AUG exhibits the strongest pulse intensity within the ribosomal decoding site

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Krkosska Bayles, Charles M. Heckert This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4105172/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Within a messenger RNA (mRNA) are the instructions for building proteins. mRNA provides this information using nucleotides in groups of three, called codons. The ribosome moves along the mRNA and reads each codon within the ribosomal decoding site. Once the codon with nucleotides AUG appears in the decoding site, protein synthesis begins. The corresponding transfer RNA (tRNA) then brings the correct protein to the ribosome. What motion is occurring within the decoding site as AUG begins this translation process? Here we show codons interacting with the decoding site’s moving parts, flippers A1492 and A1493. Using an equation for motion, both the codons and the decoding site have numbers applied to them that are closely associated with a Pulse Grading Scale (PGS). This scale is used to grade the intensity (strength) of pulsations such as those found in the wrist, the heart, and other places within a biological system. Cells in these pulsing places also contain ribosomes that are reading mRNA. Therefore, pulsing is happening during translation. When accounting for velocities, variable constants, molar masses, and acceleration and deceleration, AUG is the mRNA codon creating the strongest level of pulse strength within the ribosomal decoding site. Biological sciences/Cell biology Biological sciences/Genetics Figures Figure 1 Figure 2 1. Introduction The translation process occurs when messenger RNA (mRNA) is decoded, and the result is a series of bound amino acids 1 , 2 . The mRNA’s three nucleotides, also referred to by their positions as first base (B1), second base (B2), and third base (B3), are any combination of uracil (U), cytosine (C), adenine (A), and guanine (G) 3 . 4 . This creates sixty-four codon triplets, sixty-one of which encode the twenty amino acids plus three termination “STOP” codons 1 . Protein synthesis begins when codon AUG appears in the ribosomal decoding site 5 . The ribosome’s decoding site changes shape according to which codon is within it 6 . Here an equation is used to examine the energy involved when a codon is inside a ribosome’s decoding site. The combined molar masses of a codon’s three nucleotide bases represent each codon in the equation. If its third base is not recognized during decoding, then the masses of only the codon’s first two bases are included in the equation. The Pulse Grading Scale (PGS) is used to measure the level of pulse strength in biological systems 7 . Biological systems are made of cells containing ribosomes that are reading mRNA, therefore cells experience pulsing motion. Pulse’s three characteristics are rate, rhythm, and force 8 . The third base is not used during translation by half of the codons 6 , 9 . PGS numbers are therefore assigned to only the first two bases of all sixty-one codons and their third base is handled separately. These numbers represent initial (B1) and final (B2) velocities for the pulse rate created by that codon in the decoding site. Unlike the string of different codons creating the mRNA, the ribosome’s A-site flippers 1492 and 1493 are always present in the decoding site 10 . Their PGR reflects their constant, albeit moving, presence, making them variable constants in the equation. The pulse force (also known as volume, or strength) of the expansion and contraction of the decoding site is felt by flippers A1492 and A1493. Like observed during a heartbeat, pulse rhythm describes the pattern of expansion and contraction 11 . It will be either negative or positive as it increases and decreases from baseline 11 . These motions can be either a positive number, a negative number, or zero. Multiplying a pulse’s rate, rhythm and force and adding this to the codon’s weight creates an overall composite view of a codon and its pulse characteristics. The results show AUG is the codon creating the strongest pulse strength within the ribosome’s decoding site. This is a continuation of previous research exploring math’s ability to identify when a codon encodes with only two bases or with all three (the Watson-Crick wobble effect) 12 , and research assigning values to the codon’s third base position and to flippers A1492/1493 13 . 2. Methods 2.1 Assigning values to a codon’s first and second bases. Pulse is rated on a scale typically ranging from zero to four or five, with zero being no flow and the strongest flow rated five 14 . This rating system is reassigned here in a scale from 0–4.4, for use with the three bases of a codon. Table 1 shows values of the four base letters U, C, A, and G according to their position as the first or second base letter in the codon. These values were assigned in previous research according to their ability to accommodate the Watson-Crick wobble effect 12 . When the first base value is multiplied by the second base value and the product is greater than 3.1 then the third base of that codon also encodes, Eq. (1). B1 X B2 > 3.1 = third base encodes Table 1 . Table 1 Pulse rate values for beginning velocity (B1) and end velocity (B2). Pulse Rate: First and Second Base Values Nucleotide B1 Value B2 Value U (uracil) 2 2 C (cytosine) 1 0 A (adenine) 4 4.4 G (guanine) 0.9 3 2.2 Assigning values to two of the ribosome’s A-site adenine molecules. The A-site tunnel holds two adenine molecules that move freely, or flip 15 . These molecules A1492 and A1493 flip as a specific response to the binding of tRNA 15 . Here we apply pulse force as the energy for response, Table 2 . Values were assigned to the flippers in previous research according to their ability to accommodate the division of the sixty codons into their respective 20 different amino acid groups 13 . A codon’s first base affects A1492 (flipper one) and its second base affects A1493 (flipper two), for example AUG creates flipper values of 1 x 3 = 3 for pulse force value. Table 2 . Table 2 Pulse force values created by a codon’s first and second bases pressure the two ribosomal flippers A1492 and A1493. The range of values for pulse force is 0–3.1. This is significant because when a codon’s first and second bases are multiplied, third base encodes when their product is greater than 3.1. This suggests that the ribosomal decoding site’s environment changes when a codon exceeds 3.1, and an accommodation of third base results. Pulse Force: Flipper 1 (A1492) and Flipper 2 (A1493) mRNA’s Base Letter Flipper 1 (A1492) Flipper 2 (A1493) U (uracil) 3.1 3 C (cytosine) 0 0 A (adenine) 1 0 G (guanine) 0 0.2 2.3 Assigning pulse rhythm values. Pulse rhythm is measured as first base minus the second base of the codon (B1 – B2). This accounts for the flow specifically between the beginning and end velocities. Sometimes the first base has a larger value than the second base and vice versa, resulting in negative and positive numbers, or zero, for the pulse rhythm value. 2.4 Weight values for first, second, and sometimes, third bases . The molar mass (g/mol) of each base provides a specific mathematical description of each of a codon’s three bases. It is used to identify each codon mathematically, Table 3 . The same weight applies to the molecule regardless of its base position. Third base mass is added into the equation only when it is encoding. When only the first two bases encode then the third base mass is not used. Table 3 . Table 3 The weight of each molecule comprising the first, second, and sometimes the third, Nucleotides: g/mol mass Base letter g/mol U (uracil) 112.09 C (cytosine) 111.10 A (adenine) 135.13 G (guanine) 151.13 3. Results Table 4 describes the pulsing force within the ribosomal decoding site as each codon passes through it. Pulse rate, the value for (B1 X B2), is identified in the equation first so that B3’s role as encoding or not encoding is established, Eq. (2). When the product is greater than 3.1 then B3 does not encode. (2) (B1 X B2) X (B1 Flip X B2 Flip) X (B1 - B2) + (B1 g/mol + B2 g/mol + B3 g/mol) Pulse force is the B1 and B2 Flip columns. Flippers A1492 and A1493 reflect the force inside the decoding site according to which first and second base is presenting in the site. The pulse force is found in a range from zero to 3.1. The pulse rhythm is set by the Accelerate/Decelerate column. The pulse rhythm has a range from + 4 to -3.5. Pulse rate, force, and rhythm are multiplied to provide a value for the decoding site. The weight of the first and second bases, and the third when its being encoded, are added to the equation, and identify the codon being examined. As Table 4 shows, AUG creates the strongest level of pulse intensity. Table 5 lists the variables used in Table 4 . Figure I is a graph showing the pulse strength created by all the codons, plus the pulse levels for their three bases. Figure II graphs the beginning and ending pulse rates, the pulse forces felt by the two flippers, and the rhythm that accompanies each codon. Table 4 . . Table 4 Pulse Strength Chart. Codon AUG creates the strongest pulse strength inside the Codon Amino Acid Pulse Rate : Initial Final B1 B2 Pulse Force : A1492 A1493 B1 Flip B2 Flip Pulse Rhythm : Acceleration/ Deceleration Codon Recognition : Nucleotides' g/mol First Second Third Codon's Pulse Strength U = 2 C = 1 A = 4 G = 0.9 U = 2 C = 0 A = 4.4 G = 3 When B1 = U = 3.1 C = 0 A = 1 G = 0 When B2 = U = 3 C = 0 A = 0 G = 0.2 B1 - B2 U = 112.09 C = 111.1 A = 135.13 G = 151.13 U = 112.09 C = 111.1 A = 135.13 G = 151.13 When B1 X B2 > 3.1: U = 112.09 C = 111.1 A = 135.13 G = 151.13 B1 X B2 X B1 Flip X B2 Flip X (B1 - B2) + B1 g/mol + B2 g/mol + B3 g/mol AUG met 4 2 1 3 2 135.13 112.09 151.13 446.35 AGG arg 4 3 1 0.2 1 135.13 151.13 151.13 439.79 GAG glu 0.9 4.4 0 0 -3.5 151.13 135.13 151.13 437.39 AUA ile 4 2 1 3 2 135.13 112.09 135.13 430.35 AGA arg 4 3 1 0.2 1 135.13 151.13 135.13 423.79 AAG lys 4 4.4 1 0 -0.4 135.13 135.13 151.13 421.39 GAA glu 0.9 4.4 0 0 -3.5 151.13 135.13 135.13 421.39 UGG trp 2 3 3.1 0.2 -1 112.09 151.13 151.13 410.63 AUU ile 4 2 1 3 2 135.13 112.09 112.09 407.31 AUC ile 4 2 1 3 2 135.13 112.09 111.1 406.32 AAA lys 4 4.4 1 0 -0.4 135.13 135.13 135.13 405.39 AGU ser 4 3 1 0.2 1 135.13 151.13 112.09 400.75 AGC ser 4 3 1 0.2 1 135.13 151.13 111.1 399.76 UAG STOP 2 4.4 3.1 0 -2.4 112.09 135.13 151.13 398.35 GAU asp 0.9 4.4 0 0 -3.5 151.13 135.13 112.09 398.35 GAC asp 0.9 4.4 0 0 -3.5 151.13 135.13 111.1 397.36 CAG gln 1 4.4 0 0 -3.4 111.1 135.13 151.13 397.36 UGA STOP 2 3 3.1 0.2 -1 112.09 151.13 135.13 394.63 AAU asn 4 4.4 1 0 -0.4 135.13 135.13 112.09 382.35 UAA STOP 2 4.4 3.1 0 -2.4 112.09 135.13 135.13 382.35 AAC asn 4 4.4 1 0 -0.4 135.13 135.13 111.1 381.36 CAA gln 1 4.4 0 0 -3.4 111.1 135.13 135.13 381.36 UUG leu 2 2 3.1 3 0 112.09 112.09 151.13 375.31 UGU cys 2 3 3.1 0.2 -1 112.09 151.13 112.09 371.59 UGC cys 2 3 3.1 0.2 -1 112.09 151.13 111.1 370.6 UUA leu 2 2 3.1 3 0 112.09 112.09 135.13 359.31 UAU tyr 2 4.4 3.1 0 -2.4 112.09 135.13 112.09 359.31 UAC tyr 2 4.4 3.1 0 -2.4 112.09 135.13 111.1 358.32 CAU his 1 4.4 0 0 -3.4 111.1 135.13 112.09 358.32 CAC his 1 4.4 0 0 -3.4 111.1 135.13 111.1 357.33 UUU phe 2 2 3.1 3 0 112.09 112.09 112.09 336.27 UUC phe 2 2 3.1 3 0 112.09 112.09 111.1 335.28 GGU gly 0.9 3 0 0.2 -2.1 151.13 151.13 0 302.26 GGG gly 0.9 3 0 0.2 -2.1 151.13 151.13 0 302.26 GGC gly 0.9 3 0 0.2 -2.1 151.13 151.13 0 302.26 GGA gly 0.9 3 0 0.2 -2.1 151.13 151.13 0 302.26 GUU val 0.9 2 0 3 -1.1 151.13 112.09 0 263.22 GUG val 0.9 2 0 3 -1.1 151.13 112.09 0 263.22 GUC val 0.9 2 0 3 -1.1 151.13 112.09 0 263.22 GUA val 0.9 2 0 3 -1.1 151.13 112.09 0 263.22 CGU arg 1 3 0 0.2 -2 111.1 151.13 0 262.23 CGG arg 1 3 0 0.2 -2 111.1 151.13 0 262.23 CGC arg 1 3 0 0.2 -2 111.1 151.13 0 262.23 CGA arg 1 3 0 0.2 -2 111.1 151.13 0 262.23 GCU ala 0.9 0 0 0 0.9 151.13 111.1 0 262.23 GCG ala 0.9 0 0 0 0.9 151.13 111.1 0 262.23 GCC ala 0.9 0 0 0 0.9 151.13 111.1 0 262.23 GCA ala 0.9 0 0 0 0.9 151.13 111.1 0 262.23 ACU thr 4 0 1 0 4 135.13 111.1 0 246.23 ACG thr 4 0 1 0 4 135.13 111.1 0 246.23 ACC thr 4 0 1 0 4 135.13 111.1 0 246.23 ACA thr 4 0 1 0 4 135.13 111.1 0 246.23 CUU leu 1 2 0 3 -1 111.1 112.09 0 223.19 CUG leu 1 2 0 3 -1 111.1 112.09 0 223.19 CUC leu 1 2 0 3 -1 111.1 112.09 0 223.19 CUA leu 1 2 0 3 -1 111.1 112.09 0 223.19 UCU ser 2 0 3.1 0 2 112.09 111.1 0 223.19 UCG ser 2 0 3.1 0 2 112.09 111.1 0 223.19 UCC ser 2 0 3.1 0 2 112.09 111.1 0 223.19 UCA ser 2 0 3.1 0 2 112.09 111.1 0 223.19 CCU pro 1 0 0 0 1 111.1 111.1 0 222.2 CCG pro 1 0 0 0 1 111.1 111.1 0 222.2 CCC pro 1 0 0 0 1 111.1 111.1 0 222.2 CCA pro 1 0 0 0 1 111.1 111.1 0 222.2 Table 5 . Table 5 Variables used to determine codon pulse strength. The pulse values are assigned to a codon’s nucleotides and to a ribosome’s decoding site flippers A1492 and A1493. The g/mol for of the nucleotides create a unique identifier for each codon. Variables Used to Determine Codon Pulse Strength Nucleotide Pulse rate Pulse Force Codon Recognition B1 B2 B1 FLIP B2 FLIP G/MOL U 2 2 3.1 3 112.09 C 1 0 0 0 111.1 A 4 4.4 1 0 135.13 G 0.9 3 0 0.2 151.13 4. Discussion Velocity is measured when a codon’s first base is multiplied by its second base. This describes how fast the codon is moving and in which direction. This concept is slightly different than speed, which only expresses how fast an object is moving 16 . Pulsing motion often embodies twisting motion as well as forward, for example food going down the esophagus, blood moving in blood vessels, and peristalsis in the intestinal tract 17 . Therefore, translating cells in biological systems are engaged in twisting, pulsing motion as their mRNA codons present to a ribosome’s decoding site. When an object is stationary its velocity is zero 18 . Codons with a second base C (cytosine) as their ending pulse rate, are stationary as far as describing their influence on pulse because they have a value of zero. The remaining codons (those with no second base C) move in one direction while influencing the pulse rate. Velocity is positive when an object is moving one direction, and negative when it moves the opposite direction 18 . Since none of the codons have a negative value then none of them move backwards. Flippers A1492 and A1493’s positions are critical for recognizing the first two Watson-Crick base pairs 19 . When bound, they interact with neighboring nucleotides, and they bulge out and protrude from their helix 20 . In the free, or unbound state, A1492/93 do not actively participate the specific interactions though they can adopt flexible conformations 21 . They become molecular switches by altering the mRNA’s shape and function 22 . In Table 4 , third base is used when the initial pulse rate set by B1, multiplied by the final pulse rate set by B2, is a product greater than 3.1. The two flippers have set 0–3.1 as their volume range, therefore third base is read only when the codon’s pulse rate exceeds the volume of the decoding site. A Pulse Grading Scale describes the intensity, or force, of the pulsations when feeling for a pulse, for example, on the inside of the wrist 8 . A typical scale will rate a pulse from zero to about three or four, with zero being an absent pulse, 1 + is weak, 2 + is normal, 3 + is bounding and full, and 4 + is an exceptionally strong pulse 8 . Deciding where the boundary is between these numbers is open to interpretation by the pulse taker who’s working with a scale using whole numbers. Here we explore pulse intensity at the nano scale in which the translation process is operating, and many of the values are decimal numbers which suggests precision. However, some play could be expected in the PGS ratings in other applications due to this being the nature of the scale. Table 4 may be summed up as follows. The codon’s first two bases enter the ribosome’s decoding site with a pulsing burst of energy. If their force exceeds the decoding site’s normal capacity, the flexible decoding site will stretch and accommodate the codon’s third as well. If the codon’s first and second bases are below the energy that is needed to stretch the encoding site, then the third base’ mass is not read. The force a codon will place on the decoding site’s volume capacity is the Codon’s Pulse Strength. The codon with the strongest pulse is the initiation codon AUG. There are various equations of motion, and they describe many fundamental qualities 23 . Different variables and equations can be applied to explore other aspects of the amino acids. Our research goals will continue to apply mathematical concepts to translation and other biological processes. Declarations Competing Interests The authors declare no competing interests. Author Contribution B. K. K. B. wrote the main manuscript text and prepared Tables 1-3 and Figures I and II. C. M. H. and B. K. K. B. prepared Tables 4 and 5. Both authors reviewed the manuscript. Acknowledgments The authors thank the anonymous reviewers for their valuable suggestions. This work is privately funded. Data Availability The datasets generated and analyzed for this study will be available in the Dryad repository upon preprint acceptance. References Clancy, S., & Brown, W. (2008). Translation: DNA to mRNA to Protein. Nature Education , 1(1), 101. 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Heckert","email":"","orcid":"","institution":"Independent Researcher","correspondingAuthor":false,"prefix":"","firstName":"Charles","middleName":"M.","lastName":"Heckert","suffix":""}],"badges":[],"createdAt":"2024-03-15 05:59:49","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4105172/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4105172/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":53956030,"identity":"84b66e68-1196-47d5-a286-3df3ccd6bef2","added_by":"auto","created_at":"2024-04-02 17:15:29","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":61605,"visible":true,"origin":"","legend":"\u003cp\u003eThe blue bar shows the codon’s pulse strength. First, second and third bases of the\u003c/p\u003e\n\u003cp\u003ecodons are in green, dark blue, and brown respectively.\u003c/p\u003e","description":"","filename":"1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4105172/v1/a8c6f6286b778c24104397cc.jpg"},{"id":53956031,"identity":"fa152ccb-3b42-4cd9-871f-ea2c1fd2ebdd","added_by":"auto","created_at":"2024-04-02 17:15:30","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":86811,"visible":true,"origin":"","legend":"\u003cp\u003ePulse rate, force, and rhythm applied to the 20 amino acids.\u003c/p\u003e","description":"","filename":"2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4105172/v1/c8cf94ecd264b6146a24748a.jpg"},{"id":60128417,"identity":"7c5f819c-93f2-4713-b977-0a2a06926443","added_by":"auto","created_at":"2024-07-12 06:34:37","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1109744,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4105172/v1/3570b144-c318-44d0-abde-e25ba459f1fa.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"AUG exhibits the strongest pulse intensity within the ribosomal decoding site","fulltext":[{"header":"1. Introduction","content":"\u003cp\u003eThe translation process occurs when messenger RNA (mRNA) is decoded, and the result is a series of bound amino acids\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e,\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e. The mRNA\u0026rsquo;s three nucleotides, also referred to by their positions as first base (B1), second base (B2), and third base (B3), are any combination of uracil (U), cytosine (C), adenine (A), and guanine (G) \u003csup\u003e\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e.\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e\u003c/sup\u003e. This creates sixty-four codon triplets, sixty-one of which encode the twenty amino acids plus three termination \u0026ldquo;STOP\u0026rdquo; codons\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u003c/sup\u003e. Protein synthesis begins when codon AUG appears in the ribosomal decoding site\u003csup\u003e\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe ribosome\u0026rsquo;s decoding site changes shape according to which codon is within it\u003csup\u003e\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u003c/sup\u003e. Here an equation is used to examine the energy involved when a codon is inside a ribosome\u0026rsquo;s decoding site. The combined molar masses of a codon\u0026rsquo;s three nucleotide bases represent each codon in the equation. If its third base is not recognized during decoding, then the masses of only the codon\u0026rsquo;s first two bases are included in the equation.\u003c/p\u003e \u003cp\u003eThe Pulse Grading Scale (PGS) is used to measure the level of pulse strength in biological systems\u003csup\u003e\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u003c/sup\u003e. Biological systems are made of cells containing ribosomes that are reading mRNA, therefore cells experience pulsing motion. Pulse\u0026rsquo;s three characteristics are rate, rhythm, and force\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe third base is not used during translation by half of the codons\u003csup\u003e\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e,\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e\u003c/sup\u003e. PGS numbers are therefore assigned to only the first two bases of all sixty-one codons and their third base is handled separately. These numbers represent initial (B1) and final (B2) velocities for the \u003cem\u003epulse rate\u003c/em\u003e created by that codon in the decoding site.\u003c/p\u003e \u003cp\u003eUnlike the string of different codons creating the mRNA, the ribosome\u0026rsquo;s A-site flippers 1492 and 1493 are always present in the decoding site\u003csup\u003e\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e\u003c/sup\u003e. Their PGR reflects their constant, albeit moving, presence, making them variable constants in the equation. The \u003cem\u003epulse force\u003c/em\u003e (also known as volume, or strength) of the expansion and contraction of the decoding site is felt by flippers A1492 and A1493.\u003c/p\u003e \u003cp\u003eLike observed during a heartbeat, \u003cem\u003epulse rhythm\u003c/em\u003e describes the pattern of expansion and contraction\u003csup\u003e\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u003c/sup\u003e. It will be either negative or positive as it increases and decreases from baseline\u003csup\u003e\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u003c/sup\u003e. These motions can be either a positive number, a negative number, or zero.\u003c/p\u003e \u003cp\u003eMultiplying a pulse\u0026rsquo;s rate, rhythm and force and adding this to the codon\u0026rsquo;s weight creates an overall composite view of a codon and its pulse characteristics. The results show AUG is the codon creating the strongest pulse strength within the ribosome\u0026rsquo;s decoding site. This is a continuation of previous research exploring math\u0026rsquo;s ability to identify when a codon encodes with only two bases or with all three (the Watson-Crick wobble effect)\u003csup\u003e\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u003c/sup\u003e, and research assigning values to the codon\u0026rsquo;s third base position and to flippers A1492/1493\u003csup\u003e13\u003c/sup\u003e.\u003c/p\u003e"},{"header":"2. Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003e2.1 \u003cem\u003eAssigning values to a codon\u0026rsquo;s first and second bases.\u003c/em\u003e\u003c/h2\u003e \u003cp\u003ePulse is rated on a scale typically ranging from zero to four or five, with zero being no flow and the strongest flow rated five\u003csup\u003e\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u003c/sup\u003e. This rating system is reassigned here in a scale from 0\u0026ndash;4.4, for use with the three bases of a codon. Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e shows values of the four base letters U, C, A, and G according to their position as the first or second base letter in the codon. These values were assigned in previous research according to their ability to accommodate the Watson-Crick wobble effect\u003csup\u003e\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u003c/sup\u003e. When the first base value is multiplied by the second base value and the product is greater than 3.1 then the third base of that codon also encodes, Eq.\u0026nbsp;(1).\u003c/p\u003e \u003cp\u003e \u003col\u003e \u003cspan\u003e \u003cli\u003e \u003cp\u003eB1 X B2\u0026thinsp;\u0026gt;\u0026thinsp;3.1\u0026thinsp;=\u0026thinsp;third base encodes\u003c/p\u003e \u003c/li\u003e \u003c/span\u003e \u003c/ol\u003e \u003c/p\u003e \u003cp\u003eTable\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003ePulse rate values for beginning velocity (B1) and end velocity (B2).\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"3\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003ePulse Rate:\u003c/p\u003e \u003cp\u003eFirst and Second Base Values\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNucleotide\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eB1\u003c/p\u003e \u003cp\u003eValue\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eB2\u003c/p\u003e \u003cp\u003eValue\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eU (uracil)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC (cytosine)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eA (adenine)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e4.4\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eG (guanine)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003e2.2 \u003cem\u003eAssigning values to two of the ribosome\u0026rsquo;s A-site adenine molecules.\u003c/em\u003e\u003c/h2\u003e \u003cp\u003eThe A-site tunnel holds two adenine molecules that move freely, or flip\u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e. These molecules A1492 and A1493 flip as a specific response to the binding of tRNA\u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e. Here we apply pulse force as the energy for response, Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e. Values were assigned to the flippers in previous research according to their ability to accommodate the division of the sixty codons into their respective 20 different amino acid groups\u003csup\u003e\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u003c/sup\u003e. A codon\u0026rsquo;s first base affects A1492 (flipper one) and its second base affects A1493 (flipper two), for example AUG creates flipper values of 1 x 3\u0026thinsp;=\u0026thinsp;3 for pulse force value.\u003c/p\u003e \u003cp\u003eTable\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003ePulse force values created by a codon\u0026rsquo;s first and second bases pressure the two ribosomal flippers A1492 and A1493. The range of values for pulse force is 0\u0026ndash;3.1. This is significant because when a codon\u0026rsquo;s first and second bases are multiplied, third base encodes when their product is greater than 3.1. This suggests that the ribosomal decoding site\u0026rsquo;s environment changes when a codon exceeds 3.1, and an accommodation of third base results.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"3\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003ePulse Force:\u003c/p\u003e \u003cp\u003eFlipper 1 (A1492) and Flipper 2 (A1493)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003emRNA\u0026rsquo;s\u003c/p\u003e \u003cp\u003eBase Letter\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFlipper 1\u003c/p\u003e \u003cp\u003e(A1492)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eFlipper 2\u003c/p\u003e \u003cp\u003e(A1493)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eU (uracil)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e3.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC (cytosine)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eA (adenine)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eG (guanine)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0.2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003e2.3 \u003cem\u003eAssigning pulse rhythm values.\u003c/em\u003e\u003c/h2\u003e \u003cp\u003ePulse rhythm is measured as first base minus the second base of the codon (B1 \u0026ndash; B2). This accounts for the flow specifically between the beginning and end velocities. Sometimes the first base has a larger value than the second base and vice versa, resulting in negative and positive numbers, or zero, for the pulse rhythm value.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003e2.4 \u003cem\u003eWeight values for first, second, and sometimes, third bases\u003c/em\u003e.\u003c/h2\u003e \u003cp\u003eThe molar mass (g/mol) of each base provides a specific mathematical description of each of a codon\u0026rsquo;s three bases. It is used to identify each codon mathematically, Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e. The same weight applies to the molecule regardless of its base position. Third base mass is added into the equation only when it is encoding. When only the first two bases encode then the third base mass is not used.\u003c/p\u003e \u003cp\u003eTable\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eThe weight of each molecule comprising the first, second, and sometimes the third,\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"2\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c2\" namest=\"c1\"\u003e \u003cp\u003eNucleotides:\u003c/p\u003e \u003cp\u003eg/mol mass\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBase letter\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eg/mol\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eU (uracil)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC (cytosine)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e111.10\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eA (adenine)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eG (guanine)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e"},{"header":"3. Results","content":"\u003cp\u003eTable\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e describes the pulsing force within the ribosomal decoding site as each codon passes through it. Pulse rate, the value for (B1 X B2), is identified in the equation first so that B3\u0026rsquo;s role as encoding or not encoding is established, Eq.\u0026nbsp;(2). When the product is greater than 3.1 then B3 does not encode.\u003c/p\u003e \u003cspan\u003e \u003cp\u003e(2) (B1 X B2) X (B1 Flip X B2 Flip) X (B1 - B2) + (B1 g/mol\u0026thinsp;+\u0026thinsp;B2 g/mol\u0026thinsp;+\u0026thinsp;B3 g/mol)\u003c/p\u003e\u003c/span\u003e\u003cp\u003ePulse force is the B1 and B2 Flip columns. Flippers A1492 and A1493 reflect the force inside the decoding site according to which first and second base is presenting in the site. The pulse force is found in a range from zero to 3.1.\u003c/p\u003e \u003cp\u003eThe pulse rhythm is set by the Accelerate/Decelerate column. The pulse rhythm has a range from +\u0026thinsp;4 to -3.5.\u003c/p\u003e \u003cp\u003ePulse rate, force, and rhythm are multiplied to provide a value for the decoding site. The weight of the first and second bases, and the third when its being encoded, are added to the equation, and identify the codon being examined.\u003c/p\u003e \u003cp\u003eAs Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e shows, AUG creates the strongest level of pulse intensity. Table\u0026nbsp;\u003cspan refid=\"Tab5\" class=\"InternalRef\"\u003e5\u003c/span\u003e lists the variables used in Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e. Figure I is a graph showing the pulse strength created by all the codons, plus the pulse levels for their three bases. Figure II graphs the beginning and ending pulse rates, the pulse forces felt by the two flippers, and the rhythm that accompanies each codon.\u003c/p\u003e \u003cp\u003eTable\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e. .\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab4\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003ePulse Strength Chart. Codon AUG creates the strongest pulse strength inside the\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"11\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c9\" colnum=\"9\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c10\" colnum=\"10\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c11\" colnum=\"11\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCodon\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eAmino Acid\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c4\" namest=\"c3\"\u003e \u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003ePulse Rate\u003c/span\u003e: Initial Final\u003c/p\u003e \u003cp\u003eB1 B2\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c6\" namest=\"c5\"\u003e \u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003ePulse Force\u003c/span\u003e: A1492 A1493\u003c/p\u003e \u003cp\u003eB1 Flip B2 Flip\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003ePulse Rhythm\u003c/span\u003e: Acceleration/ Deceleration\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c10\" namest=\"c8\"\u003e \u003cp\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003eCodon Recognition\u003c/span\u003e: Nucleotides' g/mol First Second Third\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c11\"\u003e \u003cp\u003eCodon's Pulse Strength\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eU\u0026thinsp;=\u0026thinsp;2 C\u0026thinsp;=\u0026thinsp;1 A\u0026thinsp;=\u0026thinsp;4 G\u0026thinsp;=\u0026thinsp;0.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eU\u0026thinsp;=\u0026thinsp;2 C\u0026thinsp;=\u0026thinsp;0 A\u0026thinsp;=\u0026thinsp;4.4 G\u0026thinsp;=\u0026thinsp;3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eWhen B1 = U\u0026thinsp;=\u0026thinsp;3.1 C\u0026thinsp;=\u0026thinsp;0 A\u0026thinsp;=\u0026thinsp;1 G\u0026thinsp;=\u0026thinsp;0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eWhen B2 = U\u0026thinsp;=\u0026thinsp;3 C\u0026thinsp;=\u0026thinsp;0 A\u0026thinsp;=\u0026thinsp;0 G\u0026thinsp;=\u0026thinsp;0.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eB1 - B2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eU\u0026thinsp;=\u0026thinsp;112.09 C\u0026thinsp;=\u0026thinsp;111.1 A\u0026thinsp;=\u0026thinsp;135.13 G\u0026thinsp;=\u0026thinsp;151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003eU\u0026thinsp;=\u0026thinsp;112.09 C\u0026thinsp;=\u0026thinsp;111.1 A\u0026thinsp;=\u0026thinsp;135.13 G\u0026thinsp;=\u0026thinsp;151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003eWhen B1 X B2\u0026thinsp;\u0026gt;\u0026thinsp;3.1: U\u0026thinsp;=\u0026thinsp;112.09 C\u0026thinsp;=\u0026thinsp;111.1 A\u0026thinsp;=\u0026thinsp;135.13 G\u0026thinsp;=\u0026thinsp;151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003eB1 X B2 X B1 Flip X B2 Flip X (B1 - B2) + B1 g/mol + B2 g/mol + B3 g/mol\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAUG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003emet\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e446.35\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAGG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003earg\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e439.79\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGAG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eglu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-3.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e437.39\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAUA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eile\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e430.35\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAGA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003earg\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e423.79\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eAAG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003elys\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-0.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e421.39\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGAA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eglu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-3.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" 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align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-3.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e398.35\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGAC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003easp\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e 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colname=\"c4\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-2.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e302.26\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGGC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003egly\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e 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colname=\"c2\"\u003e \u003cp\u003eval\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-1.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e263.22\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e 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\u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e223.19\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCUA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eleu\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e223.19\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eUCU\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e3.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e223.19\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eUCG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e3.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e223.19\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eUCC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e3.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e223.19\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eUCA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e3.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e223.19\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCCU\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epro\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e222.2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCCG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epro\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e222.2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCCC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epro\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e222.2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCCA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003epro\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c11\"\u003e \u003cp\u003e222.2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eTable\u0026nbsp;\u003cspan refid=\"Tab5\" class=\"InternalRef\"\u003e5\u003c/span\u003e.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab5\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 5\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eVariables used to determine codon pulse strength. The pulse values are assigned to a codon\u0026rsquo;s nucleotides and to a ribosome\u0026rsquo;s decoding site flippers A1492 and A1493. The g/mol for of the nucleotides create a unique identifier for each codon.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"6\" nameend=\"c6\" namest=\"c1\"\u003e \u003cp\u003eVariables Used to Determine Codon Pulse Strength\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eNucleotide\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003ePulse rate\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003ePulse Force\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eCodon Recognition\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eB1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eB2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eB1 FLIP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eB2 FLIP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eG/MOL\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eU\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e112.09\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e111.1\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e4.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e135.13\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eG\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e151.13\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e "},{"header":"4. Discussion","content":"\u003cp\u003eVelocity is measured when a codon\u0026rsquo;s first base is multiplied by its second base. This describes how fast the codon is moving and in which direction. This concept is slightly different than speed, which only expresses how fast an object is moving\u003csup\u003e\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e\u003c/sup\u003e. Pulsing motion often embodies twisting motion as well as forward, for example food going down the esophagus, blood moving in blood vessels, and peristalsis in the intestinal tract\u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u003c/sup\u003e. Therefore, translating cells in biological systems are engaged in twisting, pulsing motion as their mRNA codons present to a ribosome\u0026rsquo;s decoding site.\u003c/p\u003e \u003cp\u003eWhen an object is stationary its velocity is zero\u003csup\u003e\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u003c/sup\u003e. Codons with a second base C (cytosine) as their ending pulse rate, are stationary as far as describing their influence on pulse because they have a value of zero. The remaining codons (those with no second base C) move in one direction while influencing the pulse rate. Velocity is positive when an object is moving one direction, and negative when it moves the opposite direction\u003csup\u003e\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u003c/sup\u003e. Since none of the codons have a negative value then none of them move backwards.\u003c/p\u003e \u003cp\u003eFlippers A1492 and A1493\u0026rsquo;s positions are critical for recognizing the first two Watson-Crick base pairs\u003csup\u003e\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u003c/sup\u003e. When bound, they interact with neighboring nucleotides, and they bulge out and protrude from their helix\u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u003c/sup\u003e. In the free, or unbound state, A1492/93 do not actively participate the specific interactions though they can adopt flexible conformations\u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e. They become molecular switches by altering the mRNA\u0026rsquo;s shape and function\u003csup\u003e\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eIn Table\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, third base is used when the initial pulse rate set by B1, multiplied by the final pulse rate set by B2, is a product greater than 3.1. The two flippers have set 0\u0026ndash;3.1 as their volume range, therefore third base is read only when the codon\u0026rsquo;s pulse rate exceeds the volume of the decoding site.\u003c/p\u003e \u003cp\u003eA Pulse Grading Scale describes the intensity, or force, of the pulsations when feeling for a pulse, for example, on the inside of the wrist\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u003c/sup\u003e. A typical scale will rate a pulse from zero to about three or four, with zero being an absent pulse, 1\u0026thinsp;+\u0026thinsp;is weak, 2\u0026thinsp;+\u0026thinsp;is normal, 3\u0026thinsp;+\u0026thinsp;is bounding and full, and 4\u0026thinsp;+\u0026thinsp;is an exceptionally strong pulse\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u003c/sup\u003e. Deciding where the boundary is between these numbers is open to interpretation by the pulse taker who\u0026rsquo;s working with a scale using whole numbers. Here we explore pulse intensity at the nano scale in which the translation process is operating, and many of the values are decimal numbers which suggests precision. However, some play could be expected in the PGS ratings in other applications due to this being the nature of the scale.\u003c/p\u003e \u003cp\u003eTable\u0026nbsp;\u003cspan refid=\"Tab4\" class=\"InternalRef\"\u003e4\u003c/span\u003e may be summed up as follows. The codon\u0026rsquo;s first two bases enter the ribosome\u0026rsquo;s decoding site with a pulsing burst of energy. If their force exceeds the decoding site\u0026rsquo;s normal capacity, the flexible decoding site will stretch and accommodate the codon\u0026rsquo;s third as well. If the codon\u0026rsquo;s first and second bases are below the energy that is needed to stretch the encoding site, then the third base\u0026rsquo; mass is not read. The force a codon will place on the decoding site\u0026rsquo;s volume capacity is the Codon\u0026rsquo;s Pulse Strength. The codon with the strongest pulse is the initiation codon AUG.\u003c/p\u003e \u003cp\u003eThere are various equations of motion, and they describe many fundamental qualities\u003csup\u003e\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u003c/sup\u003e. Different variables and equations can be applied to explore other aspects of the amino acids. Our research goals will continue to apply mathematical concepts to translation and other biological processes.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e \u003ch2\u003eCompeting Interests\u003c/h2\u003e \u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e \u003c/p\u003e\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eB. K. K. B. wrote the main manuscript text and prepared Tables 1-3 and Figures I and II. C. M. H. and B. K. K. B. prepared Tables 4 and 5. Both authors reviewed the manuscript.\u003c/p\u003e\u003ch2\u003eAcknowledgments\u003c/h2\u003e \u003cp\u003eThe authors thank the anonymous reviewers for their valuable suggestions. This work is privately funded.\u003c/p\u003e\u003ch2\u003eData Availability\u003c/h2\u003e \u003cp\u003eThe datasets generated and analyzed for this study will be available in the Dryad repository upon preprint acceptance.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eClancy, S., \u0026amp; Brown, W. (2008). Translation: DNA to mRNA to Protein. \u003cem\u003eNature Education\u003c/em\u003e, 1(1), 101.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAsano, K., Ito, K. (2013). Translation Elongation. In: Dubitzky, W., Wolkenhauer, O., Cho, KH., Yokota, H. (eds) Encyclopedia of Systems Biology. 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DOI: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1371/journal.pone.0111811\u003c/span\u003e\u003cspan address=\"10.1371/journal.pone.0111811\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eThe Physics Hypertextbook - Equations of Motion. Author: Glenn Elert. URL: Equations of Motion \u0026ndash; The Physics Hypertextbook. Accessed: 13 March, 2024.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-4105172/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4105172/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eWithin a messenger RNA (mRNA) are the instructions for building proteins. mRNA provides this information using nucleotides in groups of three, called codons. The ribosome moves along the mRNA and reads each codon within the ribosomal decoding site. Once the codon with nucleotides AUG appears in the decoding site, protein synthesis begins. The corresponding transfer RNA (tRNA) then brings the correct protein to the ribosome. What motion is occurring within the decoding site as AUG begins this translation process? Here we show codons interacting with the decoding site\u0026rsquo;s moving parts, flippers A1492 and A1493. Using an equation for motion, both the codons and the decoding site have numbers applied to them that are closely associated with a Pulse Grading Scale (PGS). This scale is used to grade the intensity (strength) of pulsations such as those found in the wrist, the heart, and other places within a biological system. Cells in these pulsing places also contain ribosomes that are reading mRNA. Therefore, pulsing is happening during translation. When accounting for velocities, variable constants, molar masses, and acceleration and deceleration, AUG is the mRNA codon creating the strongest level of pulse strength within the ribosomal decoding site.\u003c/p\u003e","manuscriptTitle":"AUG exhibits the strongest pulse intensity within the ribosomal decoding site","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-04-02 17:15:24","doi":"10.21203/rs.3.rs-4105172/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"08f5ed29-b0a3-47e3-bd23-c1d1f6d40b6b","owner":[],"postedDate":"April 2nd, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":30072210,"name":"Biological sciences/Cell biology"},{"id":30072211,"name":"Biological sciences/Genetics"}],"tags":[],"updatedAt":"2024-07-12T06:26:30+00:00","versionOfRecord":[],"versionCreatedAt":"2024-04-02 17:15:24","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-4105172","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4105172","identity":"rs-4105172","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}