Biomolecules classification

Karakoc, E., Cherkasov, A., and Sahinalp, S.C. (2006) Distance based algorithms for small biomolecule classification and structural similarity search. Bioinformatics 15,243-251. 

IUPAC classification, mesoporous materials are defined as porous materials with diameters in the range 2-50 nm, which is rather dose to the dimensions of functional biomolecules such as proteins. Therefore, unexplored phenomena and functions could be observed for biomolecules confined in mesopore channels due to their restricted motion and orientation. In this chapter, we briefly introduce recent developments on the immobilization of biomolecules in mesoporous media, where the use of mesoporous silica and mesoporous carbon are mainly discussed. 

The molecules that form the foundation of living systems are often organized into four categories. They are the primary metabolites nucleic acids, proteins, carbohydrates, and lipids. The categories can be grouped together in different ways, based on features that they have in common. For example, nucleic acids, proteins, and polysaccharides are polymeric. Nucleic acids and proteins are further related because they are templated polymers. Other classification systems are also possible.1 Interest in the development of size-expanded versions of biomolecules has grown over the past... 

Lipids, relatively nonpolar chemical substances found in plant, bacterial, and animal cells, are among the most ubiquitous of biomolecules. In this experiment, a lipid extract of ground nutmeg will be purified by chromatography on a silica gel column. Analysis of the lipid extract by thin-layer chromatography will provide the classification of the components in the extract. The unknown lipids will be further characterized by saponification and analysis of the fatty acid content by gas chromatography. For an abbreviated experiment, students may be provided samples of natural oils and fats that can be analyzed by saponification and gas chromatography. 

Regarding the functionality and structural perfection of biomolecules as the ultimate objective of supramolecular and macromolecular chemistry, it can be easily anticipated that the current situation is an intermediate state. Supramolecular chemistry will include the formation of structurally more flexible molecular assemblies of increased size, while macromolecular chemists will develop new means of approaching the structural exactness of biomolecules and low molecular weight chemistry ultimately leading to standards where the traditional classifications in chemistry will become obsolete. 

Under what circumstances is a biomolecule classified as a lipid Is the classification based on a particular characteristic structure or on some physical property ... 

The reactions of biomolecules can be described by the methods of organic chemistry, which requires the classification of compounds according to their fimctional groups. The reactions of molecules are based on the reactions of their respective functional groups. 

Vitamins are a chemically and functionally inhomogeneous group of biomolecules. As a gross classification distinction is usually made between (1) fat-soluble and (2) water-soluble vitamins. Owing to their insolubility in water the fat-soluble vitamins A, D, E, and K can be accumulated in fat tissue and excessive intake causes hypervitaminoses. The water-soluble vitamins - vitamin Bj, vitamin B2, niacin, vitamin Bg, folic acid, pantothenic acid, biotin, vitamin B12, and ascorbic acid - can generally only be stored in a small amount and intake exceeding actual need is excreted in the urine. 

Also in chemistry artificial neural networks have found wide use. They have been used to fit spectroscopic data, to investigate quantitative structure-activity relationships (QSAR), to predict deposition rates in chemical vapor deposition, to predict binding sites of biomolecules, to derive pair potentials from diffraction data on liquids, " to solve the Schrodinger equation for simple model potentials like the harmonic oscillator, to estimate the fitness function in genetic algorithm optimizations, in experimental data analysis, to predict the secondary structure of proteins, to predict atomic energy levels, " and to solve classification problems from clinical chemistry, in particular the differentiation between diseases on the basis of characteristic laboratory data. ... 

The large number of independent variables for biomolecules, in particular, warrants their classification as large-.scale and rules out the u.se of many algorithms that are effective for a small number of variables. However, as will be discus.sed, effective techniques are available today that achieve rapid convergence even for large systems. In practice, these optimization algorithms must be modest in storage requirements for macromolecular applications and economical in computations, which are dominated by the function and derivative evaluations. 

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