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 |
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; |
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code | number | codon | AA | no. of zeros | no.of 1 | code | number | codon | AA | no. of zeros | no. of 1 |
acu | Thr(T) | cca | Pro(P) | ||||||||
aca | ccu | ||||||||||
acc | ccc | ||||||||||
acg | ccg | ||||||||||
uca | Ser(S) | gca | Ala(A) | ||||||||
ucu | gcu | ||||||||||
ucc | gcc | ||||||||||
ucg | gcg | ||||||||||
cga | Arg(+ve) | ggu | Gly(G) | ||||||||
cgu | ggc | ||||||||||
cgg | gga | ||||||||||
cgc | ggg | ||||||||||
aga | (R)Arg(+ve) | gua | Val(V) | ||||||||
agg | guu | ||||||||||
agu | Ser | guc | |||||||||
agc | gug | ||||||||||
caa | Gln(Q) | cuu | Leu | ||||||||
cag | cuc | ||||||||||
aau | Asn(N) | cua | |||||||||
aac | cug | ||||||||||
gau | (D)Asp(-ve) | ugu | Cys(C) | ||||||||
gac | ugc | ||||||||||
gaa | (E)Glu(-ve) | uga | Trp(W) | ||||||||
gag | ugg | ||||||||||
uau | Tyr(Y) | uuu | Phe(F) | ||||||||
uac | uuc | ||||||||||
uaa | STOP | auu | Ile(I) | ||||||||
uag | auc | ||||||||||
aaa | (K)Lys(+ve) | aua | Met(M) | ||||||||
aag | aug | ||||||||||
cau | His(H) | uua | Leu(L) | ||||||||
cac | uug | ||||||||||
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 |
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
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* | ||||