Biomolecules families

Part One into practical applications of fractionating specific groups of biological macromolecules. The general format of these chapters is a brief discussion of the chemical and biological properties of the biomolecule family, followed by detailed HPLC methods that have been used suceessfiilly for their analysis. Part Three addresses detection methods that are especially suited for qualitatively and quantitatively analyzing the complex mixtures and minute quantities encountered in biochemistry. 

In terms of their molecular structures, the nucleotide and protein realms are usually considered to be rather independent of each other. However, these two families of molecules are covalently linked in the translational aminoacyl- RNAs and ribonucleoproteins as well as in the nucleoproteins involved in cellular and viral replication. In these hybrid biomolecules, a (deoxy)ribose phosphate moiety serves as the structural connection between the nucleoside and peptide moieties. 

There is, therefore, a need for original coxibs, and one might think to look into the medicinal flora of Asia and the Pacific, as an increasing body of evidence suggests the families Apocynaceae, Clusiaceae, Asteraceae, Polygonaceae, Lamiaceae, and Con-volvulaceae to elaborate ast sources of biomolecules which are able to inhibit the enzymatic activity of COX. 

As A. and B. Pullman showed more than 40 years ago, the purine base adenine occupies a unique situation in the purine family in comparison to the other purines, it has the greatest resonance energy per -electron, i.e., it is more stable, and thus likely to have been incorporated preferentially into biomolecules (Pullman, 1972). 

Direct labeling of a biomolecule involves the introduction of a covalently linked fluorophore in the nucleic acid sequence or in the amino acid sequence of a protein or antibody. Fluorescein, rhodamine derivatives, the Alexa, and BODIPY dyes (Molecular Probes [92]) as well as the cyanine dyes (Amersham Biosciences [134]) are widely used labels. These probe families show different absorption and emission wavelengths and span the whole visible spectrum (e.g., Alexa Fluor dyes show UV excitation at 350 nm to far red excitation at 633 nm). Furthermore, for differential expression analysis, probe families with similar chemical structures but different spectroscopic properties are desirable, for example the cyanine dyes Cy3 and Cy5 (excitation at 548 and 646 nm, respectively). The design of fluorescent labels is still an active area of research, and various new dyes have been reported that differ in terms of decay times, wavelength, conjugatibility, and quantum yields before and after conjugation [135]. New ruthenium markers have been reported as well [136]. 

A new member of the family of nonheme diiron enzymes recently discovered is called rubrerythrin. This metaUoprotein is formally classified as an oxidoreductase (rubredoximoxygen oxidoreductase). The diiron(III,in) active site structure is displayed in Figure 2(f). This biomolecule possesses two histidines coordinated to one iron and one histidine coordinated to the second iron. A carboxylate bridges the two irons and there are carboxylate ligands also coordinated to each iron. The purpose of this enzyme in the strict anaerobe is to safely reduce oxygen to water. 

Biomolecules are organic compounds found in biological systems. Many are relatively small, with molecular weights of less than 1000 g/mol. There are four main families of these small molecules—simple sugars, nucleotides, amino acids, and lipids. Many simple biomolecules are used to synthesize larger compounds that have important cellular functions, as shown in Figure 3.9. 

Starch and cellulose are two polymers that belong to the family of biomolecules called carbohydrates (Figure 5.1). 

Molecular topology [155-158,190-199] presents a systematic framework for general shape analysis methods applicable, in principle, to all molecules. The same framework is also the basis for special shape analysis methods designed to exploit the typical features of some special, distinguished molecular families, such as the folding properties of polypeptides, proteins, and other chain biomolecules. Molecular topology and the associated topological shape analysis approaches form the basis of the present book. 

Biomolecules such as proteins and oligonucleotides present mass spectra that are complicated by the presence of multiply charged families of ions. The parent species, for example, generated by a soft ionization method such as FAB of ESI, will yield several m/z peaks in which m is equal to a constant plus (protein) or minus (nucleic acid) a variable number of proton masses, while z is a variable. Egg white lysozyme, for example, yields ESI-mass spectra with fine parent peaks between m/z values of 1194 and 1791 the corresponding z values are 12-8 [see Fig. 15.9(a)]. 

Larger analytes with more protonation-deprotonation sites yield larger families of peaks for each fragment, and the overlap of mlz ranges for different fragment families can further complicate the spectra of biomolecules. For this reason, soft ionization methods, that produce few fragments, are particularly useful for biomolecule MS. 

Mass cytometry uses stable isotopes as lanthanide series because of the huge number of elements of this family and their similar chemical structure, allowing their incorporation into the same tag (45,46). They also exhibit very low background due to their intrinsic low natural abundance (45-47). These rare earth elements are relatively biocompatible and easily conjugated to biomolecules by broad availability and simple protocols. Finally, they proffer high sensitivity for traces of molecules in biological samples, being attractive markers for their use in the clinical routine (47). 

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