DOI: 10.5061/dryad.tht76hf5r
title: Data from: The twenty amino acids are identified by unique numbers assigned to the uracil, cytosine, adenine, and guanine found in the three base positions of the sixty-four messenger RNA genetic codons

description: A codon’s three bases consist of any combination of uracil, cytosine,
 adenine, or guanine and these encode the twenty amino acids. When the
 codon’s first two bases are given specific values, and those values are
 multiplied, then the third base of the codon is used during translation
 only when the product is greater than three. Here we show that those
 values plus more variables within the ribosomal decoding site results in
 specific flow values for each of the twenty amino acid groups. These
 results are demonstrated in a flow chart showing the unidirectional flow
 which is expected during the translation process. All twenty amino acids
 can be represented by numbers that describe their relationship to each
 other and to the decoding site. We anticipate our findings will increase
 discussion about using a number system to better understand the
 translation process.
description: There are sixty-one codons that are read by the ribosome and
 these encode the twenty amino acids. Our dataset assigns numbers to each
 of the 61 codons.  These numbers are calculated by assigning numerical
 values to the uracil, guanine, adenine, and cytosine that comprise mRNA
 during translation. Values are also assigned to the site within the
 ribosome that reads these codons. Twenty values result and they break the
 sixty-one codons into their respective twenty protein classes. For
 example, there are six codons that encode for serine and the value chart
 shows all six have the same value of 9.1, which is unique to serine and
 not found representing any of the other nineteen amino acid groups. Flow
 charts are used to show these values calculated in a unidirectional flow
 as is expected during translation.
description: # Each of the twenty amino acids in the codon dictionary has its own
 numerical value Table 1.
 The standard codon dictionary. The triplet codons consist of three bases
 of uracil (U), cytosine (C), adenine (A), and guanine (G). This creates
 sixty-four codon triplets, sixty-one of which encode the twenty amino
 acids. UAA, UAG, and UGA are termination codons that do not encode
 protein. Fig. 1. The codon dictionary flow chart. The sixty-one encoding
 triplets follow a three-step flow chart. First, the triplets with the
 second base A always use their third base during translation as they
 encode for proteins. Second, the codons exhibiting a C as their second
 base do not use their third base during the encoding process. Finally, the
 first bases C and G do not encode unless their second base was an A, which
 was already taken care of in the first step.   The remaining two first
 base possibilities are U and A and they do encode unless their second base
 was a C, which was taken care of in the second step of the flow chart.
 Table 2. Base letters values. See Table 5. Assigning certain numbers to
 the codons’ first and second bases and then multiplying them will predict
 which amino acids need their third bases to encode. Because the flow chart
 begins with analysis of the second base letter A, it is given the highest
 value. Next, second base C never encodes a third base so its value is
 assigned zero. The remaining bases fall in between these two extremes.
 When the codon’s first base value is multiplied by its second base value,
 and the product is greater than 3, then that codon’s third base is part of
 the encoding process. Table 3. Third base value. See Table 5. When third
 base *does not* encode then 4 is added to its value. When third base
 *does* encode then 0.9 is added to the codon’s flow value as long as the
 third base letter is U or C. No amount is added when the third base letter
 is A or G. There are two special circumstances when calculating flow
 amount for the third base. When first base multiplied by the second base
 equals 8 and third base is an A, then an additional 0.9 is added to the
 total flow amount for that codon. In the second circumstance when the
 product of the first and second bases equals two, then an additional 0.1
 is added to that codon’s total flow calculation. Table 4. Ribosomal Flp
 Values, see Table 5. To determine values for the twenty amino acid
 categories that the sixty-one codons fall within the ribosome is also
 assigned some values. The ribosome’s A-site tunnel holds two adenine
 molecules (A) that move freely, or “flip”. T  They are assigned flip
 values that react to a codon’s first and second bases, identified as “B1
 Flipper” and “B2 Flipper”.  Table 5. Arranged in descending order, the
 amino acids break up into twenty flow field values when combining a
 codon’s three base values with the ribosomal flip values. The result is
 twenty Codon Flow Values, one value for each of the twenty amino acids.
 For example, leucine (leu), serine (ser), and arginine (arg) are encoded
 by six codons each, and each set of six has its own unique number.
 Methionine (met) is encoded by only one codon AUG, and it is also the only
 encoding codon with a value of 10. The first column on the left, column 1,
 lists the codon. Column 2 shows the amino acid encoded by that codon.
 Columns 3 and 4 are the values assigned to the first (B1) and second (B2)
 bases of the codon, see Table 2. The next three columns 5, 6, and 7 show
 the numbers assigned to the codon's third base (B3), see Table 3.
 Columns 8 and 9 hold the codon's first base (B1 Flip) and second base
 (B2 Flip) ribosome flip values, see Table 4. The far right column #10
 shows the resulting Codon Flow Value, created by combining all the
 columns. The remaining columns are raw data for setting up commands to
 created the columned graph and are each labeled according to their task.
 Table 5 was prepared using XLSX spreadsheet to compute each column. Fig.
 2. Flow Chart describing the values assigned to each codon. A flow chart
 shows an orderly pattern for describing a codon’s flow value. The value
 for (B1 X B2) must be established first so that B3 can be calculated.
 After the third base’s value is calculated, it is added to Base 1 and 2
 values and Flip 1 & 2 values.  The codon’s flow value is established.
 Fig.3. The 64 codons with numbers assigned in graph form. This graph
 places all 64 codons in descending order for easy analysis. For example,
 leucine has six codons that encode it and all six have the same flow value
 number. The remaining nineteen amino acids also possess one flow value
 that is unique to them. Data was derived from the following sources: *
 Each table, figure, and graph were created by the authors B. Bayles and C.
 Heckert.