Acid Bases Worksheet by vwi13045

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Acid Bases Worksheet document sample

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									   This worksheet is designed to help you simulate the experiments that led
to the "cracking" of the genetic code.

  If you can't see the "protein" produced, hit the PgDn key.

        0             In cell A6, enter a 0, 2, 3 or 4. This number repre-
                      sents the number of bases that repeat, if there is repetition.
                      Zero means that the polypeptide is assembled randomly.
RNA base %
% of A -      1.000
% of G -      0.000              Enter values from 0 to 1 in B10 - B13
% of C -      0.000              Then hit the F9 key
% of U -      0.000
Total -           1        Cell B14 will show Error if the sum of B10 - B13 isn't 1, or if the wrong value is in Cell
                           Don't use the data if an Error is shown in cell B14!


To produce another polypeptide, hit the F9 key           To see frequencies, see cells A24 - B50
    Polypeptide- lys lys lys lys lys lys lys lys lys lys lys lys
     amino acid # -    1    2      3    4   5    6     7    8     9   10   11    12
         If the "protein" is less than 12 amino acids long, the STOP signal has been generated.


Percentages (based on up to 100 amino acids):
These percentages are
meaningless, unless cell          Probabilities of getting each triplet of RNA bases, with
A6 is zero.                       random assembly, based on the fractions entered above.
                                  You won't see anything in column O if cell A6 isn't zero.
ala              0                triplet(s)                                    probability
asn              0                AAA                                                    1
arg              0                AAC, ACA, or CAA                                       0
asp              0                AAG, AGA, or GAA                                       0
cys              0                AAU, AUA, or UAA                                       0
gln              0                ACC, CAC, or CCA                                       0
glu              0                AGG, GAG, or GGA                                       0
gly              0                AUU, UAU, or UUA                                       0
his              0                CCC                                                    0
ilu              0                CCG, CGC, or GCC                                       0
leu              0                CGG, GCG, or GGC                                       0
lys            100                CCU, CUC, or UCC                                       0
met              0                CUU, UCU, or UUC                                       0
phe              0                GGG                                                    0
pro              0        GGU, GUG, or UGG                 0
ser              0        GUU, UGU, or UUG                 0
thr              0        UUU                              0
try              0        ACG, AGC, CAG, CGA, GAC or GCA   0
tyr              0        ACU, AUC, CAU, CUA, UAC or UCA   0
val              0        AGU, AUG, GAU, GUA, UAG or UGA   0
total          100        CGU, CUG, GCU, GUC, UCG or UGC   0
STO              0



These percentages are
displayed even if the
chain is stopped, which
isn't realistic.
he wrong value is in Cell B6.
Table for initial Nitrogen base
   0      1       1     1
A    C       G      U

Random Chain
mRNA -    A       A     A         A   A   A     A    A    A     A    A     A     A     A     A    A     A
"protein"



Repeated doublet
mRNA -    A     A       A         A   A   A     A    A    A     A    A     A     A     A     A    A     A
"protein"


Repeated triplet
mRNA -     A     A      A         A   A   A     A    A    A     A    A     A     A     A     A    A     A
"protein"


Repeated quadruplet
mRNA -    A    A        A         A   A   A     A    A    A     A    A     A     A     A     A    A     A
"protein"


      Random numbers for use in generating a random sequence of bases, or the beginning of a repeating sequence.
              0.3 0.7 0.3 0.2 0.9 0.1 0.1 0.4 0.6 0.3 0.7 0.6                        0 0.6 0.8 0.1 0.6


      Sum of fractions of A, C, G, U
          1
      Signal - is correct entry in Nrn1 cell B6?
           1
      Artificial mRNA sequence actually used:
              A    A     A      A     A      A   A   A    A     A    A     A     A     A     A    A     A

      Numeric "equivalent" of mRNA sequence:
            100     10     1 100       10     1 100     10     1 100      10    1 100      10    1 100      10
                   111                111              111               111              111              111
                 lys                lys              lys               lys              lys              lys
                 lys                lys              lys               lys              lys              lys
      The Genetic code, for translating, using the numbers in rows 38 and 66:
            111 lys
            112 asn
            113 lys                                              Numeric equivalent for percentage of amino acids
            114 asn                                               111
            121 thr                                               111         111 100
            122 thr                                               111         112     0
            123 thr                                               111         113     0
            124 thr                                               111         114     0
            131 arg                                               111         121     0
            132 ser                                               111         131     0
133   arg    111   132   0
134   ser    111   133   0
141   met    111   134   0
142   ilu    111   141   0
143   met    111   142   0
144   ilu    111   143   0
211   gln    111   144   0
212   his    111   211   0
213   gln    111   212   0
214   his    111   213   0
221   pro    111   214   0
222   pro    111   221   0
223   pro    111   231   0
224   pro    111   241   0
231   arg    111   311   0
232   arg    111   312   0
233   arg    111   313   0
234   arg    111   314   0
241   leu    111   321   0
242   leu    111   331   0
243   leu    111   341   0
244   leu    111   411   0
311   glu    111   412   0
312   asp    111   413   0
313   glu    111   414   0
314   asp    111   421   0
321   ala    111   431   0
322   ala    111   432   0
323   ala    111   433   0
324   ala    111   434   0
331   gly    111   441   0
332   gly    111   442   0
333   gly    111   443   0
334   gly    111   444   0
341   val    111         0
342   val    111
343   val    111
344   val    111
411   STOP   111
412   tyr    111
413   STOP   111
414   tyr    111
421   ser    111
422   ser    111
423   ser    111
424   ser    111
431   STOP   111
432   cys    111
433   try    111
434   cys    111
441   leu    111
442   phe    111
443 leu   111
444 phe   111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
          111
             A       A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A               A




             A       A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A               A




             A       A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A               A




             A       A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A               A



 peating sequence.
                 0.8 0.5 0.3 0.4            1 0.6 0.2 0.1 0.7 0.5 0.6 0.7                          0 0.6 0.8 0.4 0.4                    1 0.2




             A       A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A               A


                   1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10               1
                             111                 111                 111                 111                 111                 111
                           lys                 lys                 lys                 lys                 lys                 lys
                           lys                 lys                 lys                 lys                 lys                 lys



e of amino acids
                                                                                                                                   continued
continued   continued
A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A




    0.1 0.4 0.6 0.5 0.7 0.7 0.8 0.2 0.4 0.8 0.3 0.1 0.1 0.2 0.9 0.2                                           1 0.6 0.5




A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A


100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100
        111                 111                 111                 111                 111                 111
      lys                 lys                 lys                 lys                 lys                 lys
      lys                 lys                 lys                 lys                 lys                 lys




A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A
    0 0.4 0.9 0.6 0.4 0.6 0.1 0.5 0.8 0.7 0.8 0.1                                  0 0.4 0.8 0.5 0.1 0.5 0.6




A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A


100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100
        111                 111                 111                 111                 111                 111
      lys                 lys                 lys                 lys                 lys                 lys
      lys                 lys                 lys                 lys                 lys                 lys
A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A




    0.3 0.8 0.4 0.4 0.2 0.7 0.3 0.5 0.3 0.8 0.6 0.4 0.1 0.3 0.8 0.5 0.3 0.2 0.2




A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A


   10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10
  111                 111                 111                 111                 111                 111                 111
lys                 lys                 lys                 lys                 lys                 lys                 lys
lys                 lys                 lys                 lys                 lys                 lys                 lys




A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A
    0.4 0.8 0.4 0.8 0.4 0.8 0.7                     0 0.7 0.6 0.8 0.1 0.4 0.2 0.4 0.6 0.2 0.4 0.5




A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A


   10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10
  111                 111                 111                 111                 111                 111                 111
lys                 lys                 lys                 lys                 lys                 lys                 lys
lys                 lys                 lys                 lys                 lys                 lys                 lys
A      A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A




    0.7 0.7 0.1          0 0.2 0.9 0.1            0 0.9 0.7 0.6 0.4 0.7 0.2 0.9                          0 0.5 0.4 0.7




A      A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A


     1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1
               111                 111                 111                 111                 111                 111
             lys                 lys                 lys                 lys                 lys                 lys
             lys                 lys                 lys                 lys                 lys                 lys




A      A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A
    0.3 0.9 0.9 0.7 0.2 0.3 0.3 0.7 0.6 0.4 0.7 0.4 0.1 0.9 0.8 0.6 0.9 0.9 0.3




A     A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A


     1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1
               111                 111                 111                 111                 111                 111
             lys                 lys                 lys                 lys                 lys                 lys
             lys                 lys                 lys                 lys                 lys                 lys
A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A




    0.6 0.9 0.8 0.2 0.8 0.3 0.8 0.9                       1 0.5 0.3           1 0.4 0.3 0.1 0.7 0.3 0.5 0.6




A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A


100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100
        111                 111                 111                 111                 111                 111
      lys                 lys                 lys                 lys                 lys                 lys
      lys                 lys                 lys                 lys                 lys                 lys




A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A
    0.4 0.9 0.5 0.5 0.1 0.4 0.9 0.6                       1 0.3 0.9 0.9 0.9 0.9 0.8 0.8 0.1 0.6 0.5




A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A


100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100
        111                 111                 111                 111                 111                 111
      lys                 lys                 lys                 lys                 lys                 lys
      lys                 lys                 lys                 lys                 lys                 lys
A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A




    0.3 0.7 0.3 0.9 0.9              0 0.5 0.6 0.4 0.6 0.6 0.7 0.5                          0 0.3 0.2 0.4 0.5 0.9




A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A


   10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10
  111                 111                 111                 111                 111                 111                 111
lys                 lys                 lys                 lys                 lys                 lys                 lys
lys                 lys                 lys                 lys                 lys                 lys                 lys




A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A
    0.5 0.2 0.8 0.4 0.8 0.4 0.8 0.3 0.3 0.9 0.7 0.3 0.4 0.6 0.6 0.4 0.5 0.8 0.6




A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A


   10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10
  111                 111                 111                 111                 111                 111                 111
lys                 lys                 lys                 lys                 lys                 lys                 lys
lys                 lys                 lys                 lys                 lys                 lys                 lys
A      A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A




    0.8 0.3 0.4 0.5 0.3              1       0 0.8       1 0.1 0.3 0.2 0.6 0.6 0.6 0.9 0.8 0.8 0.5




A      A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A


     1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1
               111                 111                 111                 111                 111                 111
             lys                 lys                 lys                 lys                 lys                 lys
             lys                 lys                 lys                 lys                 lys                 lys




A      A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A
    0.5 0.6 0.3 0.8 0.5 0.5                  0 0.5 0.2 0.8 0.9 0.3 0.3 0.9 0.1                           0 0.6 0.1 0.2




A      A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A


     1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1
               111                 111                 111                 111                 111                 111
             lys                 lys                 lys                 lys                 lys                 lys
             lys                 lys                 lys                 lys                 lys                 lys
A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A




    0.2 0.4 0.8 0.1 0.8 0.5 0.9 0.9 0.9 0.7 0.5 0.2 0.4 0.1 0.6 0.8 0.5 0.3 0.7




A     A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A    A


100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1 100
        111                 111                 111                 111                 111                 111
      lys                 lys                 lys                 lys                 lys                 lys
      lys                 lys                 lys                 lys                 lys                 lys




A     A       A    A      A       A
    0.8 0.7 0.4 0.8 0.5 0.4




A      A       A    A      A       A


100       10       1 100      10       1
         111                 111
       lys                 lys
                                                                                                                    left
A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A




                                                                                                                    to
                                                                                                                    and
    0.3 0.1 0.3 0.1 0.4 0.4                 0 0.8 0.6           1 0.8 0.2 0.9 0.9 0.7 0.8 0.3




                                                                                                                    below
A       A    A      A       A    A      A       A    A      A       A    A      A       A    A      A       A



                                                                                                                    continued
   10       1 100      10       1 100      10       1 100      10       1 100      10       1 100      10       1
  111                 111                 111                 111                 111                 111
lys                 lys                 lys                 lys                 lys                 lys
lys                 lys                 lys                 lys                 lys                 lys
    Marshall W. Nirenberg was the first U. S. Government employee to win a Nobel prize in
physiology or medicine. When the work simulated in this spreadsheet was done, the cracking
of the genetic code seemed a far-off and elusive goal. However, Nirenberg conceived the idea
of going about it not by attempting to see what DNA bases determine what amino acids, but
what RNA bases do. He developed a cell-free system, consisting of ribosomes, an energy
source, and all of the naturally occurring amino acids. Then he prepared an artificial messenger
RNA, consisting of nothing but Uracil, and added it to his cell-free system. Lo and behold,
the resulting polypeptide chain consisted of nothing but phenylalanine! The only question
was to determine whether U, UU, UUU, UUUU, UUUUU, or UUUUUU was the RNA code for
phenylalanine.
   Using enzymes which created repeating doublet (AGAGAGAG. . .), triplet (AGCAGCAGC. . .)
or quadruplet (ACCGACCGACCG . . .) artificial mRNAs, Nirenberg and others answered that
question, and, in fairly short order, determined the so-called genetic dictionary, that is, what
triplets of bases (codons) determine the presence of what amino acids.
   The doublets, triplets, or quadruplets are generated using the first 2, 3, or 4 bases as a pattern for
the rest of the sequence. The first 2, 3 or 4 are chosen by chance from the pool of bases available.
Thus, if the system is provided with 95% U and 5% A, and a repeating triplet is to be generated,
most of the time, that repeating triplet will be UUU, but occasionally it will be UUA, UAU, or AUU, and,
even more rarely, an AAU, AUA, or UAA. By comparing the results from repeating mRNAs with
that from random mRNAs, and using careful logic, it was possible to deduce the entire genetic code.


 Some genetics textbooks have Nirenberg in the index. All of them should have information on
cracking the genetic code, and a table or chart giving the actual code.


 This simulation was written by Martin LaBar, Southern Wesleyan University,
Central, SC 29630. My phone is currently 864-644-5270, and my e-mail address is mlabar@swu.edu
This worksheet is freeware. Feel free to use, distribute, and modify it as you see fit.

  -Colossians 1:16-17
al messenger


RNA code for

CAGCAGC. . .)
nswered that


s as a pattern for
 ases available.
 be generated,
A, UAU, or AUU, and,
 g mRNAs with
ntire genetic code.


formation on




 mlabar@swu.edu

								
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