Biochemistry Nucleic acids

In Chapter 1 we saw that a major achievement of the first half of the twentieth cen tury was the picture of atomic and molecular structure revealed by quantum mechan ICS In this the last chapter we examine the major achievement of the second half of that century—a molecular view of genetics based on the structure and biochemistry of nucleic acids... 

This chapter lists some representative examples of biochemicals and their origins, a brief indication of key techniques used in their purification, and literature references where further details may be found. Simpler low molecular weight compounds, particularly those that may have been prepared by chemical syntheses, e.g. acetic acid, glycine, will be found in Chapter 4. Only a small number of enzymes and proteins are included because of space limitations. The purification of some of the ones that have been included has been described only briefly. The reader is referred to comprehensive texts such as the Methods Enzymol (Academic Press) series which currently runs to more than 344 volumes and The Enzymes (3rd Edn, Academic Press) which runs to 22 volumes for methods of preparation and purification of proteins and enzymes. Leading referenees on proteins will be found in Advances in Protein Chemistry (59 volumes. Academic Press) and on enzymes will be found in Advances in Enzymology (72 volumes, then became Advances in Enzymology and Related Area of Molecular Biology, J Wiley Sons). The Annual Review of Biochemistry (Annual Review Inc. Patio Alto California) also is an excellent source of key references to the up-to-date information on known and new natural compounds, from small molecules, e.g. enzyme cofactors to proteins and nucleic acids. 

The first dynamical simulation of a protein based on a detailed atomic model was reported in 1977. Since then, the uses of various theoretical and computational approaches have contributed tremendously to our understanding of complex biomolecular systems such as proteins, nucleic acids, and bilayer membranes. By providing detailed information on biomolecular systems that is often experimentally inaccessible, computational approaches based on detailed atomic models can help in the current efforts to understand the relationship of the strucmre of biomolecules to their function. For that reason, they are now considered to be an integrated and essential component of research in modern biology, biochemistry, and biophysics. 

One of the most important and exciting advances in modern biochemistry has been the application of spectroscopic methods, which measure the absorption and emission of energy of different frequencies by molecules and atoms. Spectroscopic studies of proteins, nucleic acids, and other biomolecules are providing many new insights into the structure and dynamic processes in these molecules. 

P. Berg (Stanford) the biochemistry of nucleic acids, with particular regard to recombinant-DNA. 

Bentin T., Nielsen P. E. Enhanced peptide nucleic acid binding to supercoiled DNA possible implications for DNA breathing dynamics. Biochemistry 1996 35 8863-8869. 

Kaihatsu K., Braasch D.A., Cansizo-GLU A., Corey D.R. Enhanced strand invasion by peptide nucleic acid-peptide conjugates. Biochemistry 2002 41 11118-11125. 

Lee R., Kaushik N., Modak M.J., Vi-NAYAK R., Pandey V. N. Polyamide nucleic acid targeted to the primer binding site of the HlV-1 RNA genome blocks in vitro HlV-1 reverse transcription. Biochemistry 1998 37 900-910. 

Karras J.G., Maier M.A., Lu T, Watt A., Manoharan M. Peptide nucleic acids are potent modulators of endogenous pre-mRNA splicing of the murine inter-leukin-5 receptor-alpha chain. Biochemistry 2001 40 7853-7859. 

Belotserkovskii B.P., Zarling D.A. Peptide nucleic acid (PNA) facilitates multistranded hybrid formation between linear double-stranded DNA targets and RecA protein-coated complementary single-stranded DNA probes. Biochemistry 2002 41 3686-3692. 

C. G., Janowski B.A., Corey D. R. Inhibition of gene expression inside cells by peptide nucleic acids effect of mRNA target sequence, mismatched bases, and PNA length. Biochemistry 2001 40 53-64. 

Adams RLP, Knowler JT, Leader DP The Biochemistry of the Nucleic Acids, 11th ed. Chapman Hall, 1992. 

The discovery of the base-paired, double-helical structure of deoxyribonucleic acid (DNA) provides the theoretic framework for determining how the information coded into DNA sequences is replicated and how these sequences direct the synthesis of ribonucleic acid (RNA) and proteins. Already clinical medicine has taken advantage of many of these discoveries, and the future promises much more. For example, the biochemistry of the nucleic acids is central to an understanding of virus-induced diseases, the immune re-sponse, the mechanism of action of drugs and antibiotics, and the spectrum of inherited diseases. 

In the version of evolutionary theory popularised by Dawkins (1976), the fundamental unit of life is a gene, a conceptual abstraction clothed in the biochemistry of the nucleic acid DNA. The purpose, or telos, of this gene is replication - to make copies of itself - copies which because of random chemical and physical processes maybe more or less accurate. The particular chemical structure of DNA provides a mechanism whereby such faithful copying can readily occur - as James Watson and Francis Crick pointed out... 

Wyman TB, Nicol F, Zelphati O, ScariaPV, Plank C, Szoka FC (1997) Design, synthesis, and characterization of a cationic peptide that binds to nucleic acids and permeabilizes bilayers. Biochemistry 36 3008-3017... 

Cimino, C.P., Camper, H.B., Isaacs, S.T., and Hearst, J.E. (1985) Psoralens as photoactive probes of nucleic acid structure and function Organic chemistry, photochemistry, and biochemistry. Annu. Rev. Biochem. 54, 1151-1193. 

Metz, D.H., and Brown, G.L. (1969) The investigation of nucleic acid secondary structure by means of chemical modification with a carbodiimide reagent. I. The reaction between N-cyclohexyl-N -b-(4-methylmorpholinium)ethyl carbodiimide and model nucleotides. Biochemistry 8, 2312-2328. 

Rosenberg, M., Wiebers, J.L., and Gilham, P.T. (1972) Interactions of nucleotides, polynucleotides, and nucleic acids with dihydroxyboryl-subsdtuted celluloses. Biochemistry 11, 3623-3628. 

Figure 2.16 Orientations found in DNA helices. (Adapted with permission from Figure 2.11 of Saenger, W. Principles of Nucleic Acid Structure, Springer-Verlag, New York, 1984 copyright 1984, Springer-Verlag, New York and Figure 1.22 A, B, C of Cowan, J. A. Inorganic Biochemistry, An Introduction, 2nd ed., Wiley-VCH, New York, 1997. Copyright 1997, Wiley-VCH.)...

Equation 4.9 has been extensively applied to study the mechanisms of electrophilic (e.g., protonation) reactions, drug-nucleic acid interactions, receptor-site selectivities of pain blockers as well as various other kinds of biological activities of molecules in relation to their structure. Indeed, the ESP has been hailed as the most significant discovery in quantum biochemistry in the last three decades. The ESP also occurs in density-based theories of electronic structure and dynamics of atoms, molecules, and solids. Note, however, that Equation 4.9 appears to imply that p(r) of the system remains unchanged due to the approach of a unit positive charge in this sense, the interaction energy calculated from V(r) is correct only to first order in perturbation theory. However, this is not a serious limitation since using the correct p(r) in Equation 4.9 will improve the results. 

Electrophoresis is for separating ions, since only ions will migrate under the influence of an electric field, negative ions to the positive electrode and positive ions to the negative electrode. Scientists have found electrophoresis especially useful in biochemistry experiments in which charged amino acid molecules and other biomolecules need to be separated. Thus, application to protein and nucleic acid analysis has been popular (see Chapter 16). 

Radioactive isotopes provide a very convenient way of monitoring the fate or metabolism of compounds that contain the isotopes. When used in this way, the isotope is described as a tracer and compounds into which the radioactive atom has been introduced are said to be labelled or tagged. The labelled molecules need only comprise a very small proportion of the total amount of the unlabelled radioactive substance because they act in the same way as the non-radioactive substance but can be detected very much more easily. The varied applications of tracers in biochemistry range from studies of metabolism in whole animals or isolated organs to sensitive quantitative analytical techniques, such as radioimmunoassay. Phosphorus-32 is used in work with nucleic acids, particularly in DNA sequencing and hybridization techniques. In these instances the isotope is used as a means of visualizing DNA separations by autoradiographic techniques. 

Davidson, J.N. (1950). The Biochemistry of the Nucleic Acids. Methuen, London. Dixon, M. Webb, E.C. (1958). The Enzymes. Longmans, Green Co., London. Ferdinand, W.H. (1976). The Enzyme Molecule. Wiley Sons. 

F. Brun, J. J. Toulme, and C. Helene, Interactions of aromatic residues of proteins with nucleic acids. Fluorescence studies of the binding of oligopeptides containing tryptophan and tyrosine residues to polynucleotides, Biochemistry 14, 558-563 (1975). 

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