4.3. Assignment of amino acids side chains to blocks of a genetic code triplets

 

It's time to try to answer the question posed at the end of Section 2.3. Why the amino acids are assigned exactly to the given triplets, instead of others?

 

Let's lead comparison of the side chains, classified on the basis of concepts of physical operators of connectivity and anti- connectivity, with a table of the triplet genetic code (Fig. 38) obtained by transformation of triangular matrixes of the Supermatrix to triplets (Section 3.3.).

 

 

According to the definition given in Section 4.1., the operators of anti-connectivity are the side chains of amino acids of the protein, preventing the formation of hydrogen bonds NiH....Oi-4=C. Its properties should be non-polar amino acids.

 

In the matrixes describing the acyclic conformations of the graph and protein, х3 = 0 (in pairs of variables x3x4: blocks 00 <---> C, 01 <---> U).

 

As we have mentioned (Section 4.2.), side chains of amino acids that function as anti-connectivity operators belong in a genetic code to blocks of triplets C and U. To see this, take a look at Figure 38.

 

In block C, as follows from the figure, are located Pro (proline), Ala (alanine) - non-polar amino acids not capable to formation of hydrogen bonds, Ser (serine), Thr (threonine) - weakly polar amino acids that form hydrogen bonds with the Oi-3=C.

 

Similarly, in the block U are located Leu (leucine), Val (valine), Phe (phenylalanine) and Leu (leucine), Ile (isoleucine) and Met (methionine) - non-polar amino acids not capable to formation of hydrogen bonds.

 

 

 

 

According to Section 4.1., operators of connectivity - the side chains of amino acids that contribute to fixing the hydrogen bond NiH....Oi-4=C. These side chains should be able to form hydrogen bonds.

 

In a matrix х3 = 1 (in pairs of variables x3x4: blocks 10 <---> G, 11 <---> A), i.e. these operators recreate cyclic 4-link protein fragments.

 

The side chains of amino acids working as operators of connectivity (Section 4.2.), are in a genetic code in blocks of triplets G and A. In these blocks, triplets with G and A in the second position encode polar amino acids, which can form hydrogen bonds with the Oi-4=C.

 

Really (Fig. 38), in block G are Arg (arginine), Gly (glycine), Cys (cysteine) and Trp (tryptophan) and Ser (serine) and Arg (arginine).

 

The block A contains the amino acids His (histidine) and Gln (glutamine), Asp (aspartic) and Glu (glutamic acid), Tyr (tyrosine), Asn (asparagine) and Lys (lysine).

 

 

Thus, there is full compliance of the group properties of amino acids, considered as operators of anti-connectedness and connectedness, to those conformations of proteins that are encoded by triplets in blocks of the given structure of the genetic code.

Fig. 38. The table of  triplet genetic code

 

The triplets received by coding of triangular matrixes of the Supermatrix, and amino acids corresponding to these triplets are shown.

Thus we have in general found the answer to the question at the beginning of this section: why the amino acids correspond exactly to the given triplets, instead of others. The answer is that the amino acids correspond to the triplets, which encode the protein conformation, reconstituted by these amino acids in the role of physical operators.

 When considering the amino acid side chains in Section 4.2. you've probably noticed that as the length of the side-chain increases hydrogen bond angle is changed: at the short side chains it is less than 90 degrees, at the long - more than 90 degrees. This could mean that the side chains of different lengths may create a "tug" in NiH...Oi-4=C, aimed in different directions. This observation was the starting point for further analysis of this sphere. Part of this analysis, associated with the reconstruction of symmetrical conformations of four-link graph and protein, carried out in Section 4.4.

 

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