4.2.1. The Hydrogen Atom Content
From
Table A1 in
Appendix A, the total number of hydrogen atoms in the side chains of all the amino acids coded by the 61 sense codons is equal to
. Let us note from the start that, in this count, we take for the (singular)
imino acid proline, as a special case, five hydrogen atoms in its side chain. We will return to this important point later, in
Section 5, with brand new results. A quick look at
Table 5 of our Fibonacci-like sequences reveals that the number of hydrogen atoms, mentioned above, is showing itself in multiple instances: first, ostensibly, as the ninth member of the sequence
(
; second, from the relation (viii) in Equation (2) which, we recall, is valid, particularly for
:
; third, from the recurrence relation of the sequence
; fourth, from the sum
This last equation will be considered in detail below, as it has great importance concerning the computation of the degeneracy of the genetic code in various formats. By isolating the last term
, we have
This relation is important and will play a prominent role in this section and later (in
Section 6). Equation (10) gives the number of hydrogen atoms in the amino acids’ side chains, distributed into two parts: 139 hydrogen atoms in 23 amino acids (17 amino acids with no “degeneracy” at the
first base position and the six entities
,
and
), on the one hand, and
hydrogen atoms in the remaining side chains of the amino acids encoded by the
degenerate codons, on the other (see
Appendix A for the calculations from the table). This is the equivalent “
” pattern for the hydrogen content. Next, as we have
from the recurrence relation of the sequence
, we can cast the relation above as follows:
This is the hydrogen atom content in the usual pattern “
(117 hydrogen atoms in the side chains of 20 amino acids and 241 hydrogen atoms in the side chains of the amino acids coded by the 41 degenerate codons; see
Table A1 in
Appendix A). Note that 22 is the number of hydrogen atoms in the side chains of serine, arginine and leucine, corresponding to one codon for each one of them (see
Table A1 in
Appendix A). It is also just the right factor that connects the two patterns “
” and “
”.
By restricting the sum in Equation (10), as shown below, we have
This hydrogen atom partition corresponds to Rakočević’s
Cyclic Invariant Periodic System (CIPS) classification of the amino acids, where there are 133 (225) hydrogen atoms in the amino acids side chains in the secondary superclass (primary superclass), [
15]. The above hydrogen atom partition is only one unit from another one, which is twice relevant. By transferring the first member of the sequence,
, from the sum to the other factor, we obtain
First, this hydrogen atom pattern corresponds to 132 hydrogen atoms in all the side chains of the 3 sextets coded by 18 codons, on the one hand, and 226 hydrogen atoms in all the side chains of the remaining 17 amino acids coded by 43 codons, on the other (see below). Here, we see that the three sextets are set apart, and this has, we think, a link with the subject of
Section 4.2.2 below. Second, this pattern also describes the distribution of hydrogen atoms in the side chains of the amino acids in the two classes of the aminoacyl t-RNA synthetases: 226 hydrogen atoms in the side chains of all the amino acids coded by 29 codons in Class-I and 132 hydrogen atoms in the side chains of all the amino acids coded by 32 codons in Class-II; see [
7]. Note the codon pattern “
”, the same as in Equation (8) above.
4.2.2. The Hydrogen Atom Content in the “Ideal” Symmetry Classification Scheme
In this section, we consider the hydrogen atom content for the “ideal” symmetry classification scheme, [
10], which occupies an important place in this work, as it has a tight relation with the choice of the “seeds” of our Fibonacci-like series. As promised at the beginning of
Section 3, this is the right place to explain and justify the choice of the initial conditions of the sequences
and
, as defined in
Section 3, having importance in this section (more will be said about the “seeds” of the other sequences in
Section 4.2.5, which is devoted to their choice). Concerning
, the “seeds” are
and
(see
Table 5). These are chosen, respectively, to be the number of
hydrogen atoms in arginine’s and serine’s side chains (
) and in leucine’s side chain (9). Their sum, which is the recurrence relation,
is the number of hydrogen atoms in the side chains of these three amino acids (see Equation (12)). The “seeds” of
,
and
, are chosen to be, respectively, the number of
atoms in the side chains of arginine and leucine (
) and in the side chain of serine (
). Here, as for hydrogen, we have the recurrence relation
which is the number of atoms in the side chains of these three amino acids (see
Table A1 in
Appendix A).
We show, in this section and also in the next ones, using all the resources offered by our Fibonacci-like series and their properties, that these three sextets (more precisely, their hydrogen and atoms numbers), as “seeds”, will create the entire hydrogen atom, atom and even nucleon content of the whole set of amino acids, including the degeneracy, much like the creation of the 64 codons from the three sextets in the “ideal” symmetry scheme, [
10], mentioned above.
Now, we return to the subject of this section. First, using the relation (v)
in Equation (2), we can derive the hydrogen atom content in the two sets: the “leading” group and the “nonleading” group. We have, for
(see
Table 5 and also
Appendix C)
It can be seen, from
Table 4 and also, in parallel, from an evaluation using the data in
Table A1 in
Appendix A, that there are
and
hydrogen atoms in the side chains of the amino acids in the “leading” group and in the “nonleading” group, respectively. Moreover, concerning the latter, there are
hydrogen atoms in the side chains of the amino acids, the codons of which have the
same first two bases, UU, CC, AA and GG (in the four corners of
Table 4), and
hydrogen atoms in the side chains of the amino acids located in the four boxes in the center of the table, the codons of which have
different first two bases, UG, GU, AC and CA. Equation (14) above faithfully describes, therefore, this pattern. Now, we move further to accurately describe the hydrogen atom content involving the amino acids of the “
core” comprising serine, arginine and leucine. To see this, we invoke the following two relations:
It could be verified that they give the same result and both hold (see
Appendix C). They can also be transformed into each other, using the relation (viii) in Equation (2),
. For
, they give
and
, respectively, with a common value of 358, the total number of hydrogen atoms in the side chains of all the amino acids encoded by the 61 sense codons. These relations are of interest for what follows. In the first relation, as we have seen above,
is the number of hydrogen atoms in the side chains of the amino acids in the “leading” group, and
is the number of hydrogen atoms in the side chains of the amino acids in the “nonleading” group. In the second relation,
is the number of hydrogen atoms in the side chains of the amino acids in the part of the “core” belonging to the “leading” group (
,
), and
is the number of hydrogen atoms in the side chains of all the remaining amino acids in the other part of
Table 4, comprising, in particular, the part of the “core” belonging to the “nonleading” group, that is,
. The authors write in their paper [
10], “The sextets as initial building blocks for the creation of their new scheme of the genetic code generate by themselves the patterns of A+U rich/C+G rich, purine/pyrimidine, weak-strong and amino-keto symmetries”. They also add that, in their approach, “the symmetries are a consequence of sextet’s dynamics”. To go further and show agreement with what has just been said, we can use our Fibonacci-like sequences to reveal the exact hydrogen atom content of the “core”, constituted by the three sextets. As mentioned above, the “core” has two parts: one that belongs to the “leading” group and the other that belongs to the “nonleading” group. Let us consider the former with 114 hydrogen atoms. Using Euler’s totient function φ and also the so-called “reduced” totient function or Carmichael’s function λ(n) (see
Appendix B), we have for the number 114 φ
and
. Subtracting these from the number 114, we obtain
and by rearranging, we obtain
This is the correct content of the part of the “core” in the “leading” group:
hydrogen atoms (
) in arginine’s side chain (
), 36 hydrogen atoms
in leucine’s side chain (
) and 18 hydrogen atoms (
) in serine’s side chain (
). Let us, alternatively, add the above-mentioned two functions to the number 114. We have
This is the number of hydrogen atoms in the side chains of the amino acids of the “nonleading” group, where the isolated number 18 is now
re-interpreted as the number of hydrogen atoms in the side chain of leucine
the “seed” of the “nonleading” group, that is,
(see above). We have thus established the exact hydrogen atom content in the “ideal” symmetry scheme of the genetic code where the sextets play a prominent role. Note, finally, that, as λ
has been used two times, once as the number of hydrogen atoms in
and once as the number of hydrogen atoms in
, we can summarize all of what has been said above by adding λ
= 18 to Equation (17) and write the exact hydrogen atom content of the entire “core”
constituted by
and
, respectively. (The
codons of the “core” are underlined in
Table 4.) Of course, after subtracting the number
from the total sum
in Equation (14) above, we are left with
the number of hydrogen atoms in the side chains of the 17 amino acids outside the “core”. We have thus seen that the “seeds” of the sequences
and
are capable of creating the hydrogen atom structure in good agreement with the “ideal” symmetry classification scheme (see also
Section 4.2.4 below).
As a by-product of the results obtained in this section, we have found, unexpectedly, a way to derive from the number of hydrogen atoms in the part of the “core” in the “leading” group,
and in the rest,
comprising the part of the “core” in the “nonleading” group (see above), and only from these, the very chemical structure of the building blocks of RNA: the four ribonucleotides
uridine monophosphate (UMP),
cytidine monophosphate (CMP),
adenosine monophosphate (AMP) and
guanosine monophosphate (GMP). Using the functions
and λ (see
Appendix B), we have
,
and
(see
Appendix B, where the details of the computations are given as examples). First, we have, from these three quantities,
This is the total number of atoms in the four ribonucleotides: 56 in the four nucleotides U (12 atoms), C (13 atoms), A (15 atoms) and G (16 atoms) and 88 in the four identical “backbones”, each with 22 atoms (see [
7] for the details of the calculation, which also includes a mathematical derivation of the number 22 above, which is part of the “
condensation” equation for the assembly of a ribonucleotide from the three units: a nucleotide, a ribose and a phosphate group with the release of two water molecules, also derived). Now, as there are 30 codons in the “leading” group (two stop codons not counted) and 31 codons in the “nonleading” group (one stop codon also not counted) (see
Table 4), we can use this decomposition for the number 61 above and finally write the relations above in the form
. Note that the above decomposition of the number 61 could also be obtained in another way, by directly using the properties of the sequence
; see
Table 5. We have, in this case,
,
and
, so by combining them, we obtain
. The above-computed quantities
,
,
and
are, respectively, the number of atoms in the four ribonucleotides UMP (C
9H
13N
2O
9P), CMP (C
9H
14N
3O
8P), AMP (C
10H
14N
5O
7P) and GMP (C
10H
14N
5O
8P), where we have indicated their elemental composition.
4.2.3. The Hydrogen Atom Content in Rumer’s Symmetry
Now, we return to the symmetries and examine the second case, Rumer’s symmetry (
Section 2.1). Let us reconsider Equation (10) and write it in the following form:
where we have used the recurrence relation of the sequence
to write the number
as
(see
Table 5). We have already mentioned in the examples following Equation (5) that, for
, one has
or
. Inserting this quantity in the above equation results in
This is the hydrogen atom content in Rumer’s division: 186 hydrogen atoms in the side chains of the amino acids in
and 172 hydrogen atoms in the side chains of the amino acids in
, where, in this latter, we have the correct partition into 84 hydrogen atoms
in the side chains of the amino acids constituting the 5 quartets and 88 hydrogen atoms
in the side chains of the amino acids constituting the 3 sextets. To obtain the details concerning the number of hydrogen atoms in
, 186, we first isolate the sum of the first four numbers in the sum in Equation (19), that is,
This is equal to the number of hydrogen atoms in the triplet isoleucine (see below). We are left, in the sum, with the three terms
. By writing the number
once as
from the relation (viii) in Equation (2), with n = 5, and twice as
from the recurrence relation of the sequence
, we obtain
Here, and from the recurrence relation of the sequence . We have, therefore, in detail, the correct number of hydrogen atoms in : in the 9 doublets, in the doublets of the 3 sextets, in the triplet, in the singlet methionine and in the singlet tryptophane.
4.2.4. The Hydrogen Atom Content in the Third Base Symmetry
In
Section 2.2, we explained that the authors extracted an inherent basic symmetry linked to the third base by partitioning the 64-codons set into four pair-wise subsets, where each one of them contains only codons having the same third base. In this way, a one-to-one correspondence exists between one member of a doubly degenerate codon pair and the other member. Here, also, for this symmetry, we could describe the hydrogen atom content, using our Fibonacci-like series. Take the relation (v) in Equation (2), the one we already considered above in Equation (14)
This relation,
as it is, is the pattern shown in
Table 3 for the gross third-base division UC/AG; more exactly, we have from the
Table 3.
Here, we note that this relation already describes, nicely, the equality of the number of hydrogen atoms in the columns third base U and third base C, where the amino acids are the same (see the penultimate row in the
Table 3). We can do better by invoking two more relations. First, we have the relation (x) in Equation (2):
which, for
, gives
(see
Appendix C). Second, we have the relation
, which also holds and gives, for
,
. Inserting the number
, from the relation just above, in the second one results in
. Collecting these results in Equation (22) above gives, finally,
This last relation completely describes, therefore, the hydrogen atom content pattern of
Table 3. The third base classification mentioned above can also be supported by the following calculation. We know, from
Section 2.2, that the doubly degenerate codons (group-II) obey a fundamental symmetry, so they must play a basic role, including, we will show, in the hydrogen atom content. We have, using the sequence
,
By subtracting this sum from the right side of Equation (22) above, which gives the total number of hydrogen atoms in the side chains of all the amino acids coded by the 61 sense codons, we obtain, by arranging,
These two numbers can be interpreted as follows: 100 hydrogen atoms in the side chains of the amino acids constituting the 9 doublets and 258 hydrogen atoms in the side chains of the amino acids constituting the remaining multiplets (5 quartets, 3 sextets, 2singlets and 1 triplet); see Equation (21) and below it. This same relation, Equation (25), could also be obtained, in another way, from the relation mentioned in
Section 4.1,
, noting that the sum in Equation (24) above is also equal to
(recall
, with k = 9). We then get back to our result as follows:
. Note also that
and
or
, which is nothing but the hydrogen atoms pattern of the present classification (see Equation (22) and
Table 3). (The function φ is defined in
Appendix B, and the factor two, which has been introduced above, is for “doubly” degenerate codons.)
4.2.5. On the Choice of the “Seeds” of the Fibonacci-like Sequences
We have explained and justified, in
Section 4.2.2, our choice of the “seeds” of the Fibonacci-like sequences
and
; they are related, respectively, to the hydrogen and atom numbers of the three sextets serine, arginine and leucine, which play a prominent role in the “ideal” symmetry classification scheme. The choice of the “seeds” of the remaining sequences,
,
and
is of another nature. These “seeds” have been found (by a trial-and-error thought process) to be fruitful. These “seeds” may, perhaps, also have some deep connection with the nature of the codons; let us outline below how.
Consider, first, the sequence
. First, we have, using Equation (6),
, with the “seeds” being the first two numbers 6 and 1, and a unit was transferred from the right side of the equation to the left side. From the Fibonacci relation
, with
, we have
or
. Next, it could be easily shown that the sequence
, in Equation (4), is related to the Lucas sequence,
so that, for
, we have
. Finally, we call, exceptionally, the term
which also obeys the recurrence relation
, that is,
or, equivalently,
. Putting together all these pieces, we end up with
. The last four terms on the left side could be interpreted as 1 triplet, 2 singlets, 5 quartets and 9 doublets, which are the 17 amino acids outside the “core” of the “ideal” symmetry classification scheme, discussed in
Section 4.2.2. As for the first two terms, in the parenthesis, they are just enough to describe the five entities
and
, forming the part of the “core” belonging to the “leading” group, on the one hand, and one for
, the part of the “core” belonging to the “nonleading” group, on the other. (The “seeds” of the sequence
, leading to the sequence of numbers
also allowed us to establish the multiplet structure of the amino acids and the Rumer’s division of the genetic code table in
Section 4.1).
Consider the “seeds” of sequence
They also lead to meaningful results. From Equation (49), defined below in
Section 5, we have, for
or
. Analogously to what we accomplished above, we call the index
and the recurrence relation
, that is,
this is the first number six in the equation above. The second number six, which is also a perfect number, could be written as the sum of its proper divisors:
(this trick was also useful in
Section 4.1). By bringing together these terms and arranging, we obtain, finally,
. This last relation could be interpreted as the sum of the number of multiplets of the standard genetic code: 1 triplet, 2 singlets, 5 quartets, 3 sextets and 9 doublets, that is, 20 amino acids (see the introduction). (The “seeds” of the sequence
also lead to meaningful results, like the distribution of hydrogen atoms in Equation (10), which, in turn, is in agreement with Equation (34); see just below).
Finally, the sequence
, defined below in Equation (26), together with its “seeds”,
and
, will lead us to establish Equations (34) and (35), below in the next section, and these latter are also shown to agree with the “ideal” symmetry classification scheme of
Section 4.2.2.