Genetic Coding

by Tom Gilmore
Copyright 2017
All graphics by Tom Gilmore
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(An Advanced Article)
It is assumed you have read the article on atomic bonding

Part I - DNA

Strands

The most common form of genetic coding involves DNA molecules, which are double-stranded helices, consisting of two long biopolymers made of alternating sugars and phosphate groups, with nucleobases attached to the sugars. 

The helices of DNA are anti-parallel, in the ratio (1:3) as illustrated below.  The dotted line indicates the 3rd empty position.

There are 4 nucleobases (Guanine, Cytosine, Adenine, and Thymine), represented by the letters G, C, A, and T.
The nucleobases are complementary, with A always paired to T, and C always paired to G.

G = (C5H5N5O)
C = (C4H5N3O)
A = (C5H5N5)
T = (C5H6N3O2) 

A simplified Geocubic Model of a DNA Strand segment (without bonding arrows or Hydrogen atoms) is shown below.  It consists of alternating sugar and phosphate groups.  The two groups act as one unit (the atoms enclosed in the oval).  The unit circled is 6 cubes tall, advances forward 6 cubes, but has a net movement to the left of just 2 cubes.  This is a ratio of 2:6 or 1:3 and that accounts for the spirals being offset by thirds.

The Phosphate group is a Phosphorus(15) atom bonded to 4 Oxygen(8) atoms (group of 5 atoms at bottom shown below).  The “sugar” group is 5 atoms in an unclosed roughly pentagonal arrangement of 4 Carbon(6) atoms and 1 Oxygen(8) atom.  The 2 groups of 5 atoms are connected by a single Carbon atom between them.  (Hydrogen atoms are not shown).

The nucleobases attach to the sugar group at the left-most Carbon atom of each sugar group as indicated by the red arrow.

Actually the spiral strings do not extend as a helix spiral, but bend at some of the joints between the sugar/phosphate units (the oval above), and end up as a complex compact ball.

DNA Nucleobases

All 4 nucleobases of DNA incorporate a hexagonal ring.  Cytosine (C4H5N3O) and Guanine (C5H5N5O) are shown below.  The standard conventional schematic of the molecule is shown in green.  In the standard schematics, Carbon atoms are assumed to be at the empty vertices, and generally only some of the Hydrogen atoms are specified (this is done to cover-up not understanding the 3 dimensional structure).  Below the conventional schematic the same diagram is shown in black, fully filled in with all the constituent atoms, and with arrows indicating the direction of the atomic bonds involved.

In the case of Guanine the conventional schematic is wrong.  There is a conventional misconception that “pentagonal rings” can exist, but the cubic matrix precludes this.  In the green diagram this invalid pentagonal group is at lower right. Aside from the cubic impossibility of a pentagonal group, Nitrogen can only take on Neon-form(10), and must only receive Spheres (3 of them), so the bottom Nitrogen cannot attach to the Carbon atom above it because that Carbon is in Neon-form(10) and thus only receives Spheres.

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Beneath the completed and corrected schematics in black, the Geocubic Model of the molecules is shown.  The dotted arrows represent the intermolecular attraction that attaches Cytosine to Guanine  The attraction is between a Void Hydrogen in one of the nucleobases to an active Element ((Oxygen(8) or Nitrogen(7)) in the complementary nucleobase. 

(Both diagrams of C and G are upright, but because the DNA strands flow in opposite directions, the C or G Nucleobase will be inverted in relation to the other).

A Simplified Schematic of DNA

The anti-parallel DNA strands are shown below with the Base pair A—T attached. 

In this simplified schematic, the atomic numbers of the atoms are shown in red.  Since Nitrogen(7), Oxygen(8), and Phosphorus(15) are always in Neon-form(10), the 10 is assumed for them and not shown.  Carbon(6) can take either the Neon-form(10) or Helium-form(2), so 10 is assumed unless 2 is shown in black next to the 6.  The Hydrogen atoms are a transfer of 1 sphere, either in or out, represented by green arrows.  The black dotted arrows represent the intermolecular attraction.  The circled green arrows are Hydrogen atoms that are dislodged when the nucleobases attach to the DNA strings

The diagram is 2 dimensional, so the Base pairs appear to be parallel to the DNA strands, but the Base pairs are 7 cubes tall and the intervals are 6 cubes tall, so they would not fit parallel.  Instead the Base pairs are oriented perpendicular to the DNA strands.

Codons (Sets of 3)

Only from 5 to 10 percent of DNA has been tied to the coding system that produces proteins from amino acids.  The remainder is not yet understood (often called junk DNA), but may be involved in defining the Bio-Form.

Genetic coding involves 3 successive nucleobases called "codons".  In the process of interpreting the genetic coding, the DNA strands in the Nucleus are replicated in both (opposite) directions, forming two single helix strands termed “replicated DNA” or RNA.  During replication the nucleobase Uracil (U) C4H4N3O2 is substituted for Thymine (T).

The conversion just removes an extraneous Carbon atom from the molecule, as shown circled in the simplified diagram below.  Two of the 3 Hydrogen atoms bonded to the removed Carbon atom are also removed, but the 3rd Hydrogen closes up the Carbon atom that the CH3 was attached to.

The following data concerning coding is derived from published conventional consensus.

A “nucleic acid sequence” is a succession of letters that indicate the order of nucleobases within a DNA molecule.

For example, the following complementary double helix strand of DNA translates (substituting U for T) to 2 strands as follows:

A C G C A T G
 !  !   !  !   !   !  !   à  A C G C A U G  and  C A U G C G U
T G C G T A C

The replica is called messenger RNA (mRNA). 

The replica passes through the Nucleus membrane of the cell, where ribosomes use what are termed translation RNA (tRNA) to construct proteins from amino acids in the sequence of the codons (the codons each associate to an amino acid).

The strands of mRNA nucleobases are read in groups of 3, but advancing in single code steps.  For example ACGCAUG is read as ACG, then CGC, then GCA, then CAU, until the Start codon (AUG) is encountered and triggers the start of building a protein, beginning with the amino acid Methionine (Met.).  Once AUG is encountered, the codes are read in groups of 3.

There are 19 additional amino acids that may be added by subsequent codons.  Each codon (set of 3) that follows adds its associated amino acid to the protein, until one of 3 Stop codons are encountered.  There are 20 standard amino acids that are associated with the mRNA codons   Sets of 2 mRNA codes would only allow for coding 16 (4x4) amino acids, so sets of 3 mRNA codes are required, making 64 (4x4x4) possible codons.  All 64 codes are valid, but only 20 amino acids result.  The associations are shown below, organized by the first two nucleobase codes.  Multiple associations common to the first 2 codes are indicated by the small-case letters x, y, and z (coded in purple at upper right).  The amino acids (in red) show their standard abbreviations.


Chart by Tom Gilmore

The possible number of different proteins is enormous.  The finished protein is routed to the location where it is to function, and that location determines the function based on what is termed a "cell community effect".

In a protein, the amino acid sequence emulates the DNA nucleobase coding.  The emulation involves a structural change from a hexagonal ring (in the DNA nucleobases) to a tetrahedral chain (in the amino acid).  The purpose of this chemical translation is to make the amino acids carry the DNA codes in a disposable (consumable and/or bio-degradable) protein.

Proteinogenic amino acids (those used in building proteins) are a small subset of all the chemically potential amino acids.  The human metabolism can construct 11 of the coded amino acids, but 9 of the coded amino acids (termed essential) must be consumed, mostly from proteins that contain them.  The consumed protein is broken down to extract the essential amino acids.  A few amino acids are sometimes added in a post-translational (after the coded protein is finished) biosynthesis process.  The many variations and exceptions to the general standard amino acids and proteins suggest that the genetic codes have been externally amended, and this indicates an intervention in the supposed determinative link between DNA chemistry and the organic expression. 

The complementary sequencing of C to G and A to T insures exact duplication when the DNA strands split during cell division, since the complementary nucleobase is automatically reattached to each of the split strands from the chemical soup in the cell. 

The complementary sequencing results from the intermolecular attachments, in that for the A—T pair there are only 2 points of attraction, and for the C—G pair there are 3 points of attraction at different spatial locations from the 2 in the A – T pair.

Coding systems do not evolve through random mutation, and are not reasonably attributed to natural selection,

DNA Duplication

The following data concerning duplication is derived from published conventional consensus.

DNA is packaged in chromosomes that are spread out and isolated in the cell, possibly to prevent mix-ups during cell division when the spiral strands are split and replicated.  During duplication a chemical called a Helicase breaks the weak intermolecular Hydrogen attraction and "unzips" the strands, straightening them into separate linear strands with their separated Nucleobases attached. 

From a soup of chemicals an enzyme (catalyst) reconstructs (in a linear process) an exact complementary replica upon each strand, but this process only operates in one of the two strand directions.  In the strand of the other direction, short segments are constructed in the direct-process direction and then the segments are fused together.  (How this could have evolved is mysterious). 

Once split into separate linear strands, for each split strand, as the inverted strand and the complementary nucleobases are (rather mysteriously) constructed, the intermolecular Hydrogen attraction bends the straightened strands back into helix spirals.

It appears that only a small percentage of the total DNA is used for defining genetic traits, and it is not known if the remainder has any purpose (it is likely that it defined the Bio-Form).

In sexual reproduction the DNA is “unzipped” and a single strand, with its Nucleobases attached, is produced in the egg and the sperm.  When fertilization takes place, these strands are joined, but coming from differing DNA the Nucleobases in sequence are not always complementary, and one of these mismatches must be replaced.  The mechanism for the determination of which mismatch to replace is a mystery.

Because the identical DNA is duplicated to all cells in an organism, the specialization of cell form and function must be controlled by a biological form that identifies relative location within an organism and modifies the cell accordingly.  (It is known that embryonic stem–cells if relocated in an organism will alter their form and function to match their location.)  Although the Bio-Form has not yet been detected, and it is unclear how it functions in relation to genetic deformities, it is clear that the known genetic coding itself is not responsible for the organic design, or for the autonomic organic functions such as heartbeat, digestion, breathing, and sleep, let alone accounting for thought and will.

The intricate organic coding detailed in this article suggests the coding has been designed by an intellect as a mechanism of structuring the life-force built into the Cosmos. 

Part II – Geocubic Model of Amino Acids

Geocubic Conventions

In the following set of Geocubic diagrams of amino acids, the cubes with bold black front squares are Carbon(6) atoms, red are Nitrogen(7), blue are Oxygen(8), yellow is Sulfur(16), and the plain cubes are Hydrogen(1).  There are many potential amino acids but only 20 are genetically coded.

Amino acids are considered to combine amino NH2 (attached with a red arrow) and carboxylic acid COOH (attached with a blue arrow).  There are 2 additional atoms (CH) that are common to all amino acids, so all other atoms in the amino acid beyond NH2 (CH) COOH or (C2H4O2N) are considered to be a "side chain" specific to each amino acid.  The tetrahedral bonding of the Carbon and Nitrogen atoms produces zig-zag linkages that are conventionally referred to as chains.  Naming the non-common atoms a “side chain” is an oversimplification. 

One discrepancy is that, depending on the constraints of the constituent atoms, the Nitrogen atom claimed to be amino (NH2) may have only one Hydrogen atom attached (NH).  Also, the problem with using the term “side chain” is that the excess atoms over the atoms common to all amino acids, for the most part, do not extend to the “side” of the chain.

In the following amino acid illustrations, 2 ways of expressing the chemical formula are used.  The conventional notation is to specify the counts of the 4 different atoms (CHNO), as with Alanine (C3H7NO2).  The preferable Geocubic Model notation is based on the actual tetrahedral Carbon/Nitrogen chain, color coded to match the colors in the illustration.  Sometimes the chain includes Oxygen(8) or Sulfur(16).

Only the blue COOH is the same for every amino acid (it should have been named for the amino tail of Nitrogen).

For the simplest coded amino acid, Glycine (C2H5O2N), diagrammed below, the “side chain” is simply (H), one excess Hydrogen atom.

 

Notice that in Glycine the amino and the carboxylic acid attach directly to each other.  The Carbon atom is forced to the end of the chain 

The reason for this is that in a tetrahedral Carbon/Nitrogen chain the atoms must alternate between Helium-form(2) and Neon-form(10), alternating sending and receiving spheres, the chain starts with the Carbon(6) in COOH, which is in Helium-form(2), and Nitrogen(7) can only take Neon-form(10).  Thus, if the other Carbon in this molecule linked directly to the Carbon in the COOH, it would be in Neon-form(10) and the Nitrogen(7) could not attach. 

Carbon(6) + 4 à Neon-form(10)
Carbon(6) – 4
à Helium-form(2)
Nitrogen(7) +3
à Neon-form(10) 

Carbon(6) can take either Neon-form(10) or Helium-form(2), but Nitrogen(7) can only take Neon-form(10), so it must attach to Carbon atoms that are in Helium-form(2).

The next simplest coded amino acid is Alanine, which has an excess (side chain) of CH3.   

Element Substitutions

Serine and Cysteine have identical chain structures, except Serine incorporates an Oxygen(8) atom in the chain, and Cysteine incorporates a Sulfur(16) atom.
For Sulfur(16), adding 2 spheres reaches the next inert form, Argon-form(18). 

Oxygen(8) +2 à Neon-form(10)
Sulfur(16) +2
à Argon-form(18)

Isomers of a molecule are differing arrangements of the same count of constituent atoms.  Both Serine and Cysteine have one isomer (an alternate chemical arrangement).  In these isomers the position of the Nitrogen(7) is switched with the Oxygen(8)/Sulfur(16) atom.  In the diagram just above of the Cysteine Isomer the Nitrogen and Sulfur positions are switched (for the Serene isomer, the Nitrogen and Oxygen are switched).

Above is shown one of the Isomers of Methionine (Met.). 

Lysine is an example of an amino acid with an additional NH2 as shown below. 

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