Biological macromolecules nucleic acids

Like most other types of biological macromolecules, nucleic acids adopt highly organized three-dimensional structures. The dominant factors that determine nucleic acid... 

This part of the chapter focuses on the interactions of Cr complexes in various oxidation states with biological macromolecules (nucleic acids, proteins, and... 

Abstract Replication is a fundamental process that is critical to life as we know it. While replication today is carried out by complex biochemical machineries that have been evolving for bilhons of years, it must have originated with relatively small molecules in simple systems. Here we explore this concept, focusing on the physicochemical characteristics and prebiotic potential of two classes of biological macromolecules nucleic acids and lipids. We discuss the informational and catalytic capabilities of DNA and RNA, the thermodynamic limits of information transfer, the structure and function of lipid membranes, and the formation and maintenance of primitive protocells . 

The unique properties of oligonucleotides create crosslinking options that are far different from any other biological molecule. Nucleic acids are the only major class of macromolecule that can be specifically duplicated in vitro by enzymatic means. The addition of modified nucleoside triphosphates to an existing DNA strand by the action of polymerases or transferases allows addition of spacer arms or detection components at random or discrete sites along the chain. Alternatively, chemical methods that modify nucleotides at selected functional groups can be used to produce spacer arm derivatives or activated intermediates for subsequent coupling to other molecules. 

Biological macromolecules amino acids proteins nucleic acids... 

Molecular biology also involves organic chemistry, physics, and biophysical chemistry as it deals with the physicochemical structure of macromolecules (nucleic acids, proteins, lipids, and carbohydrates) and their interactions. Genetic materials including DNA in most of the living forms or RNA (ribonucleic acid) in all plant viruses and in some animal viruses remain the subjects of intense study. 

The current chapter focuses on soft materials based on the main types of biological molecules and macromolecules - lipids, proteins, nucleic acids and polysaccharides. The fascinating topics of biological motors, nucleic acid replication machinery and other systems, known collectively as bionanomachines, is only briefly touched on in the final section. 

Owing to their inherent structural and biological properties, nucleic acids are fascinating macromolecules. Indeed, deoxyribonucleic acid (DNA) exhibits an incomparable capability for molecular recognition and plays a crucial role in heredity mechanisms as well as protein synthesis. However, a current focus of... 

PDB files were designed for storage of crystal structures and related experimental information on biological macromolecules, primarily proteins, nucleic acids, and their complexes. Over the years the PDB file format was extended to handle results from other experimental (NM.R, cryoelectron microscopy) and theoretical methods... 

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.)... 

The overall scope of this book is the implementation and application of available theoretical and computational methods toward understanding the structure, dynamics, and function of biological molecules, namely proteins, nucleic acids, carbohydrates, and membranes. The large number of computational tools already available in computational chemistry preclude covering all topics, as Schleyer et al. are doing in The Encyclopedia of Computational Chemistry [23]. Instead, we have attempted to create a book that covers currently available theoretical methods applicable to biomolecular research along with the appropriate computational applications. We have designed it to focus on the area of biomolecular computations with emphasis on the special requirements associated with the treatment of macromolecules. 

This volume thus presents a current and comprehensive account of computational methods and their application to biological macromolecules. We hope that it will serve as a useful tool to guide future investigations of proteins, nucleic acids, and biological membranes, so that the mysteries of biological molecules can continue to be revealed. 

All biological organisms have the ability to reproduce themselves. The instructions for self-replication are stored and transmitted by macromolecules called nucleic acids. There are two types of nucleic acids, one that stores genetic information and one that transmits the information. Genetic information is stored in molecules of deoxyribonucleic... 

Synthetic examples include the poly(meth)acrylates used as flocculating agents for water purification. Biological examples are the proteins, nucleic acids, and pectins. Chemically modified biopolymers of this class are carboxymethyl cellulose and the lignin sulfonates. Polyelectrolytes with cationic and anionic substituents in the same macromolecule are called polyampholytes. 

Fasman, G. D. (Ed.), Prediction of Protein Structure and the Principles of Protein Conformation, Plenum Press, New York 1989 Jurnak, F., and A. McPherson (Eds), Biological Macromolecules and Asembliesy Vol. 2, Nucleic Acids and Interactive Proteins, John Wiley Sons, New York, 1985. 

Molecular biology involves the study of the major macromolecules, DNA, RNA, and protein. The central dogma ofmolecular biology is illustrated in Fig. 2. The central dogma shows the relationship among the macromolecules in the processes of transcription and translation. Figure 2 also gives the relationship between immunoelectron microscopy and in situ hybridization. In situ hybridization allows one to localize a specific nucleic acid sequence. Immunoelectron microscopy is an essential component to the technique of in situ hybridization when applied at the EM level. 

Protein Data Bank (http //www.rcsb.org/pdb), international repository of experimentally resolved stmctures of biological macromolecules (proteins, nucleic acids, viruses), including anotations. 

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