Binary Codes for CODONS
POLAR AMINO ACIDS [32 codons, cg=44; au=52,ag=56,cu=40 total =96] [c=24,g=20,a=36,u=16][u absent in middle] In 1st & 2nd position combination of :-- pyrimidine-pyrimidine-4, purine-purine-12, mixed-16. Non repeating codon-14 & repeating codon-18 . All nucleotides occur in even no. No. of U is half of u in non-polar AA. no. of C same as in non-polar AA. * codons with grey background are frequently used codons for respective amino acids. * nu: no. of nucleons ; no: no. of atoms * If one offsets the no. of nucleons between P & NP amino acids, on P side, a=24 and on NP side, g=8,u=16. (P -NP) no.of nucleons =16 if T is there and =240 if U is there. If UAG is deducted from polar side & AUA from non-polar side, nucleons on both sides become equal. |
Non-Polar Amino Acids [32 codons, cg=52;au=44,ag=40,cu=56; total=96][c=24,g=28,a=12,u=32][a absent in middle] In 1st & 2nd position combination of :-- pyrimidine-pyrimidine-12, purine-purine-4, mixed-16; non-repeating codon-10, repeating codon-22; no. of 'c' twice that of 'a'. All nucleotides occur in even no. |
||||||||||
code | number nu no | codon | AA | no. of zeros | no.of 1 | code | number nu no | codon | AA | no. of zeros | no. of 1 |
-- | Thr(T)-aaRSIIa | -- | Pro(P)-aaRSIIa | ||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | Ser(S)-aaRSIIa | -- | Ala(A)-aaRSIIc | ||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | Arg(+ve)-aaRSIc | -- | Gly(G)-aaRSIIc | ||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | (R)Arg(+ve) | -- | Val(V)-aaRSIa | ||||||||
-- | -- | ||||||||||
-- | |||||||||||
-- | Ser | -- | |||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | Gln(Q)-aaRSIc | -- | Leu-aaRSIa | ||||||||
-- | -- | ||||||||||
-- | |||||||||||
-- | Asn(N)-aaRSIIb | -- | |||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | (D)Asp(-ve)-aaRSIIb | -- | Cys(C)-aaRSIa | ||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | (E)Glu(-ve)-aaRSIc | -- | opal/Trp(W)-aaRSIb | ||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | Tyr(Y)-aaRSIb | -- | Phe(F)-aaRSIIc | ||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | STOP-aaRSIb (ochre) | -- | Ile(I)-aaRSIa | ||||||||
-- | STOP-aaRSIb (amber) | -- | |||||||||
-- | -- | ||||||||||
-- | (K)Lys(+ve)-aaRSIIb | -- | Met(M)-aaRSIa | ||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | His(H)-aaRSIIa | -- | Leu(L)-aaRSIa | ||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
-- | -- | ||||||||||
AA | pure repeating codons | pure non-repeating codons | mixed codons | AA | pure repeating codons | pure non-repeating codons | mixed codons | ||||
03 | 01 | 06 | 03 | nil | 07 | ||||||
name | Lys,Glu,Asn | Asp | His,Tyr, Gln,Ser,Arg,Thr | Phe,Gly,Pro | Leu,Met,Ile, Trp,Cys,Val, Ala | ||||||
*codons under grey background are optimal codons for corresponding AA. optimal codons mentioned for Ser,Thr, Arg,Ala,Val,Gly to be rechecked. * aug is the initiating codon , but in some prokaryotes, gug is the initiating codon. * It is observed that optimal codons normally have a or c in their 3rd position. |
*codons under violet background are optimal codons if no. of codons for each of them is greater than 1. |
* some AA exhibit 2 fold, some 3 fold and 4 fold, some 6 fold degeneracy w.r.t codons. All the codons coding for same AA are called synonymous codons. Initially, this "degeneracy" seemed a bit wasteful, but evidence has been accumulating that the synonymous codons actually do behave differently, leading to different functional outcomes (see ENV's coverage, here and here). The first clues came from observations that different synonymous codons affected the rate of translation in the ribosome. Apparently there is an "optimal" codon that translates quickly, while others cause a bit of delay. Like many written languages, the genetic code is filled with synonyms: differently spelled "words" that have the same or very similar meanings. For a long time, biologists thought that these synonyms, called synonymous codons, were in fact interchangeable. Recently, they have realized that this is not the case and that differences in synonymous codon usage have a significant impact on cellular processes, so scientists have advanced a wide variety of ideas about the role that these variations play. |
Under polar aa, (ser,thr,his)-aaRSIIa (asp,asn,lys)-aaRSIIb (glu,gln,arg)-aaRSIc (tyr)-aaRSIb Under nonpolar aa, (leu,ile,val,met,cys)-aaRSIa (ala,gly,phe)-aaRSIIc (trp)-aaRSIb (pro)-aaRSIIa |
The aa (trp,pro) are slightly polar in nature and hence under the category of aaRS of polar aa. But in our categorization above, we have put them under nonpolar aa. | *Anagram of codons in Polar Segment also
remain in polar and anagram of non-polar segment remain in non-polar.
Exceptions:4 codons(ucg-gcu,ser-ala),(cgu-ugc,Arg-cys), (agu-uga,ser-Trp)(gca-acg, Ala-Thr) in non repeating codons & 2 codons of Pro,Gly each (cca-acc,Pro-Thr),(ccu-ucc,Pro-Ser)-(ggc-cgg,Gly-Arg)(gga-agg, Gly-Arg) in repeating codons |
Anti-Codon Code table as per polar/non-polar Amino Acids
POLAR AMINO ACIDS [32
anti-codons, cg=44; au=52,ag=40,cu=56
total =96] [c=20,g=24,a=16,u=36][a absent
in middle] In 1st & 2nd position combination of :-- pyrimidine-pyrimidine-12, purine-purine-04, mixed-16. Non repeating codon-14 & repeating codon-18 . All nucleotides occur in even no. No. of A is half of u in non-polar AA. no. of G same as in non-polar AA. * codons with grey background are frequently used codons for respective amino acids. |
Non-Polar Amino Acids [32
codons, cg=52;au=44,ag=40,cu=56;
total=96][c=28,g=24,a=32,u=12][u absent in
middle] In 1st & 2nd position combination of :-- pyrimidine-pyrimidine-04, purine-purine-12, mixed-16; non-repeating codon-10, repeating codon-22; no. of 'u' half that of 'g'. All nucleotides occur in even no. |
|||||||
code | number | anti-codon | AA | code | number | anti-codon | AA | |
-(agu) | uga | Thr(T)-aaRSIIa | -(agg) | gga | Pro(P)-aaRSIIa | |||
-(ggu) | ugg | -(ggg) | ggg | |||||
-(ugu) | ugu | -(ugg) | ggu | |||||
- | -(cgu) | ugc | - | -(cgg) | ggc | |||
-(aga) | aga | Ser(S)-aaRSIIa | -(agc) | cga | Ala(A)-aaRSIIc | |||
-(gga) | agg | -(ggc) | cgg | |||||
-(uga) | agu | -(ugc) | cgu | |||||
- | -(cga) | agc | - | -(cgc) | cgc | |||
-(acg) | gca | Arg(+ve)-aaRSIc | -(acc) | cca | Gly(G)-aaRSIIc | |||
-(gcg) | gcg | -(gcc) | ccg | |||||
-(ucg) | gcu | -(ucc) | ccu | |||||
- | -(ccg) | gcc | - | -(ccc) | ccc | |||
-(ucu) | ucu | (R)Arg(+ve) | -(aac) | caa | Val(V)-aaRSIa | |||
- | -(ccu) | ucc | -(gac) | cag | ||||
-(acu) | uca | Ser | -(uac) | cau | ||||
- | -(gcu) | ucg | - | -(cac) | cac | |||
-(uug) | guu | Gln(Q)-aaRSIc | -(aag) | gaa | Leu-aaRSIa | |||
- | -(cug) | guc | -(gag) | gag | ||||
-(auu) | uua | Asn(N)-aaRSIIb | -(uag) | gau | ||||
- | -(guu) | uug | - | -(cag) | gac | |||
-(auc) | cua | (D)Asp(-ve)-aaRSIIb | -(aca) | aca | Cys(C)-aaRSIa | |||
- | -(guc) | cug | - | -(gca) | acg | |||
-(uuc) | cuu | (E)Glu(-ve)-aaRSIc | -(uca) | acu | Trp(W)-aaRSIb | |||
- | -(cuc) | cuc | - | -(cca) | acc | |||
-(aua) | aua | Tyr(Y)-aaRSIb | -(aaa) | aaa | Phe(F)-aaRSIIc | |||
-(gua) | aug | - | -(gaa) | aag | ||||
-(uua) | auu | STOP-aaRSIb | -(aau) | uaa | Ile(I)-aaRSIa | |||
- | -(cua) | auc | - | -(gau) | uag | |||
-(uuu) | uuu | (K)Lys(+ve)-aaRSIIb | -(uau) | uau | Met(M)-aaRSIa | |||
- | -(cuu) | uuc | - | -(cau) | uac | |||
-(aug) | gua | His(H)-aaRSIIa | -(uaa) | aau | Leu(L)-aaRSIa | |||
- | -(gug) | gug | - | -(caa) | aac | |||
- | - | |||||||
AA | pure repeating codons | pure non-repeating codons | mixed codons | AA | pure repeating codons | pure non-repeating codons | mixed codons | |
03 | 01 | 06 | 03 | nil | 07 | |||
name | Lys,Glu,Asn | Asp | His,Tyr, Gln,Ser,Arg,Thr | Phe,Gly,Pro | Leu,Met,Ile, Trp,Cys,Val, Ala | |||
|
|
Under polar aa, (ser,thr,his)-aaRSIIa (asp,asn,lys)-aaRSIIb (glu,gln,arg)-aaRSIc (tyr)-aaRSIb Under nonpolar aa, (leu,ile,val,met,cys)-aaRSIa (ala,gly,phe)-aaRSIIc (trp)-aaRSIb (pro)-aaRSIIa |
*Anagram of codons in Polar Segment also
remain in polar and anagram of non-polar segment remain in non-polar.
Exceptions:4 codons(ucg-gcu,ser-ala),(cgu-ugc,Arg-cys), (agu-uga,ser-Trp)(gca-acg, Ala-Thr) in non repeating codons & 2 codons of Pro,Gly each (cca-acc,Pro-Thr),(ccu-ucc,Pro-Ser)-(ggc-cgg,Gly-Arg)(gga-agg, Gly-Arg) in repeating codons |
Code table as per Essential / Non-essential Amino Acids
Non-Essential AA | Essential AA | ||||||
* all non-essential amino acids are
glucogenic (except Tyr which is both glucogenic & ketogenic). Reverse is
not necessarily true. * Young chicks require Gly but adult can
synthesize it. * a=23 u=19, c=27, g=27 , total=96 ; au=42,cg=54, ag=50, cu=46 ; Repeating codons-20, non-repeating codons-12, total no. of codons=32 * 7 pairs of codons anagram to each other:( ucc,ucg,caa,cag,aau,gau,ccg & ccu,gcu,aac,gac,uaa,uag,gcc); 7 codons who are their own anagrams(ucu,gag,uau,ccc,gcg,ggg,ugu); 11 have anagrams on opposite side. * u - absent in middle position. (even if one adds Arg,His). No. of C=No. of G; * All nucleotides occur in odd no. (even if one adds Arg, His). * With A=01,C=10,G=00,U/T=11,Sum of Non-essential AA = 932 & sum of essential AA=1084, LHS-RHS=-76. If Histidine is brought to Non-essential AA & ggg, gga of Glycin taken to Essential, Codon no. remains unaltered and difference becomes zero. * For non-polar, non-essential AA, a is absent in 1st position. |
* Lys, Leu (red color) are purely ketogenic. Phe, Trp,Ile (pink color) are both ketogenic & glucogenic. Rest are purely glucogenic. * Arg,His are partially essential in rats. * In plants, Met, Lys are produced in very small quantities. * His essential for infants. Adult body can produce Histidine. * a=25, u=29,c=21; g=21, total=96; au=54,cg=42, ag=46,cu=50;Repeating codons-20, non-repeating codons-12, Total no. of codons = 32 * 6 pairs of codons anagram to each other:( gua,guu,guc,cuu,cua,uua& aug,uug,cug,uuc,auc,auu); 9 codons who are their own anagrams(aca,cgc,aga,aaa,cac,gug,cuc,uuu,aua); 11 have anagrams on opposite side. * In non-polar AA, entire set of 16 codons with 'u' in middle position are there out of total of 18 codons barring Trp. * All nucleotides occur in odd no. (even if one subtracts Arg,His). * For polar, essential AA, u/g absent in 1st position. |
||||||
AA | P/NP | codon | No. | AA | P/NP | codon | No. |
Ser | P -aaRS II a | Thr | P-aaRS IIa | ||||
P | P | ||||||
P | P | ||||||
P | P | ||||||
P | |||||||
P | Arg | P-aaRS Ic | |||||
P | |||||||
Gln | P-aaRS Ic | P | |||||
P | P | ||||||
P | |||||||
Asn | P-aaRS IIb | P | |||||
P | |||||||
Lys | P-aaRS IIb | ||||||
Asp | P-aaRS IIb | P | |||||
P | |||||||
His | P-aaRS IIa | ||||||
Glu | P-aaRS Ic | P | |||||
P | |||||||
Tyr | P-aaRS Ib | ||||||
P | |||||||
STOP | |||||||
a=20, u=13, c=11, g=10 ,
total=54 ; au=33,cg=21, ag=30, cu=24;
repeating codons-9, non-repeating codons-9 |
a=16, u=3,
c=13, g=10 , total=42 ; au=19,cg=23, ag=26, cu=16 ; repeating codons-9, non-repeating codons-5 ; |
||||||
Pro | NP-aaRS IIa | Val | NP-aaRS Ia | ||||
NP | NP | ||||||
NP | NP | ||||||
NP | NP | ||||||
Ala | NP-aaRS IIc | Leu | NP-aaRS Ia | ||||
NP | NP | ||||||
NP | NP | ||||||
NP | NP | ||||||
NP | |||||||
Gly | NP-aaRS IIc | NP | |||||
NP | |||||||
NP | Trp | NP-aaRS Ib | |||||
NP | NP | ||||||
Cys | NP-aaRS Ia | Phe | NP-aaRS IIc | ||||
NP | NP | ||||||
a=3, u=6, c=16, g=17 , total=42 ; au=9,cg=33, ag=20, cu=23 ; | Ile | NP-aaRS Ia | |||||
repeating codons-11, non-repeating codons-3 ; | NP | ||||||
Met | NP-aaRS Ia | ||||||
NP | |||||||
<---total if His is added & gga,ggg of Gly is taken to other side | (total) | ||||||
<---Difference | a=9, u=26, c=8, g=11 ,
total=54 ; au=35,cg=19, ag=20, cu=34 ; repeating codons-11, non-repeating codons-7 |
||||||
Difference |
<total
if His is minus & gga,ggg of Gly is plus <--- Difference |
Difference | (total) | ||||
Code table as per 4-fold ( 8 slots in code table) / 2-fold degeneracy(16 slots in code table) of Amino Acids
Sl. no. | Amino Acid | No. | Sl. No. | Amino Acid | No. |
1 | Leu | 1 | Phe | ||
2 | Val | 2 | Leu | ||
3 | Ser | 3 | Ile | ||
4 | Pro | 4 | Met | ||
5 | Thr | 5 | Tyr | ||
6 | Ala | 6 | STOP | ||
7 | Arg | 7 | His | ||
8 | Gly | 8 | Gln | ||
9 | Asn | ||||
10 | Lys | ||||
11 | Asp | ||||
12 | Glu | ||||
13 | Cys | ||||
14 | Trp | ||||
15 | Arg | ||||
16 | Ser | ||||
Code Table as aaRS-I & aaRS-II linkage of Amino Acids
aaRS-I | aaRS-II | ||||
Sl. No. | Amino Acid | No. | Sl. No. | Amino Acid | No. |
1 | Leu(L) -NP | 1 | Ser(S)-P | ||
2 | Val(V) -NP | 2 | Pro(P)-NP | ||
3 | Ile(I) -NP | 3 | Thr(T)-P | ||
4 | Cys(C) -NP | 4 | His(H)-P | ||
5 | Met(M) -NP | ||||
aaRS-Ia (16 codons) | aaRS-IIa (16 codons) | ||||
6 | Tyr(Y) -P | 5 | Lys(K)-P | ||
7 | Trp(W)-NP | 6 | Asp(D)-P | ||
11 | STOP | 7 | Asn(N)-P | ||
aaRS-Ib (6 codons) | aaRS-IIb (6 codons) | ||||
8 | Arg(R) -P | 8 | Gly(G)-NP | ||
9 | Glu(E) -P | 9 | Ala(A)-NP | ||
10 | Gln(Q) -P | 10 | Phe(F)-NP | ||
aaRS-Ic (10 codons) | aaRS-IIc (10 codons) | ||||
* For c=11,a=00,u=01,g=10, aaRS-I =1012, aaRSII=1004;If 2 codons with difference 4 are interchanged, both sides become 1008. Possibilities 17-13,16-12,19-15,18-14,32-28,34-30,48-44,50-46,37-33,39-35,36-32,38-34,4-0,6-2,53-49,55-51,5-1,7-3. For exa, if it is 5-1=auu-aau. | |||||
aaRs -I and aaRS-II anti-codon table (modified)
POLAR AA | NON-POLAR AA | ||||||
aaRS-I (2-fold) | Y | aaRS-I (2-fold ) | I | ||||
E | M | ||||||
Q | C | ||||||
R2 | W(1 codon) | ||||||
STOP | |||||||
K | |||||||
aaRS-I (4-fold) | R4 | aaRS-I (4-fold) | L4 | ||||
V | |||||||
aaRS-I (total polar) | aaRS-I (total non polar) | ||||||
aaRS-I Total | |||||||
aaRS-II (2-fold) | H | aaRS-II (2-fold) | L2 | ||||
D | STOP | ||||||
N | F | ||||||
S2 | |||||||
aaRS-II (4-fold) | S4 | aaRS-II (4-fold) | P | ||||
T | A | ||||||
G | |||||||
aaRS-II (total polar) | aaRS-II (total non polar) | ||||||
aaRS-II Total | |||||||
aaRS Polar (total) | aaRS non-Polar (total) | aaRS total | |||||
Here, we have included K in aaRS-I & L2 in aaRS-2 at par with F. Since STOP codon near Y is in aaRS-1, STOP codon near W is included in aaRS-2. |
TOTAL |
Genetic Code table
u(1) | c(2) | a(3) | g(4) | |||||||||||||||||
AA | codon | no. | remark | AA | codon | no. | remark | AA | codon | no. | remark | AA | codon | no. | remark | no. | ||||
u(1) | Phe | uuu | ser | ucu | tyr | uau | cys | ugu | u | |||||||||||
uuc | ser | ucc | tyr | uac | cys | ugc | c | |||||||||||||
Leu | uua | ser | uca | stop | uaa | trp/stop | uga | a | ||||||||||||
uug | ser | ucg | stop | uag | trp | ugg | g | |||||||||||||
c(2) | Leu | cuu | pro | ccu | his | cau | arg | cgu | u | |||||||||||
Leu | cuc | pro | ccc | his | cac | arg | cgc | c | ||||||||||||
Leu | cua | pro | cca | gln | caa | arg | cga | a | ||||||||||||
Leu | cug | pro | ccg | gln | cag | arg | cgg | g | ||||||||||||
a(3) | Ile | auu | thr | acu | asn | aau | ser | agu | u | |||||||||||
Ile | auc | thr | acc | asn | aac | ser | agc | c | ||||||||||||
met/Ile | aua | thr | aca | lys | aaa | arg | aga | a | ||||||||||||
met | aug | thr | acg | lys | aag | arg | agg | g | ||||||||||||
g(4) | val | guu | ala | gcu | asp | gau | gly | ggu | u | |||||||||||
val | guc | ala | gcc | asp | gac | gly | ggc | c | ||||||||||||
val | gua | ala | gca | glu | gaa | gly | gga | a | ||||||||||||
val | gug | ala | gcg | glu | gag | gly | ggg | g | ||||||||||||
u=24 | c=8,a=8 | g=8 | u=8,c=24 | a=8,g=8 | u=8,c=8 | a=24,g=8 | u=8.c=8 | a=8,g=24 | ||||||||||||
cg/au=1/2 | cg/au=2/1 | cg/au=1/2 | cg/au=2/1 | |||||||||||||||||
LOGIC GATES |
|
Logic gates are elementary building blocks of a digital circuit. | Most logic gates have 2 inputs & 1 output. |
Each of 2 inputs is one of the two binary conditions 0 & 1. | 0 ---> OFF ; 1 ---> ON |
name of the gate | indicative no. |
AND | 1 |
OR | 2 |
XOR | 3 |
NAND | 4 |
NOR | 5 |
XNOR | 6 |
Genetic database: http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html
http://www.ncbi.nlm.nih.gov/books/NBK44863/
http://compbio.cs.princeton.edu/ancestralaa http://blast.ncbi.nlm.nih.gov/Blast.cgi
http://www.genome.jp/aaindex/ http://www.incogen.com/bioinfo_tutorials/Bioinfo-Lecture_3-pairwise-align2.html
http://www.whatabeginning.com/Misc/Genetics/Genetics_VS.htm
http://www.genome.jp/tools/clustalw/
http://www.cytoscape.org/
Here is a DNA sequence that I am going to use for testing the hypothesis. The
complete human genome can be found online here -
ftp://ftp.ensembl.org/pub/release-67...o_sapiens/dna/
Here is the NCBI index page for complete genomes - http://www.ncbi.nlm.nih.gov/genome
As you can see, I can choose any of the following - Human, microbes, organelles,
plants, viruses.
Here is the complete sequence for Chromosome 1 of human DNA
http://www.ncbi.nlm.nih.gov/nuccore/...0?report=fasta
Chromosome 1 is 249,250,621 bases long.
10 million bytes = 6 million bases approximately, so the complete chromosome
will have a download size of about 400 megabytes, which is quite big.
I have searched the first 6.5 million bases of Chromosome 1 for any pattern of
amino acids that would match the Genesis1 sequence of letters.
There is no match between amino acids sequence and Genesis1 letter sequence
within the part of Chromosome 1 searched.
Download
There are two software programs. The first is for non-overlapping codons. The
second is for overlapping codons -
A. http://www.craigdemo.co.uk/DNAsetup.zip
B. http://www.craigdemo.co.uk/OverlappingCodonSetup.zip
Extract from zip then in the dialog that appears click NEXT - EVERYONE - NEXT -
NEXT.
Note : If you do not have the dotNet 4.0 framework installed on your computer
already, you may need to install that also.
http://www.webqc.org/aminoacids.php
codon : -- binary : -- * indicates no GATE | ||||
binary code | gate | output | NOT GATE output | |
Base-1 nucleotide | ||||
Base-2 nucleotide | ||||
Base-3 nucleotide | ||||
Decimal sum | ||||
LHS - add 1 & find sum | ||||
RHS - add 1 & find sum | ||||
Base1*+Base2gate+Base3gate | ||||
Base1gate+Base2*+Base3gate | ||||
Base1gate+Base2gate+Base3* | ||||
Base1*+Base2*+Base3gate | ||||
Base1*+Base2gate+Base3* | ||||
Base1gate+Base2*+Base3* | ||||