also drag this sequence somewhere and add something so that it can be clearly seen: a special sequence can be attached to any gene, with which it will interact specific protein, and a fluorescent protein can be added to this protein. Then you can see how and with what dynamics the gene works.
The second line of research is related to high-throughput sequencing technologies. They allow you to catalog and describe large volumes of molecules and make many predictions, and then test them experimentally. Where bioinformatics appears, evolution appears. Sometimes you can understand how a process works if you know how it evolved. You can see that some of the components are very stable, while others have appeared recently. This already sets the direction for scientific research.