Frozen Evolution. Or, that’s not the way it is, Mr. Darwin. A Farewell to Selfish Gene.

Interpretation of the genetic information encoded in the DNA, i.e. transformation of information contained in the order of the individual nucleotides in the DNA linear chain to the properties of three-dimensional organisms, is performed by the molecular apparatus of the individual cells (Fig. II.6). Long DNA sections contain information that is employed to control the synthesis of the individual molecules of the proteins. During the transcription, the information contained in the relevant DNA section is first mechanically rewritten in the linear RNA chain, a molecule that has a structure very similar to that of the DNA single chain and who’s four nucleotides again pair with the corresponding DNA nucleotides. The DNA double-helix that bears the relevant regulation area at the given place, the promotor, i.e. a sequence of nucleotides to which the molecule of the enzyme synthesizing the RNA binds, acts as the template for synthesis of RNA. In a great many groups of organisms, this RNA is further modified in processes of splicing and editing (Fig. I.4). During splicing, parts of the RNA chain, introns, are spliced and the remaining parts, exons, are again covalently bonded into a single chain. In editing, the individual nucleotides within the RNA molecule are enzymatically exchanged or inserted and removed. Part of the RNA acts as messenger RNA (mRNA). During the translation, information is encoded in linear mRNA chains, which contain four different nucleotides, using the simple translation rules of the genetic code (Fig. II.7); it is translated to the linear chain of the protein containing approximately 20 different aminoacids, i.e.  twenty basic aminoacids and, as appropriate, a few supplementary aminoacids, occurring only in some proteins in some organisms. Selenocysteine is a typical example of a supplementary aminoacid and occurs in about 25 proteins in humans (Kryukov et al. 2003). Some of the proteins have a structural function and their three-dimensional shape, determined by the order of the individual amino acids in their chains, and other  biophysical properties determine the internal and external structure of the relevant cells and their parts. A great many proteins exhibit

Fig. II.6 Interpretation of genetic information. Genetic information, written as a linear sequence of deoxyribonucleotides in the DNA molecule, is first transcribed to the sequence of ribonucleotides of the RNA molecule; this RNA is modified during RNA splicing and possibly also RNA editing and is then translated during translation of the sequence of its ribonucleotides according to the rules of the genetic code to the sequence of aminoacids in the linear protein chain. The protein chain can be modified by protein splicing and covalent bonding of certain sections and covalent modifications, for example glycosylation (bonding sugars) of individual aminoacids, and can be subsequently bonded covalently or noncovalently with other similarly modified proteins to form complicated molecular complexes capable of performing a biological function.

enzymatic activity, i.e. they catalyze a particular chemical reaction, or mediate in the transport of substances and transmission of signals. Their occurrence, location, amount and properties then determine the course of biochemical and physiological processes occurring in the cell. The biophysical properties of enzymes and their products again determine the structures of the individual cells. In multicellular organisms, the course of biochemical and physiological processes also indirectly influence (through influencing the properties of the individual cells) the anatomy and function of the organs and the entire bodies of organisms. The anatomy and micro-anatomy of individual specialized organs, in animals especially the micro-anatomy of the nervous system, then determine the behaviour of the organisms, i.e. the reaction of the organisms to various combinations of external and internal stimuli.

A large amount of the information contained in the DNA is interpreted even without transcription to the RNA sequence and further to the protein sequence. The linear motifs of the alternating nucleotides act as specific binding sites for various molecules with structural or regulation functions. The nucleotide sequences in these sections thus determine not only the manner of storing long DNA sections in the cell nuclei, but directly (through bond specificity) and indirectly (through exposure or covering of binding sites) determine the timing and intensity of the rewriting of other DNA sections to the RNA or the timing and intensity of the translation of the given RNA sections to the proteins. Especially in multi-cellular organisms, apparently the most important evolutionary changes, including changes leading to radical modification of body structure, occur precisely through modification of the programs for expression of the individual genes, and not through modification of the order of nucleotides in these genes. The structure and thus the properties of the individual proteins are apparently of lesser importance here than the time order and intensity of their synthesis in the individual tissues of the organism.

Fig. II.7 Universal genetic code. The table depicts the rules for translation of the sequence of RNA nucleotides to the sequence of protein aminoacids. The universal genetic code is a triplet type, i.e. is formed by triplets of nucleotides (triplets, codons). The individual triplets do not overlap in the RNA chain and are bonded one to another directly in the mRNA molecule without any separators. In addition, the genetic code is degenerated, as most aminoacids are coded by a larger number of triplets. As the translation of the mRNA molecule always begins from one specific site, a particular RNA is always translated to the same sequence of aminoacids. The protein synthesis ends as soon as the mRNA chain contains any one of the three terminal codons.

The DNA also contains sections that are transcribed only into the RNA chains, where these RNA chains are then not further translated to proteins. In contrast to the relatively rigid double-helix DNA, single-chain RNA can form very complex spatial structures because of the mutual interactions between various sections on a single chain. Thus, shorter and longer RNA molecules can have and very frequently do have very different functions in cell physiology, especially in eukaryotic cells. Some RNA molecules also have enzymatic activity, so that they can affect not only regulation of cell function, but also directly physiological processes occurring in the cell. A great many RNA molecules apparently fulfill a structural function in multi-molecular complexes (ribosome, spliceosome). A major portion of the RNA molecules not translated to proteins apparently plays a role in gene expression regulation, in regulation of activation, inactivation, strengthening and weakening transcription and also in the similar regulation of translation (Eddy 2001). Regulation RNA is also important in regulating processes in organisms employing RNA splicing and editing, i.e. later modification of the transcripts. Study of the function of RNA in cell physiology is progressing much more slowly than similar research relating to proteins. This is a result, amongst other things, of the fact that, in prokaryotes, which serve as a very useful model for studying cellular processes, a major part of the function of RNA molecules was apparently secondarily taken over by proteins during evolution (Poole, Jeffares, & Penny 1998; Jeffares, Poole & Penny 1998).