genetic code

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Screen_shot_2018-02-02_at_12.53.50_pm lin xiang (Author)

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WHAT IS IT?

The genetic code was deciphered in the 1960s mainly by a series of ingenious experiments invented by Marshall Nirenberg's team. This model allows you to crack genetic code based on the synthesized mRNA, like Dr. Nirenberg.

HOW IT WORKS

This model generates an 18-base mRNA based on the nucleotides input by users. Only letters A, C, G, and U are accepted to generate the mRNA. There is no limit to the number of input nucleotides, as the mRNA will be generated based on the proportions of the nucleotides in the input. This gives users some control over the generated sequence. For example, an input of "UUUUA" will generate an mRNA containing more "U" than an input of "UA." E.g., 1) A means 100% of A, and A is equivalent to AA, AAA, etc. 2) UG means 50% of U and 50% of G, and UG is equivalent to GU, GGUU, or UGUG. 3) CGGA means 25% of C, 50% of G, and 25% of A.

Once correct nucleotides are input, the model will synthesize the mRNA in the simulation window. Six codons are displayed in the monitors under the simulation window.

The model will translate the sequence and provide the types of amino acids involved in the peptide synthesis. Note the displayed amino acids are not aligned with the coding order. This is what happened in the actual experiments: scientists only knew the types of amino acids and had to infer the genetic code. You need to infer the genetic code just like a scientist.

HOW TO USE IT

  1. Input nucleotides. It must be the letters A, C, G, and U.

  2. Press on "STEP-2 Synthesize mRNA"

  3. Press on "STEP-3 Translate mRNA"

THINGS TO NOTICE

  • No start codon is needed in this model.
  • Translation will be terminated when the ribosome encounters a stop codon.
  • The mRNA is read from the 5' end to the 3' end.

THINGS TO TRY

Try different compositions of A, C, G, and U to help you strategically determine the genetic code.

CREDITS AND REFERENCES

This model is made by Dr. Lin Xiang at Weber State University in 2018 and revised at the University of Kentucky in 2022. If you mention this model in a publication, we ask that you include the citations below.

Xiang, L. (2022). Genetic Code. Department of STEM Education, Unversity of Kentucky, Lexington, KY.

CC BY-NC-SA 4.0

This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/.

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globals [ n  ;RNA PXCOR POSITION
          p1 ;PEPTISE PXCORPOSITION
          RNA ;RNA string
          first-base ; item position of 1st base in RNA
          codon ;codon variable
          s-base  ;starting base item position of a codon
          f-base  ;final base item position of a codon
          amino-acid ; translated amino acid
          amino-acid-result ; report the types of amino acids
          protein-length  ;peptide length
          base-candidates  ;nucleotides input from users
          aa1 ; amino acid 1
          aa-num ; assign a number for shuffle AAs
          aa-num-list
          filtered-list ;  find % of input nucleotides
  a-%
  c-%
  g-%
  u-%

  check-index  ;record the position of the nucleotide under check
      ]

Patches-own [base]

breed [nucleotides nucleotide]
breed [units unit]
breed [peptides peptide]
breed [primes prime]

to setup

 ca

  set base-candidates STEP-1-Input-Nucleotides ;user-input "Nucleotides (Capital A C U or G only.No space)"

  ifelse length base-candidates = 0 [user-message "no nucleotide is tested" stop][capitalize-bases]

  find-percentages

  set RNA "5'-"                                    ;create 5' end
  set-default-shape nucleotides "x"               ;set default shape as X in case having an invalid base
  set n 7                                         ;set the first base position in the world
  set first-base 3

  set s-base 3
  set f-base 6
  set p1 10
  set protein-length 0
  set amino-acid-result ""
  set aa-num-list 0
  set aa1 0

  ask patches [set pcolor 9.5 + random-float 0.4 ]
  ask patches with [pycor <= min-pycor + 2 ] [set pcolor 2]

 repeat 18
  [ set RNA word RNA item random (length base-candidates) base-candidates]      ;synthesize the RNA



  set RNA word RNA "-3'"                       ;attach 3' end


 repeat 18
    [ ask patches with [pxcor = n and pycor = 4]               ;assign base to patches
      [set base item first-base RNA]
      set n n + 1
      set first-base first-base + 1]

 ask patches with [base != 0]                                  ;let assigned patches produce bases
 [sprout-nucleotides 1
      [ if base = "A"  [set shape "nn-a"]
        if base = "C"  [set shape "nn-c"]
        if base = "G"  [set shape "nn-g"]
        if base = "U"  [set shape "nn-u"]
    ]]

  create-primes 1               ;MAKE 5' END
  [set shape "5'"
    set size 1.5
    set color 0
    setxy 6.3 4.5]



   create-primes 1               ;MAKE 3' END
  [set shape "3'"
    set size 1.5
    set color 0
    setxy 24.7 4.5]


  if any? nucleotides with [shape = "x"] [user-message "Please input correct nucleotide(s) (A, U, C, G)" stop]

ribosome

reset-ticks
end 

to translate

  if f-base > 21 [user-message "Translation has been completed" stop]

   repeat 6 [
    ask units                           ;move ribosome one codon
      [set heading 90
        forward 4
        wait 0.3]


   set codon substring RNA s-base f-base                            ;detetmine the range (the codon)
   if codon = "AUG" [set amino-acid "Met" set aa-num 1]                         ;translate
   if codon = "UUU" or codon = "UUC" [set amino-acid "Phe" set aa-num 2]
   if codon = "UUA" or codon = "UUG" or codon = "CUU" or codon = "CUC" or codon = "CUA" or codon = "CUG"[set amino-acid "Leu" set aa-num 3]
   if codon = "AUU" or codon = "AUC" or codon = "AUA" [set amino-acid "Ile" set aa-num 4]
   if codon = "GUU" or codon = "GUC" or codon = "GUA" or codon = "GUG" [set amino-acid "Val" set aa-num 5]
   if codon = "UCU" or codon = "UCC" or codon = "UCA" or codon = "UCG" or codon = "AGU" or codon = "AGC" [set amino-acid "Ser" set aa-num 6]
   if codon = "CCU" or codon = "CCC" or codon = "CCA" or codon = "CCG" [set amino-acid "Pro" set aa-num 7]
   if codon = "ACU" or codon = "ACC" or codon = "ACA" or codon = "ACG" [set amino-acid "Thr" set aa-num 8]
   if codon = "GCU" or codon = "GCC" or codon = "GCA" or codon = "GCG" [set amino-acid "Ala" set aa-num 9]
   if codon = "UAU" or codon = "UAC"  [set amino-acid "Tyr" set aa-num 10]
   if codon = "CAU" or codon = "CAC"  [set amino-acid "His" set aa-num 11]
   if codon = "CAA" or codon = "CAG"  [set amino-acid "Gln" set aa-num 12]
   if codon = "AAU" or codon = "AAC"  [set amino-acid "Asn" set aa-num 13]
   if codon = "AAA" or codon = "AAG"  [set amino-acid "Lys" set aa-num 14]
   if codon = "GAU" or codon = "GAC"  [set amino-acid "Asp" set aa-num 15]
   if codon = "GAA" or codon = "GAG"  [set amino-acid "Glu" set aa-num 16]
   if codon = "UGU" or codon = "UGC"  [set amino-acid "Cys" set aa-num 17]
   if codon = "UGG" [set amino-acid "Trp" set aa-num 18]
   if codon = "CGU" or codon = "CGC" or codon = "CGA" or codon = "CGG" or codon = "AGA" or codon = "AGG" [set amino-acid "Arg" set aa-num 19]
   if codon = "GGU" or codon = "GGC" or codon = "GGA" or codon = "GGG" [set amino-acid "Gly" set aa-num 20 ]
    if codon = "UAA" or codon = "UAG" or codon = "UGA" [set amino-acid "" user-message "Translation is terminated" ask units [die]]

   set aa-num-list sentence aa-num-list aa-num    ;assign number to aa for removing duplication and shuffle
   set aa-num-list remove-duplicates aa-num-list


       ifelse amino-acid != ""                           ;if not encounter a stop codon,
        [
         create-peptides 1                            ; make amino acid
           [set size 2
            set shape "protein-unit"
            setxy p1  min-pycor + 1
            set color white]

         set p1 p1 + 2          ;set amino acids position

         set s-base s-base + 3    set f-base f-base + 3]

     [set aa-num-list remove 0 aa-num-list
      set aa-num-list shuffle aa-num-list
      show-aa
      stop]


  ]

  set aa-num-list remove 0 aa-num-list
  set aa-num-list shuffle aa-num-list

  show-aa
end 

to ribosome

 create-units 1
   [
    set shape "l-unit"
    set size 7
    set color 27
    setxy 3.5 3]
end 

to show-aa

  repeat length aa-num-list
   [set aa-num item aa1 aa-num-list
      num-to-aa
      set amino-acid-result word amino-acid-result " "
      set amino-acid-result word amino-acid-result amino-acid
      set aa1 aa1 + 1]
end 

to num-to-aa

  if aa-num = 1 [set amino-acid "Met"]
  if aa-num = 2 [set amino-acid "Phe"]
  if aa-num = 3 [set amino-acid "Leu"]
  if aa-num = 4 [set amino-acid "Ile"]
  if aa-num = 5 [set amino-acid "Val"]
  if aa-num = 6 [set amino-acid "Ser"]
  if aa-num = 7 [set amino-acid "Pro"]
  if aa-num = 8 [set amino-acid "Thr"]
  if aa-num = 9 [set amino-acid "Ala"]
  if aa-num = 10 [set amino-acid "Tyr"]
  if aa-num = 11 [set amino-acid "His"]
  if aa-num = 12 [set amino-acid "Gln"]
  if aa-num = 13 [set amino-acid "Asn"]
  if aa-num = 14 [set amino-acid "Lys"]
  if aa-num = 15 [set amino-acid "Asp"]
  if aa-num = 16 [set amino-acid "Glu"]
  if aa-num = 17 [set amino-acid "Cys"]
  if aa-num = 18 [set amino-acid "Trp"]
  if aa-num = 19 [set amino-acid "Arg"]
  if aa-num = 20 [set amino-acid "Gly"]
end 

to find-percentages

 ifelse member? "A" base-candidates
   [set filtered-list remove "A" base-candidates
      set a-% ((length base-candidates) - (length filtered-list)) * 100 / (length base-candidates)]
  [set a-% 0]

  ifelse member? "C" base-candidates
   [set filtered-list remove "C" base-candidates
      set c-% ((length base-candidates) - (length filtered-list)) * 100 / (length base-candidates)]
  [set c-% 0]

 ifelse member? "G" base-candidates
   [set filtered-list remove "G" base-candidates
      set g-% ((length base-candidates) - (length filtered-list)) * 100 / (length base-candidates)]
  [set g-% 0]

  ifelse member? "U" base-candidates
   [set filtered-list remove "U" base-candidates
      set u-% ((length base-candidates) - (length filtered-list)) * 100 / (length base-candidates)]
  [set u-% 0]
end 

to capitalize-bases
  set check-index 0
  Repeat length base-candidates
  [
  (ifelse
    item check-index base-candidates = "a" [set base-candidates (replace-item check-index base-candidates "A")]
    item check-index base-candidates = "g" [set base-candidates (replace-item check-index base-candidates "G")]
    item check-index base-candidates = "c" [set base-candidates (replace-item check-index base-candidates "C")]
    item check-index base-candidates = "u" [set base-candidates (replace-item check-index base-candidates "U")])

    set check-index check-index + 1]
end 

There are 11 versions of this model.

Uploaded by When Description Download
lin xiang 3 months ago Auto capitalize the base letters, display composition of input nucleotides Download this version
lin xiang 10 months ago Add notes Download this version
lin xiang 10 months ago Add notes Download this version
lin xiang 10 months ago Add notes Download this version
lin xiang 10 months ago Fix input issue Download this version
lin xiang 10 months ago Fix input issue Download this version
lin xiang almost 2 years ago update license Download this version
lin xiang about 4 years ago fix bug Download this version
lin xiang almost 5 years ago REFINE Download this version
lin xiang almost 5 years ago REFINE Download this version
lin xiang almost 5 years ago Initial upload Download this version

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