Nucleic acids structural building blocks

That is enough for now about proteins. Let s turn our attention to the building blocks of the nucleic acids and relate these to nucleic acid structure and function. 

Combinatorial chemistry involves the use of the basic building blocks in biochemistry, either the 20 amino acids or 4 nucleic acids, to build new molecules. All the different combinations of a set number of building blocks can be created for example, the use of 10 different amino acids can result in over 3.5 million decapeptide compounds. Huge libraries of compounds are produced, which require screening through HTS and the use of informatics to help sort out the structures and especially the activities of all these new compounds. ... 

Almost all of the calculations on polyads were performed for isolated base complexes thus neglecting effects of nucleic backbone, solvent and also of entropic contributions. Erqreriments most directly related to quantum-chemical results are gas phase investigations on base pairs.Nevertheless, it makes also sense to compare the results of quantum-chemical studies on base pairs or polyads to complete three-dimensional nucleic acid structures. One should realize, however, that there is a long way to go from results of quantum-chemical studies on building blocks to nucleic acid structure and function. The power of this approach is that it can help to separate the effects of different parts of the nucleic acid, such as backbone and bases, on the overall structure. In addition, it provides useful information on charge distribution and electrostatic potentials relevant for the determination of interaction sites with cations such as K, the most abundant cation in cells. Finally, the interaction energies can be studied in great detail. For example non-additive contributions can be determined. 

All these chiral structural standards and the corresponding families around them in proteins and nucleic acids represent, however, only the main building blocks upon which evolution has been operating. The colored loop- and knot-stretches and all the more disordered parts of protein and nucleic acid structural designs are of primary importance for the evolutionary aspects of informational and functional processings in our evolving life patterns. 

We begin with the structure and preparation of the 20 most coimnon amino acids, the building blocks of proteins. We then show how amino acids are linked by peptide bonds in the three-dimensional structure of hanoglobin and other polypeptides. Some proteins contain thousands of amino acids, but we shall see how to determine the sequence of amino acids in many polypeptides and synthesize these molecules in the laboratory. Finally, we consider how other polymers, the nucleic adds DNA and RNA, direct the synthesis of proteins in nature. 

Chirality is an essential property of life, which can be found throughout all biological self-assembled and self-organized architectures. Over many millennia nature has, through trial and error, learned how to utilize the chiral properties of the small building blocks, for example, amino acids and nucleic acids and how to express this structural property in a hierarchical process at the quaternary level. This expression of chirality at the quaternary level in turn... 

The basic structural unit of carbohydrates is the monosaccharide. Molecules in this class contain just one sugar moiety ahexose, pentose, or whatever. Monosaccharides are the building blocks of more complex carbohydrates in mnch the same sense that amino acids are the building blocks for proteins and nncleotides are the building blocks for nucleic acids. 

There is another point about the thermodynamic stability of prebiotic compounds. This is the fact that a series of thermodynamically very stable molecules seem to have been ignored in the course of prebiotic molecular evolution as building blocks of living structures. Take sugars, for example six-membered rings have not been used for the construction of nucleic acids, where only o-ribose takes the stage. Furthermore, only two types of purine and only two of the pyrimidine bases have been utilized among the many possible nucleic acids. Actually one could make a... 

If the terminal pyrophosphate is removed from a molecule of ATP, the remainder is AMP, adenosine monophosphate, one of the four building blocks of the important biological macromolecules, the nucleic acids. There are two types of nucleic acids (26) ribonucleic acid (RNA), and deoxyribonucleic acid (DNA). RNA is a polymer of four different nucleotides, one of which is AMP, the ribose phosphate of adenine. The other three nucleotides are also ribose phosphates of heterocyclic bases, guanine, cytosine, and uracil. The structure of the four bases is shown in Figure 6. 

Just as the amino acids, sugars, and nucleotides are the building blocks for formation of proteins, polysaccharides, and nucleic acids, these three kinds of macromolecule are the units from which larger subcellular structures are assembled. Fibers, microtubules, virus "coats," and small symmetric groups of subunits in oligomeric proteins all result from the packing of macromolecules in well-defined ways, something that is often called quaternary structure. 

Nucleotides are the building blocks of nucleic acids their structures and biochemistry were discussed in chapter 23. When a 5 -phosphomononucleotide is joined by a phosphodiester bond to the 3 -OH group of another mononucleotide, a dinucleotide is formed. The 3 -5 -linked phosphodiester intemucleotide structure of nucleic acids was firmly established by Lord Alexander Todd in 1951. Repetition of this linkage leads to the formation of polydeoxyribonucleotides in DNA or polyribonucleotides in RNA. The structure of a short polydeoxyribonucleotide is shown in figure 25.3. The polymeric structure consists of a sugar phosphate diester backbone with bases attached as distinctive side chains to the sugars. 

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