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RNA / DNA-bases


Synthesis, complementary traits, first annotations about mass.


The DNA-RNA-bases G and A versus C-U-T do indeed represent complementary "poles", with several polarities in origin and their synthesis.

The 6-5-member-rings of G- an A-bases originate from Inosinic acid,
the 6-member-rings of U-C-T-bases from Orotate.

In original papers G and A are called "00"-bases, U-C-T "0"-bases. Yet the G- and A-bases in their construction have the character of 0-poles of the dimension model here, U-C-T the character of 00-poles (anticentre poles).

a) G- and A-bases are constructed from a centre outwards, the U-C-T-bases inwards:The centre in G- and A-bases is made up of the smallest amino acid Gly, whose branches outwards are filled with small molecules from the surrounding anticentre.
   We have a "c - ac"-relation.

The U-C-T-bases on the contrary are created through the meeting from outwards of two bigger molecules, the amino acid Asp and carbamylphosphate, binding to form the 6-atom rings.

Principle of synthesis for the opposite codon bases:

 
b) Further, G and A then are formed along a branched way from the resulting Inosinic acid, while U, C and T are differentiated along a "linear" path of changes.

  

c) Also the relation to the P-ribose groups of the nucleotides are opposite:
construction of A- and G-bases occurs on the P-ribose group which comes first,
U-C-T bases are constructed separately with the P-ribose group added afterwards.

d) Gly and Asp, the amino acids making up parts of the polar types of bases have mass numbers which are inversions to one another:

(Cf. sum of 133 and 75 = 208, numbers reappearing in the Exponent series.)

e) Mass number sums of "0"- and "00"-bases are inversions:

G + A = 286 = 151 + 135 A (with +1 for bonds to ribose)
U+C+T = 349 = 112 + 111 + 126 A

286 /\ 349. x 10x

Also, more intricate:
2 bases with exponent 2/3 give their opposites if inverted.
(Cf. the exponent 2/3 to an elementary number chain 5-4-3-2-1 related to codon distribution to amino acids in the genetic code, see files The genetic code.)


The branched paths of synthesis for G- and A-bases:

Here we have something like a secondary polarity:

A-base gets its free N-group from the amino acid Asp,
    the N-group in the B-chain of this. (There is of course no other.)
G-base gets its free N-group from Gln,
    the N-group in the R-chain of this.

We can note too:
   Asp, 70 Z ——> A-base 70 Z
   Gln,  78 Z ——> G-base 78 Z

Codons as a mirror relation:

Asp G-A-C <——> C-A-G = Gln  
(but G-A-U <——> U-A-G = one of the Stop codons.)


Complementary forms of bases versus amino acids (ams):

There is a relation in their forms like centres-anticentres, (c—ac), as 0-00 in the model - or radial versus circular as geometrical poles of dimension degree (d-degree) 3 in our model:
- Amino acids as tetrahedrons have central C-atoms and direction outwards in 3-4- directions,
- Bases are rings as if the central atoms had got inverted to anticentre positions.

Formally, 2 amino acids N-C-C-N-C-C could be restructured to the 6-rings of the bases (if chemically possible is another question):

Actually, the contribution of the amino acid Gly to A- and G-bases corresponds to half a 6-ring (1/3 of the C-N-atoms in the 5-6-ring), and Asp with C-C-C-N, 2/3 of the 6-rings of U and C, T: 7 out of 15 C + N in purine and pyrimidine rings.
   (Also Glu and Asp contribute with singular atom groups (NHx) to the Inosine, the parent to A- and G-bases.)

Polarization in end-(R)-groups of the bases:
In the G-C-pair the bases have both O and N, keto-oxygen and nitrogen groups,
while the opposition O-N is polarized to separate bases in the A-U-pair (A-base with only a NHx-group, U (and T) with only 2 oxygen groups.
   This fact points towards the A-U-pair as expression for a secondary step or level from the viewpoint of our dimension model. Many other facts do the same in the arithmetical analysis of codons and amino acids (see those files). (That the opposite is true about the order of synthesis, representing the opposite inward direction, is natural.)

The base pairs may be ordered along 3 kinds of polarities:

a. GA <——> UC type of bases
b. GC <——> UA complementary pairing
c. GU <——> AC defined as keto-bases versus amino-bases.

The GC <—> UA- polarity is here suggested as the first one, an expression for opposite, complementary directions, i.e. d-degree 4.

The GA <—> UC-polarity could be the second one. Compare features of "radial" versus "circular" in the forms of synthesis as poles of d-degree 3. Also a certain polarity heavier — lighter in the property Mass.

The GU <—> CA polarity, founded in the O <—> N-polarity, refers to a hydrophilic-hydrophobic aspect, which concerns Charge as a property. Charge in this model assumed as a property defined in d-degree 2.
Illustrated as coordinate axes:

 

3/2/relations among bases as a polarization of 5:


Free end-groups of the 4 RNA-bases as illustrated in end-groups of amino acids Gln and Asn:


 

About mass numbers (A) and atoms in the single bases:

Intervals in mass between A-T-G-bases:
Intervals are squares illustrated by the Pythagorean' triangle.
G 151 u, A 135 u, T = 126 u. (Including +1 for bond to (deoxi-)ribose:


Approximate mass numbers of T-A-G-bases from quotients in the dimension chain with superposed odd-figure-chain:


Sum of the 4 DNA-bases with +2H for the double bonds added = 543:
543: the first triplet in the elementary number chain:


[Mass of side-chains of G+C-coded ams (R) = 544. The same number division appears there between Z- and N-numbers: 300 Z, 244 N (-/+1 in 2nd base order)]


A mass relation between base types as connected with sum of ams:
Pyrimidine ring without H: 4 C + 2 N = 76 A
Purine ring without H: 5 C + 4 N = 116 A

   76/116 = 2 x 3275,9. ≈ 3276. x 10-4. 3276 = sum of 20 + 4 double-coded ams.


A - Z - L/Lp - p - numbers as different levels in the bases:
The starting point here is the thought that activation ("excitation" ?) of an atom or molecule may imply a stepwise approach towards more superficial levels as suppression of deeper ones and therefore different number of levels in the electron shells are engaged in different stages of processes.
   Here we assume that in first steps the orbitals of the K-shell are suppressed first, designated L-level, in next step the s-orbitals of the L-shell, designated p-level. It doesn't include H-atoms of course.

Addition of different stages could then be regarded as an operation for getting the time aspect inherent (only virtual).


Here it seems as the deeper level of atomic Mass is "disintegrated" in different stages of more superficial levels - as Charge and the electron shells - in a way that agrees with the general principle in the dimension model of higher d-degrees transformed to lower ones. There is a similar, rather remarkable pattern among the coded amino acids, see The genetic code.


Number of atoms in 2 x 24 codon bases, 1st and 2nd position:
Cf. table of 20 + 4 double-coded amino acids.
- Equal number divisions +/-1 in 2 dimensions, horizontally an vertically.

Total sum of atoms = 674 = 2/3 x the sum of the exponent series 1011:
With 3rd base in codons included, assuming equal distribution, 6 of each base, 336 atoms are included:
   6 G = 6 x 16 = 96,
   6 A = 6 x 15 = 90,
   6 U = 6 x 12 = 72,
   6 C = 6 x 13 = 78      
Total sum of atoms should then become ~ the sum of the exponent series 1011.

52/3 — 42/3 — 32/3—22/3 —12/3 —0      x 102 = Sum 1011, 3 x 337.

Numbers abbreviated to integers in the exponent series:

292 + 252 + 208 + 159 + 100
    544                   467

Atoms then in the bases paired:
A+U-bases: 544 atoms -1 = 292 + 252 -1
G+C-bases: 467 atoms = 208 + 159 + 100

Including stop codons, UA-A/G and UGA, first two bases = + 2 U, 1 A, 1 G:
The same equivalence vertically and horizontally appears +/-1:
    A+G-bases: 432 ~ C + N = 433.
    U+C-bases: 297 ~ O + H = 296.

 

23 amino acids, without Ileu2 ( same 1st and 2nd base in the codons):

a. A+G-bases: atom number ~ C+N atoms (A ~ C, G ~ N)
    U+C-bases: atom number ~ O+H atoms.

b. Number 385, which guide one 12-group among amino acids, is equally divided here
    in the numbers 209 - 176 (among the Cross- and Form-coded ams +/-1).

Numbers 262-261 is the mass number of a DNA pair G + C and A + T respectively.
   Note perhaps the inverse relation between numbers around 260 and 385.
There is also the relation in number-base systems (nb-x):
    261 in nb-10 = 405 ~ 385 rewritten in nb-8.
(From files The genetic code.)

The schemes above seem connected with the function the bases have as coenzymes in relation to the different classes of substances. Roughly:
   U-base (UTP) with carbohydrates (dominating atom O),
   C-base (CTP)- with lipids (characterizing atom may be said to be H)
   G-base (GTP) with proteins (typical atom N).
A-base, less specific, most connected with energy storing and transportation.


Sum of products in the dimension chain with superposed odd-figure level
gives mass numbers of bases and amino acids:



A-base and nucleotides - some number readings in the elementary chain:

*

To
Numbers - more on mass numbers of bases and mass relations to amino acids.

 


© Åsa Wohlin
Free to distribute if the source is mentioned.
Texts are mostly extractions from a booklet series in Swedish, made publicly available in 2000.