Protein special categories

Even though cholesterol (substituted by other sterols in plants) is chemically classified as a lipid, the molecule is better grouped it into a special category, which is distinct from membrane proteins and (phospho- and sphingo-) lipids, when discussing its role in biomembrane stmcture and function. Cholesterol constitutes between 25% and 40% of the total lipid plus cholesterol fraction of most typical cell membranes. These numbers translate into a 33-66% fraction of the noncholesterol lipids, or considering its smaller size, about a 10-20%... 

Proteoglycan Special category of glycoproteins in which the saccharide chain is covalently linked to protein via an initiating xylose residue, a specific core oligosaccharide, and is followed by a glycosaminoglycan chain. 

Except the special case of large particles and proteins that enter the cell by endocy-tosis [19], the transport of molecules across biomembranes can be divided into two categories [20] active and passive transport. 

The protein sequence databases are the most comprehensive source of information on proteins. The goal of this chapter is to describe the different protein sequence databases available to researchers. It is necessary to distinguish between universal databases that cover proteins from all species and specialized data collections that store information about specific families or groups of proteins, or about the proteins of a specific organism. Two categories of universal protein sequence databases can be discerned simple archives of sequence data and annotated databases in which additional information has been added to the sequence record. The next section describes the Protein Information Resource (PIR), the oldest protein sequence database SWISS-PROT, an annotated universal sequence database and TrEMBL, the supplement of... 

There are many specialized protein sequence databases. Some of them are quite small and contain only a handful of entries others are wider in scope and larger in size. This section describes three examples of specialized protein sequence databases. As this category of databases is quite changeable, any list provided here would soon be outdated. However, under the URL http //www.expasy.ch/alinks.html Proteins is a www document that lists information sources for molecular biologists that is continually update. 

The fourth category of protein assay is amino acid analysis. This method is the most accurate and robust method for determination of protein concentration, but is appropriate only for pure proteins. In addition, it is relatively slow and requires specialized instrumentation and knowledge of the target protein s theoretical amino acid composition. 

A FIGURE 2-13 The 20 common amino acids used to build proteins. The side chain (R group red) determines the characteristic properties of each amino acid and is the basis for grouping amino acids into three main categories hydrophobic, hydrophilic, and special. Shown are the ionized forms that exist at the pH (=7) of the cytosol. In parentheses are the three-letter and one-letter abbreviations for each amino acid. 

The axons of neurons appear to have special transport processes for moving molecules into and out of the cell body (soma). The presence of special transport mechanisms in these cells is essential for their function, since neurons vary greatly in size, with some extending over 1 m, while protein synthesis occurs predominantly in the soma. Transport rates for different solutes occur in two categories slow (1-lOmm/day) and fast (100-400mm/day), and occur in the anterograde (away from the cell body) and retrograde (toward the cell body) directions. The speed of the slow processes is consistent with rates of diffusion, but the fast processes require additional mechanisms [9, 128]. 

Different sites could specialize in the hydrolysis of different categories of peptide bonds (e.g., those that join hydrophobic/hydrophilic, hydrophobic/hydrophobic, or hy-drophilic/hydrophilic amino acids, etc.) and thereby optimize the overall kinetics of degrading diverse protein sequences. 

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