Nucleic acids Macromolecules with secondary structure

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

Nucleic acids, proteins, some carbohydrates, and hormones are informational molecules. They carry directions for the control of biological processes. With the exception of hormones, these are macromolecules. In all these interactions, secondary forces such as hydrogen bonding and van der Waals forces, ionic bonds, and hydrophobic or hydrophilic characteristics play critical roles. Molecular recognition is the term used to describe the ability of molecules to recognize and interact bond—specifically with other molecules. This molecular recognition is based on a combination of the interactions just cited and on structure. 

Bioactive macromolecules like peptides, proteins, and nucleic acids have been successfully embedded in planar LbL films. An important question is the retention of the bioactivity of the film-embedded biomolecules. The structural properties and stability of the LbL films formed from synthesized polypeptides of various amino acid sequences were recently reported [50]. The authors showed that control over the amino acid sequence enables control over non-covalent interpolypeptide interaction in the film, which determines the film properties. Haynie and coworkers showed by circular dichroism spectroscopy that the extent of adsorption of poly(L-glutamic acid) (PGA) and poly(L-lysine) (PLL) in the LbL films scales with the extent of secondary structure of the polypeptides in solution [51]. Boulmedais demonstrated that the secondary structure of the film composed of these polypeptides is the same as the peptide structure in the complex formed in solution [52], as found by Fourier transform IR spectroscopy (FUR). 

Important differences between DNA and RNA appear in their secondary and tertiary structures, and so we shall describe these structural features separately for DNA and for RNA. Even though nothing in nucleic acid structure is directly analogous to the quaternary structure of proteins, the interaction of nucleic acids with other classes of macromolecules (for example, proteins) to form complexes is similar to the interactions of the subunits in an oligomeric protein. One well-known example is the association of RNA and proteins in ribosomes (the polypeptide-generating machinery of the cell) another is the self-assembly of tobacco mosaic virus, in which the nucleic acid strand winds through a cylinder of coat-protein subunits. 

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