Random Numbers
Codon Numbers
( assign any numerical value to the bases )
Distribution of
Repeating Base & Non-repeating Base codons
in
Amino Acids
| Amino Acid | Total codons | codons-repeating | % of repeat codons | codons-nonrepeating |
| Trp | 01 | 01 | - | |
| Met | 01 | - | 01 | |
| 02 | 02 | 01 | 50% | 01 |
| Lys | 02 | 02 | - | |
| His | 02 | 01 | 01 | |
| Glu | 02 | 02 | - | |
| Asp | 02 | - | 02 | |
| Gln | 02 | 01 | 01 | |
| Asn | 02 | 02 | -- | |
| Tyr | 02 | 01 | 01 | |
| Cys | 02 | 01 | 01 | |
| Phe | 02 | 02 | -- | |
| 09 | 18 | 12 | 66% | 06 |
| Ile | 03 | 02 | 01 | |
| 01 | 03 | 02 | 66% | 01 |
| Thr | 04 | 02 | 02 | |
| Gly | 04 | 04 | - | |
| Val | 04 | 02 | 02 | |
| Ala | 04 | 02 | 02 | |
| Leu | 04 | 02 | 02 | |
| 05 | 20 | 12 | 60% | 08 |
| Ser | 06 | 02 | 04 | |
| Arg | 06 | 04 | 02 | |
| Pro | 06 | 06 | - | |
| 03 | 18 | 12 | 66% | 06 |
| termination | 03 | 01 | 33% | 02 |
| Total | 64 | 40 | 62.5% | 24 |
*overall per cent of repeat codons is 62.5%. Percentage of repeat codons in 4-codon, 3-codon and 2-codon AA id 66% each which is quite close to overall ratio.
* repeat codons for trp,met is 50% which indicates coding for these AA was done subsequently.
* termination repeating codon is 33% which indicates it appeared in later stage. In fact OCHRE is used in lower organisms , and in the Heterotrich Ciliate Condylosoma
nuclear code, it codes for gln.UAA usage normally decreases with increase G+C pressure. UAA is also the least error prone stop codon variant. It is more robust to mutation
and mistranscription.
* It is also observed that highly expressed genes predominantly end with UAA ensuring termination with either of the 2 release factors RF1/RF2.
Frequency Distribution of Amino Acids (AA/aa)
| no. of codons in AA | no. of AA | total codons | Presence of Base in middle | Absence of base in middle |
| 1 codon aa | 2 | 02 | C | |
| 2 codon aa | 9 | 18 | A or G | C |
| 3 codon aa | 1 | 03 | C/G/A | |
| 4 codon aa | 5 | 20 | C or U | A |
| 5 codon aa | - | -- | --- | |
| 6 codon aa | 3 | 18 | C,G,U | A |
| termination codon | 03 | C | ||
| TOTAL | 20 | 64 | ||
|
As a mathematical exercise, assign any value to bases in 1,2,3 positions and click, numbers shall be generated for each codon. Codons having same numbers are assumed to represent particular amino acids. How many aa can be generated through different no. assigned to bases ? One can experiment. |
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Distribution of Bases
(total no. of codon:64 ; total no.of bases: 64*3=192)
| Bases | polar aa(10) | nonpolar aa(10) | initiation codon* | termination codon | total |
| A | 33 | 10 | 01 | 04 | 48 |
| U | 14 | 30 | 01 | 03 | 48 |
| C | 24 | 24 | - | - | 48 |
| G | 19 | 26 | 01 | 02 | 48 |
| Total | 90 | 90 | 03 | 09 | 192 |
*Met is included in non-polar aa but the bases are not included. They are shown separately in initiation codon.
Distribution of Bases position wise
(In each position, total no. of a base = 64*3/(3*4)=16)
| Bases | 1st position | 2nd position | 3rd position | Total |
| A | 16 | 16 (polar aa) | 16 | 48 |
| U | 16 | 16 (non-polar aa) | 16 | 48 |
| C | 16 | 16 (aaRS-II,8 polar,8 non-polar) | 16 | 48 |
| G | 16 | 16 | 16 | 48 |
| Total | 64 | 64 | 64 | 192 |
AA distribution codon alphabet wise with a particular base in first & second position
(for 6 codon aa, 2 codons are made - from the total list to keep aa no. 20)
| Base in 1st & 2nd position | U | C | A | G | Total |
| U | 02-01(aa) | 01 | 01 | 02 | 06 - 01 |
| 1codon aa | -- | -- | -- | 01 | 01 |
| 2codon aa | 01 | -- | 01 | 01 | 03 |
| 3codon aa | -- | -- | -- | -- | -- |
| 4codon aa | -- | -- | -- | -- | -- |
| 6codon aa | 01 | 01 | -- | -- | 02 |
| termination codon | -- | -- | 02 | 01 | 03 |
| C | 01 (aa) | 01 | 02 | 01 | 05 |
| 1codon aa | -- | -- | -- | -- | -- |
| 2codon aa | -- | -- | 02 | -- | 02 |
| 3codon aa | -- | -- | -- | -- | -- |
| 4codon aa | -- | 01 | -- | -- | 01 |
| 6codon aa | 01 | -- | -- | 01 | 02 |
| termination codon | -- | -- | -- | -- | -- |
| A | 02 (aa) | 01 | 02 | 02-02 | 07-02 |
| 1codon aa | 01 | -- | -- | -- | 01 |
| 2codon aa | -- | -- | 02 | -- | 02 |
| 3codon aa | 01 | -- | -- | -- | 01 |
| 4codon aa | -- | 01 | -- | -- | 01 |
| 6codon aa | -- | -- | -- | 02 | 02 |
| termination codon | -- | -- | -- | -- | -- |
| G | 01(aa) | 01 | 02 | 01 | 05 |
| 1codon aa | -- | -- | -- | -- | -- |
| 2codon aa | -- | -- | 02 | -- | 02 |
| 3codon aa | -- | -- | -- | -- | -- |
| 4codon aa | 01 | 01 | -- | 01 | 03 |
| 6codon aa | -- | -- | -- | -- | -- |
| termination codon | -- | -- | -- | -- | -- |
| Total | |||||
| 1codon aa | 01 | -- | -- | 01 | |
| 2codon aa | 01 | -- | 07 | 01 | |
| 3codon aa | 01 | -- | -- | ||
| 4codon aa | 01 | 03 | -- | 01 | |
| 6codon aa | 02-01 | 01 | -- | 03-02 | |
| termination codon | -- | -- | -- | ||
| 06-01(aa) | 04 | 07 | 06-02 | 23-03=20 |
Distribution of aaRS-I & aaRS-II in codon table
| U | C | A | G | no. of aa | ||
| U | II, non-polar | II, polar | I, polar | I, non-polar* | U C A G |
6(1 common aa)+*+* |
| I, non-polar | ||||||
| I, non-polar | ||||||
| C | I, non-polar | II, non-polar | II, polar | I, polar | U/C A/G |
5 |
| I, polar | ||||||
| A | I, non-polar | II, polar | II, polar | II, polar | U C A G |
7(2 common aa) |
| II, polar | I, polar | |||||
| I, non-polar | ||||||
| G | I, non-polar | II, non-polar | II, polar | II, non-polar* | U/C A/G |
5 |
| I, polar | ||||||
| 5 | 4 | 7+* | 5(1 common aa) +* | 23(includes 3 aa common) +* +* |
(C in middle --> all aaRS-II, U in 1st --> all non-polar, aaRS-I except Phe which being a large molecule should have been associated with aaRS-I. To explore if something with Ala which is associated with aaRS-IIc as is Phe)
Distribution of aaRS-I & aaRS-II in codon table
(cytochrome oxidase of Human mitochondria)
| U | C | A | G | no. of aa | ||
| U | II, non-polar | II, polar - Ser | I, polar | I, non-polar* |
U/C
A/G
|
6(1 common aa)+* |
| I, non-polar- Leu | ||||||
| I, non-polar | ||||||
| C | I, non-polar - Leu | II, non-polar | II, polar | I, polar -Arg |
U/C A/G |
5 |
| I, polar | ||||||
| A | I, non-polar | II, polar | II, polar | II, polar - Ser |
U/C
A/G
|
7(2 common aa) |
| II, polar | I, polar- Arg | |||||
| I, non-polar | ||||||
| G | I, non-polar | II, non-polar | II, polar | II, non-polar* |
U/C A/G |
5 |
| I, polar | ||||||
| no. of aa | 5 | 4 | 7+* | 5(1 common aa) | 23(includes 3 aa common)+* |
(C in middle --> all aaRS-II, U in 1st --> all non-polar, aaRS-I except Phe which being a large molecule should have been associated with aaRS-I. To explore if something with Ala which is associated with aaRS-IIc as is Phe)
Distribution of Doublets in codon table
(cytochrome oxidase of Human mitochondria)
| U | C | A | G | |
| U | NP | P | P | NP |
| C | NP | NP | P | P |
| A | NP | P | P | P |
| G | NP | NP | P | NP |
| Polar (P) & Non-Polar (NP) Amino Acids (aa) |
|
NP- 8 blocks; P- 8 blocks * U in middle -> all NPs *A in middle -> all Ps *C in middle - 50% P, 50% NP --- CC ->NP *G in middle - 50% P, 50% NP --- GG ->NP *with 1st base as U or C, polarity of C & G blocks are opposite i.e. if C block is polar, G block is NP and vice versa. *with 1st base as A or G, polarity of C & G blocks are identical i.e. if C block is polar, G block is also polar and vice versa. |
| Degeneracy |
|
* click on blue colored NP, all yellow colored cells are doubly degenerate and black colored cells are fully degenerate. 8 blocks are fully degenerate 8 blocks are doubly degenerate. * C in middle -> blocks fully degenerate * A in middle -> blocks doubly degenerate * U / G in middle -> doubly degenerate w.r.t. U & A -> fully degenerate w.r.t. C & G. |
| aaRS distribution |
|
* C in middle -> aaRS-II - 4 blocks - 16 codons * U in middle -> aaRS-I - 4 blocks - 16 codons (presume Phe to be of aaRS-I though it is aaRS-II) * A in middle -> AA ->aaRS-II * G in middle ->GG ->aaRS-II * AG & GA -> aaRs-II (upper part) & aaRS-I (lower part) *aaRS-I has 10+1(include Phe) aa, terminating codons -. total aggregate 32 codons Polar aa- Arg(6 codon), nil (4 codons), Glu, Gln, Tyr (all 2 codons) Non-Polar aa - nil(6 codon), Leu,Val (both 4 codons),Trp,Ile,Met,Cys,Phe (all 2 codons) *aaRS-II has 10-01(exclude Phe) aa, total aggregate 32 codons Polar aa- Ser(6 codon), Thr,Gly (both 4 codons), Asp, Asn,Cys,His (all 2 codons) Non-Polar aa - Pro(6 codon),
Ala (4 codons),Nil
(2 codons-Phe has been excluded) |
Distribution of A among Amino Acids (total -48)
| Codons with | codon no. in polar aa | no. of bases in polar aa | codon no. in non polar aa | no. of bases in non polar aa | initiating codon no. | no. of bases in initiating codon | terminating codon. no | no. of bases in terminating codons |
total A |
| 1 A | 16 | 16 | 08 | 08 | 01 | 01 | 02 | 02 | 27 |
| 2 A | 07 | 14 | 01 | 02 | - | - | 01 | 02 | 18 |
| 3 A | 01 | 03 | -- | -- | -- | - | - | - | 03 |
| Total | 24 | 33 | 09 | 10 | 01 | 01 | 03 | 04 | 48 |
| nil A | 06 | -- | 21 | -- | -- | -- | -- | -- | -- |
Distribution of U among Amino Acids (total -48)
| Codons with | codon no. in polar aa | no. of bases in polar aa | codon no. in non polar aa | no. of bases in non polar aa | initiating codon no. | no. of bases in initiating codon | terminating codon. no | no. of bases in terminating codons |
total U |
| 1 U | 10 | 10 | 13 | 13 | 01 | 01 | 03 | 03 | 27 |
| 2 U | 02 | 04 | 07 | 14 | - | - | - | - | 18 |
| 3 U | -- | -- | 01 | 03 | -- | - | - | - | 03 |
| Total | 12 | 14 | 21 | 30 | 01 | 01 | 03 | 03 | 48 |
| nil U | 18 | -- | 09 | -- | -- | -- | -- | -- | -- |
Distribution of C among Amino Acids (total -48)
| Codons with | codon no. in polar aa | no. of bases in polar aa | codon no. in non polar aa | no. of bases in non polar aa | initiating codon no. | no. of bases in initiating codon | terminating codon. no | no. of bases in terminating codons |
total C |
| 1 C | 16 | 16 | 11 | 11 | - | - | - | - | 27 |
| 2 C | 04 | 08 | 05 | 10 | - | - | - | - | 18 |
| 3 C | - | - | 01 | 03 | - | - | - | - | 03 |
| Total | 20 | 24 | 17 | 24 | - | - | - | - | 48 |
| nil C | 10 | -- | 13 | -- | 01 | - | 03 | - | -- |
Distribution of G among Amino Acids (total -48)
| Codons with | codon no. in polar aa | no. of bases in polar aa | codon no. in non polar aa | no. of bases in non polar aa | initiating codon no. | no. of bases in initiating codon | terminating codon. no | no. of bases in terminating codons |
total G |
| 1 G | 13 | 13 | 11 | 11 | 01 | 01 | 02 | 02 | 27 |
| 2 G | 03 | 06 | 06 | 12 | - | - | - | - | 18 |
| 3 G | 01 | 03 | -- | -- | - | - | - | - | 03 |
| Total | 17 | 22 | 17 | 23 | 01 | 01 | 02 | 02 | 48 |
| nil G | 14?? | -- | 12?? | -- | - | - | 01 | - | -- |
Frequency of bases among 64 Codons ( Base A )
( frequency of other bases C, U, G are also same )
| Frequency of A in codon | Codons with repeating bases | Codons with non-repeating bases | Total |
| 1 ( A,-,-; -,A,-; -,-,A ) | 09 | 18 | 27 |
| 2 (A,-,A;A,A,-;-,A,A) | 09 | -- | 09 |
| 3 (A,A,A) | 01 | -- | 01 |
| Nil(-,-,-) | 21 | *06 | 27 |
| Total | 40 | 24 | 64 |
Worksheet for above calculation of Frequency
| no. of bases -(m)= | 4 |
| Each codon consists of n. number of bases, here n= | 3 |
| Total no. of codons mn | 43 =64 |
| no. of codons with non-repeating bases -> mPn | 4!/(4-3)! =24 |
| no. of codons with repeating bases= (64-24)= | 40 |
| codons with 3 no. of A = (1/4)*(1/4)*(1/4)*64= | 01 |
| codons with nil A = (3/4)*(3/4)*(3/4)*64= | 27 |
| codons with 2 no. of A = [(1/4)*(1/4)*(3/4)*64]+[(1/4)*(3/4)*(1/4)*64]+[(3/4)*(1/4)*(1/4)*64]= (1/4)*(1/4)*(3/4)*3*64 | 09 |
| codons with 1 no. A = [(1/4)*(3/4)*(3/4)*64]+[(3/4)*(3/4)*(1/4)*64]+[(3/4)*(1/4)*(3/4)*64]= (3/4)*(3/4)*(1/4)*3*64 | 27 |
| * in codons with non-repeating bases aggregating 24, total no. bases is 24*3=72 and each base has a frequency of 72/4=18 codons. So no. of codons with non repeating bases where A is absent is 24-18=06 | 06 |
| While doing the above exercise, one can think of three 4 sided dice being rolled and outcome calculated. |