Why do we look like our parents?
What is heredity?
What is the genetic code? When did scientists discover the "atoms of heredity"? How did life on Earth originate? "Snob" publishes a fragment of Sergei Yastrebov's book "From Atoms to Wood. Introduction to the modern science of Life".
People have always known that heredity exists. Signs are transmitted from ancestors to descendants in humans, animals, and plants. A simple peasant who lived a century or two ago might not have exactly any theoretical ideas about the structure of nature, but he knew for sure that children were supposed to be like their parents. And this had a clear practical significance for him: in Russian villages, the bride was looked after "by breed", striving to ensure that she did not have hereditary diseases, cripples or crazy people in her family. No less vivid was the experience of breeding domestic animals and plants. None of the people who had anything to do with agriculture doubted the existence of heredity.
It is noteworthy that none of the three pre-revolutionary editions of Dahl's dictionary contain the word "heredity". Obviously, this phenomenon seemed so natural to the popular consciousness that a special designation was not required for it. Rather, on the contrary, the surprise was caused by too obvious deviations from the exact inheritance (they say, "who are you born into?"). For such deviations, the concept of "variability" has been coined in science. In general – it is worth paying attention to – heredity is usually spoken of if it is at least potentially not absolutely accurate, that is, if at least some variability is still present. These concepts are complementary.
It was clear to anyone who tried to comprehend the phenomenon of heredity: children receive something from their parents that decisively affects their qualities. How can this "transmitted something" be called? The father of biological sciences, Aristotle, used the rather complex concept of "entelechy" here. Aristotelian entelechy is an immaterial entity that determines the shape and structure of a developing organism. The life of this concept turned out to be very long, some biologists turned to it in the first half of the XX century. But now entelechy has finally been replaced by another concept, much clearer: hereditary information.
The most important fact for understanding all modern biology is the following: hereditary information is digital.
Why did entelechy disappear from science? Not least because no one has ever been able to quantify it. The information is quite measurable, as any user of a modern computer knows perfectly well. But hereditary information by its nature does not fundamentally differ from the one that is recorded and copied in technical devices.
There are two ways to record information – analog and digital. With analog recording, the encoding parameter can change arbitrarily gradually: for example, the shape of the sound track on a vinyl record (if anyone else remembers what it is nowadays) repeats the shape of the very sound wave that needs to be recorded. In digital recording, the encoding parameter can take only a few strictly defined values without any gaps between them. The limiting case of digital writing is binary code, where the encoding parameter can take only two values: either 0 or 1. The technology of writing plain text is also typically digital. There is a strictly defined set of letters, intermediate states between which are not provided.
The most important fact for understanding all modern biology is the following: hereditary information is digital. In the XVIII century, the French physicist Pierre Louis Moreau de Maupertuis guessed this. And 100 years later, the well–known Gregor Mendel came to the same conclusion - he was also a physicist, but he became interested in botany and became a first-class specialist in it. Moreover, if Maupertuis relied on observations, then Mendel proved the digital nature of hereditary information already experimentally. Of course, neither Maupertuis nor Mendel knew the terms we use now, but they would certainly agree with our formulation about digital recording.
The discoveries of Maupertuis, Sagre and Mendel were imperfect in one important aspect for us. The particles they took for elementary units of heredity were not really such at all. All these "makings" and "factors" are quite amenable to fragmentation into smaller parts (as we now know for sure). In the XIX century, there simply were no methods to see this. But in the XX century, with the beginning of the so–called studies of the fine structure of the gene, it immediately became clear that the "atoms of heredity" - if they exist in nature – should be much smaller.
The DNA chain is quite similar to the text, where some information is written in a four-letter alphabet. With the peculiarity that this chain is double.
And yet the proponents of discreteness were ultimately right. Indivisible carriers of hereditary information do exist. These are nucleotides. Here they are the very "letters" that the genetic text is written with. It should be noted that a nucleotide is a fairly large molecule by the standards of conventional chemistry. And if it is split into parts, then they will no longer be carriers of hereditary information. Thus, the "atom of heredity" can be considered detected.
In justification of the researchers of the past centuries, it must be said that they guessed a lot correctly. The fact is that discreteness exists at different levels. Nucleotides combine into much larger complexes, which are extremely stable and very often (although not always!) in fact, they behave as independent units from each other. That's exactly what Mendel recorded. Well, neither he nor his predecessors had any idea about the existence of the nucleotides themselves: the time for this has not yet come.
But by the middle of the XX century biochemists have definitely found out that the main carrier of hereditary information is DNA. A DNA molecule is, simply put, a long chain of nucleotides, which come in four types: adenine (A), thymine (T), guanine (G) or cytosine (C). So, the genetic "alphabet" is four–letter. In general, nothing special. There are only two "letters" in the binary code, in the most popular version of the Latin alphabet there are 26, but here there are four.
The DNA chain is quite similar to the text, where some information is written in a four-letter alphabet. With the peculiarity that this chain is double. It should be noted, however, that such a feature is not absolutely necessary for storing genetic information: it's just useful, but no more. Duplication of the DNA molecule significantly increases the reliability of the system (if one chain collapses for some reason, there is a second one), but it does not add anything to the very content of the messages recorded by the nucleotide text.
Whole genomes usually consist of millions of nucleotides, and sometimes billions. And in principle, all these nucleotides can be counted, modern biochemical methods quite allow this to be done.
However, what are these messages? Just by the time biologists figured out the genetic role of DNA, the answer (received by other biologists and turned out to be correct) was ready. Large stable nucleotide complexes – genes – must somehow carry information about the structure of proteins, those very huge molecules that do almost everything in the cell. A set of genes (genome) defines a set of proteins (proteome) in some way unknown to us so far. It was this conclusion that took shape in the minds of biologists by the mid-1950s.
Here it is necessary to make a reservation that the genome is actually not only a set of genes. Genomes usually have other sections of DNA that are not included in any genes (but we are not interested in them yet). As for the genes themselves, each of them includes thousands of nucleotides, and very often tens of thousands. Whole genomes usually consist of millions of nucleotides, and sometimes billions. And in principle, all these nucleotides can be counted, modern biochemical methods quite allow this to be done.
How does the genome encode proteins?
To begin with, any protein is a chain of amino acids. And always linear, that is, non-branching. This is where it becomes very important. The order of amino acids in the chain is called the primary structure of the protein. All other levels of the structure – secondary, tertiary and quaternary – relate already to the folding of the amino acid chain in volume, in three-dimensional space.
And here comes the most important fact, which actually relates to physical chemistry, but - suddenly – turns out to be key to understanding such a subtle matter as heredity. This fact is as follows. The primary structure of a protein (that is, the amino acid sequence), as a rule, uniquely determines all other levels of its structure, that is, the entire stacking of the molecule in volume. That is why a simple linear sequence of nucleotides – in other words, a nucleotide text – can completely determine all the properties of any arbitrarily complex protein molecule. After all, the primary structure of such a molecule is also linear, and it can also be considered a text. Only the "letters" in these texts are different.
And the following question immediately arises before us: how is the nucleotide "alphabet" translated into amino acid?
Sergey Yastrebov's book "From Atoms to Wood" was published by Alpina non-fiction publishing house.
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