Binary Codes for CODONS

Nucleotide Bases Binary Code
A
G
U/T
C
   
           Difference in   ⇒  number  no.of zeros   
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;

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          
                                         
Base

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*