2. Table on amino acids and codons. - First observations


The investigation started in the 1980th - without prejudices - with a table of 20 + 4 codons (Table I) with and A-, N- and Z-numbers of side-chains (R) of the coded amino acids (ams), 4 ams having two different codons. Most common isotopes were used.
   Hence, codons where the choice of purine bases U and C in 3rd position or of pyrimidine bases A and G in 3rd position makes no difference was counted as one and the same, as when 3rd base makes no difference at all (called "2-base-coded", generally in the literature called "degenerated"). The 4 ams with double codons are Arg CG + AG-A/G, Ser UC + AG-U/C, Leu CU + UU-A/G and Ileu AU-U/C + AUA, only differing in 3rd base type.

In these files all numbers will refer to atomic mass (nucleon number) and to side-chains (R) of ams where nothing else is mentioned.

Table 1: Codons and A-, N, Z-numbers in side chains of 20 + 4 amino acids:

1st base
2nd base
Ams
N
Z
A
..........
A
Z
N
Ams
1st base
2nd base
G1
G
Gly
-
1
1
1
1
-
Gly
G
G2
C
Ala
6
9
15
101
56
45
Arg1
C
U
Val
18
25
43
130
69
61
Trp
U
A
Asp
28
31
59
47
25
22
Cys
U
A
Glu
34
39
73
31
17
14
Ser2
A
101
56
45
Arg2
A
Sum
5
86
105
191
411
224
187
6
Sum
C1
G
Arg1
45
56
101
15
9
6
Ala
G
C2
C
Pro
18
24
42
42
24
18
Pro
C
U
Leu1
24
33
57
31
17
14
Ser1
U
A
Gln
33
39
72
45
25
20
Thr
A
A
His
38
43
81
Sum
5
158
195
353
133
75
58
4
G1+C1
10
244
300
544
544
299
245
10
G2+C2
U1
G
Cys
22
25
47
43
25
18
Val
G
U2
G
Trp
61
69
130
57
33
24
Leu1
C
C
Ser1
14
17
31
57
33
24
Leu2
U
U
Leu2
24
33
57
91
49
42
Phe
U
U
Phe
42
49
91
57
33
24
Ile1
A
A
Tyr
50
57
107
57
33
24
Ile2*
A*
75
41
34
Meth
A
Sum
6
213
250
463
437
247
190
7
A1
G
Ser2
14
!7
31
59
31
28
Asp
G
A2
G
Arg2
45
56
101
73
39
34
Glu
G
C
Thr
20
25
45
72
39
33
Gln
C
U
Ile1
24
33
57
81
43
38
His
C
U
Ile2*
24
33
57
107
57
50
Tyr
U
U
Meth
34
41
75
58
31
27
Asn
A
A
Asn
27
31
58
73
42
31
Lys
A
A
Lys
31
42
73
Sum
8
219
278
497
523
282
241
7
U1+A1 14   432 528 960   960 529 431   14 U2+A2

*Ile, AU-codon, only differing in type of 3rd base.


First observations:

First to notice is that the mass sums of the two main groups with G+C-codons and U+A-codons become the same in 1st and 2nd base order, 544 and 960.
    It implies that mass sums of ams with mixed codons changing position between the groups are the same, 385 (Table 2). These groups showed astonishing regularities, which seemed to support the hypothesis that mass distribution of ams on different codons wasn't a random one. Note the approximately equal sums horizontally and vertically, Table 2:

Table 2: Mixed codons 12 amino acids, sum 385:

The table is closer studied in file The two 12-groups of ams.

It led to a division of the 24 codons in 2 main groups of 12 ams, the other = 2 times 367, (Table 3), which doesn't show the same regularity as the other:

     
Table 3: Non-mixed codons. 12 amino acids, sum 734:
   
This way of counting and organizing codons seems deviating from most other research.


We get 4 subgroups of codons, here called Form-, Cross-, Pair- and RNA-codons:

Form-coded:  GA, AG, UC, CU, 6 ams, sum 352
Cross-coded: GU, UG, CA, AC, 6 ams, sum 418...2 x 385 = 770
    These two in Table 2.
Pair-coded:    GG, CC, UU, AA, 6 ams, sum 322
RNA-coded:  GC, CG, UA, AU, 6 ams, sum 412...2 x 367 = 734
    These two in Table 4.

Note in Table 3:
G1 + A1, 175 + 177 = 352, give the same mass as the Form-coded ams,
U1 + C1, 208 + 210 = 418, give the same mass as the Cross-coded ams.

Before going on with the analysis, two annotations:

Survey of totals:
With mass in unbound backbone chains (B, B-chains) à 74 A, - 1 in the four ams Arg1 and 2, Lys and Pro. and mass 56 in bound ams, this gives following survey of totals:

24 ams: R: 1504, B unbound 1772, sum 3276 A,
24 ams: R: 1504, B bound 1344, sum 2848 A.
N-Z: R: 828 Z, 676 N, R+B: 1516 N, 1760 Z, unbound ams.

Cf. for instance codon domains when we count on two sets of ams R+B, 1st plus 2nd base order, file 17 short files, 2.6.


Simple variations of the elementary number chain 5-4-3-2-1-0:

There are some simple variations of the elementary number chain (5-4-3-2-1-0), closer dealt with in files in section II, files 12-16, that more or less approximately give the division between some main codon groups of ams, G+C and U+A, but also other more detailed ones.
   Hypothetically such simpler chains on integers 5→0 with exponents 4, 1, 3, 2 could underlie the more developed and differentiated chain in this section, precede this in a perhaps "inflationary" evolution of the code or represent underlying levels? Here only a couple of examples:
   Reading the simple chain as triplets 543+432+321+210 gives 543 (G-C-group -1, U-A-group 960 +3,

Fig 2-1: The triplet series 543 - 432 etc.

Sum 1506 = total of 20 + 4 ams R, +2.

With exponent 4 the main division 544 - 960 (+2) derives from first three numbers 54-44-34 plus/minus 3rd number 81: G-C-group 544 = 625 - 81, U-A-group 960 (+2) = 625 + 256 + 81.

With exponent 2 in the 2x2-chain behind the periodic system, times a factor 16, several different codon-groups of ams appear (+/-1), the main division showed in figure. 2-2:

Fig. 2-2: Relations to 2x2-series, 34-26-60 times a factor 16:

Total sum of the chain, 110, times 16 = 1760, the total Z of the 24 ams (R+B).
   See further file Simpler number chains about the 2x2-chain.

 

To The exponent 2/3 series (ES)

© Åsa Wohlin
Individual research
E-mail: a.wohlin@u5d.net


 

Links and Notes

Table 24 amino acids (ams)
R-chsins, A, Z, N

Abbreviations
- ways of writing -

Background model

Files here:

0. Amino acids and codon bases.
Why this coding system?





All these files in one document,
pdf, 118 pages

To 17 short files.
- partly other material -

The 17 files as one document,
pdf

 

An earlier version (2007)
with more material
on the same subject, 73 pages
:

Latest updating
2017-01-16

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