Nucleic acids The Basis of All Biologic Life, Including Men, Women, and Children ---------------------------------- The nucleic acids are very long polymers. The unit or monomer from which they are built is a substance called a nucleotide. Each nucleotide consists of three components: 1. a molecule of phosphoric acid 2. one purine, or one pyrimidine base 3. one pentose sugar Two types of purines are found in nucleotides: adenine and guanine. Three types of pyrimidines are involved: thymine, cytosine, and uracil. Two types of sugars occur in nucleotides: deoxyribose and ribose In the structure of the nucleotide, the pentose sugar forms the central unit with one phosphoric acid unit and one purine or pyrimidine base covalently linked to carbon atoms of the sugar molecule. Nucleotide units are joined by bonds between the alternating phosphate molecule of one nucleotide and the sugar molecule of the next nucleotide to result in a sugar-to-phosphate-to- sugar-to-phosphate linkage. Two (2) specific carbon atoms of the pentose sugars are solely devoted to this sugar-to-phosphate link; the entire DNA, or RNA chain from beginning to end, is held together and defined by this main carbon-to-phosphorus chemical linkage. Apart from the four (4) carbon atoms defining the cyclic structure of the pentose sugars, the third carbon atom is solely devoted to the purpose of bonding to either one type of purine, or one pyrimidine base. The fourth carbon atom of deoxyribose or ribose is involved with internal hydrogen bonding to lend further support and strength to this critical and fragile structure. Two types of nucleic acids are found in protoplasm: deoxyribonucleic acid (DNA) ribonucleic acid (RNA) Base Constituents and Pairing ----------------------------- nucleic acid purines pyrimidines base pairing sugar ------------ ------- ----------- ------------ ----- DNA Adenine Thymine G--C deoxyribose Guanine Cytosine A--T RNA Adenine Uracil none ribose Guanine Cytosine none Computing the number of Nucleic Base Sequence Combinations ---------------------------------------------------------- We are now interested in examining the total number of possible combinations of DNA or RNA base sequences given a known polymer length. In DNA, the base pairing of purine to pyrimidine is uniform and constant: guanine is always paired (hydrogen bonded) with cytosine and Adenine with Thymine, while in RNA there is no pairing to worry about. Therefore, we can do away with the DNA pairing as we can infer this. If we have one nucleotide whose pentose sugar is deoxyribose, then we know that deoxyribose can have four (4) different possible bases bonded to that specific carbon atom, namely Adenine, Guanine, Thymine, or Cytosine. Thus, for one nucleotide, there are four (4) possible distinct nucleotide constructions. If we have a polymer consisting of two nucleotides, then we have 4^2 = 16. Meaning that there are now 16 possible base sequence arrangements of two (2) phosphorous-sugar-phosphorous-sugar linked nucleotides. From the DNA bases, we have the following combinations using base name abbreviations: AGCT A-G, A-C, A-T, A-A G-A, G-C, G-T, G-G C-A, C-G, C-T, C-C T-A, T-G, T-C, T-T Thus, the general formula is computed as: 4 to the exponent known polymer length or 4^polymer_length Discovering the actual base sequence permutation for a particular life form, is, of course, another matter, but can be done! Observe that with a DNA polymer composed of two nucleotides, there is redundancy: A-G and G-A are 'identical'. It would only depend upon which order the chemist viewed the polymer. For a life form of this simplicity, this redundancy is not critical. However, for longer base sequences, this redundancy may translate to a specific gene of vital biologic importance; in long base sequences, any redundancy is critical. Further, this type of redundancy cannot be avoided mathematically, or chemically, and it is the placement of such redundant sequences of variable length which give the entire DNA or RNA strand its peculiar characteristics from a combinatorial point of view. (The combinatorics of the Data Encryption Algorithm are exactly the same; the DNA model is a perfect analogy to what goes on in the algorithm. With the DEA, however, the above general formula is: 10^one-time-pad size.)