Threesology Research Journal

Trigrams or Bigrams?...page 2
Threes or Twos?

(The Study of Threes)
http://threesology.org



The following is another attempt to use Bigrams as so-called "Trigrams":


Amino acid positioning on the I Ching Matrix

Phe   . . Leu . . . Ser . . . . -
1 63  44 62 . 13 61 . 33 60. . 10 59   6 58 . 25 57 . 12 56
ttt ttc tta ttg tct tcc tca tcg
Tyr --------- . Ochre . Amber Cys   -----  . Umber . Trp 
9 55   57 54 . 37 53 . 53 52 61 51  59 50  . 42 49 . 20 48
tat tac taa tag tgt tgc tga tgg
Leu . . . . .. . Pro . . . . .
14 47 50 46 . 30 45 . 56 44 . 38 43  64 42 . 21 41 . 35 40
ctt ctc cta ctg cct ccc cca ccg
His . . Gln . . . Arg . . . . .
26 39 18 38 . 22 37 . 52 36 . 41 35   4 34 . 27 33 . 23 32
cat cac caa cag cgt cgc cga cgg
Ile . . . . Met Thr . . . . .
43 31    28 30 . 49 29 . 31 28 . 58 27 47 26 . 17 25 . 45 24
att atc ata atg act acc aca acg
Asn . . Lys . . . Ser . . Arg . .
 5 23 48 22 . 63 21 . 39 20 . 60 19 29 18 . 3 17 .  8 16
aat aac aaa aag agt agc aga agg
Val . . . . . . Ala . . . . .
34 15 32 14 . 55 13 . 62 12 . 54 11 40 10 . 51 9 . 16 8
gtt gtc gta gtg gct gcc gca gcg
Asp . . Glu . . . Gly . . . . .
11 7 46 6 . 36 5 . 15 4 . 19 3  7  2 . 24 1 . 2 0
gat gac gaa gag ggt ggc gga ggg

Amino acid three letter code
First number is I ching number -- Second number is the binary value of the DNA codon and I Ching Hexagram.

--- Amino acids and I Ching ---
http://www.cancun.com/sipp5/amino.stm




trigram genetic code analogy


In humanity's early attempts to unravel the genetic code, it was determined that in order for us to account for the 20 amino acids used in the synthesis of most proteins, there would have to be a code that would, at its very minimal, contain at least 20.  As can be seen in the following chart, a singlet code would only provide us with 4 amino acid "words," and a doublet code would only provide us with 16 "words."  It is obvious that both of these code formulas fall short of the minimum requirement of 20, but that a triplet code satisfies this need quite easily by having a 64 "word vocabulary":


Singlet code (4 "words")
Doublet code (16 "words")
Triplet code (64 "words")
AAA   AAG   AAC   AAT
AGA   AGG   AGC   AGT
ACA   ACG   ACC   ACT
ATA   ATG   ATC   ATT
GAA   GAG   GAC   GAT
GGA   GGG   GGC   GGT
A AA   AG   AC   AT GCA   GCG   GCC   GCT
G GA   GG   GC   GT GTA   GTG   GTC   GTT
C CA   CG   CC   CT CAA   CAG   CAC   CAT
T TA   TG   TC   TT CGA   CGG   CGC   CGT
CCA   CCG   CCC   CCT
CTA   CTG   CTC   CTT
TAA   TAG   TAC   TAT
TGA   TGG   TGC   TGT
TCA   TCG   TCC   TCT
TTA   TTG   TTC   TTT

With the understanding that it takes three nucleotides to make up one "word" (called a codon), it is interesting to find that a sequence of codons (that we might refer to as a sentence), uses three "punctuation marks" called "stop codons," to end the sentence. There are 3 "stop" codons in RNA and 3 "stop" codons in DNA, along with 1 start codon for each, as is indicated in the following two tables. (We are thus presented with a 3 to 1 ratio formula that has cropped up in other areas:


Note that for each table, the left-hand column gives the first nucleotide of the codon, the 4 middle columns give the second nucleotide, and the last column gives the third nucleotide.


The RNA Codons:

U C A G
U UUU Phenylalanine (Phe) UCU Serine (Ser) UAU Tyrosine (Tyr) UGU Cysteine (Cys) U
UUC Phe UCC Ser UAC Tyr UGC Cys C
UUA Leucine (Leu) UCA Ser UAA    STOP UGA    STOP A
UUG Leu UCG Ser UAG    STOP UGG Tryptophan (Trp) G
C CUU Leucine (Leu) CCU Proline (Pro) CAU Histidine (His) CGU Arginine (Arg) U
CUC Leu CCU Pro CAC His CGC Arg C
CUA Leu CCA Pro CAA Glutamine (Gln) CGA Arg A
CUG Leu CCG Pro CAG Gln CGG Arg G
A AUU Isoleucine (Ile) ACU Threonine (Thr) AAU Asparagine (Asn) AGU Serine (Ser) U
AUC Ile ACC Thr AAC Asn AGC Ser C
AUA Ile ACA Thr AAA Lysine (Lys) AGA Arginine (Arg) A
AUG Methionine (Met) or
START
ACG Thr AAG Lys AGG Arg G
G GUU Valine Val GCU Alanine (Ala) GAU Aspartic acid (Asp) GGU Glycine (Gly) U
GUC (Val) GCC Ala GAC Asp GGC Gly C
GUA Val GCA Ala GAA Glutamic acid (Glu) GGA Gly A
GUG Val GCG Ala GAG Glu GGG Gly G




The Genetic Code (DNA):

These are the codons as they are read on the (5' to 3') strand of DNA. Except that the nucleotide thymidine (T) is found in place of uridine (U), they read the same as RNA codons. However, mRNA is actually synthesized using the (3' to 5') as the template.

(This table could well be called the Rosetta Stone of life.)

The DNA Codons:

TTT Phe TCT Ser TAT Tyr TGT Cys
TTC Phe TCC Ser TAC Tyr TGC Cys
TTA Leu TCA Ser TAA STOP TGA STOP
TTG Leu TCG Ser TAG STOP TGG Trp
CTT Leu CCT Pro CAT His CGT Arg
CTC Leu CCC Pro CAC His CGC Arg
CTA Leu CCA Pro CAA Gln CGA Arg
CTG Leu CCG Pro CAG Gln CGG Arg
ATT Ile ACT Thr AAT Asn AGT Ser
ATC Ile ACC Thr AAC Asn AGC Ser
ATA Ile ACA Thr AAA Lys AGA Arg
ATG Met***    (START) ACG Thr AAG Lys AGG Arg
GTT Val GCT Ala GAT Asp GGT Gly
GTC Val GCC Ala GAC Asp GGC Gly
GTA Val GCA Ala GAA Glu GGA Gly
GTG Val GCG Ala GAG Glu GGG Gly
*** When within gene; at beginning of gene, ATG signals start of translation.

The genetic code is almost universal.   The same codons are assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microorganisms.   However, some exceptions have been found.  Most of these involve assigning one or two of the three STOP codons to an amino acid instead.


Mitochondrial genes:


When mitochondrial mRNA from animals or microorganisms (but not from plants) is placed in a test tube with the cytosolic protein-synthesizing machinery (amino acids, enzymes, tRNAs, ribosomes) it fails to be translated into a protein.  The reason for this is that these mitochondria use UGA to encode tryptophan (Trp) rather than as a chain terminator. When translated by cytosolic machinery, synthesis stops where Trp should have been inserted.


In addition, most

  • Animal mitochondria use AUA for methionine not isoleucine and
  • All vertebrate mitochondria use AGA and AGG as chain terminators.
  • Yeast mitochondria assign all codons beginning with CU to threonine instead of leucine (which is still encoded by UUA and UUG as it is in cytosolic mRNA).


Plant mitochondria use the universal code, and this has permitted angiosperms to transfer mitochondrial genes to their nucleus with great ease.


The above table information and accompanying comments are adapted from:


--- The Genetic Code ---
http://www.ultranet.com/~jkimball/BiologyPages/C/Codons.html



Your Questions or Comments are welcomed: Contact Herb O. Buckland (herbobuckland@hotmail.com}