Primary structure, definition

In contrast, RNA occurs in multiple copies and various forms (Table 11.2). Cells contain up to eight times as much RNA as DNA. RNA has a number of important biological functions, and on this basis, RNA molecules are categorized into several major types messenger RNA, ribosomal RNA, and transfer RNA. Eukaryotic cells contain an additional type, small nuclear RNA (snRNA). With these basic definitions in mind, let s now briefly consider the chemical and structural nature of DNA and the various RNAs. Chapter 12 elaborates on methods to determine the primary structure of nucleic acids by sequencing methods and discusses the secondary and tertiary structures of DNA and RNA. Part rV, Information Transfer, includes a detailed treatment of the dynamic role of nucleic acids in the molecular biology of the cell. 

Disulfide bridges are, of course, true covalent bonds (between the sulfurs of two cysteine side chains) and are thus considered part of the primary structure of a protein by most definitions. Experimentally they also belong there, since they can be determined as part of, or an extension of, an amino acid sequence determination. However, proteins normally can fold up correctly without or before disulfide formation, and those SS links appear to influence the structure more in the manner of secondary-structural elements, by providing local specificity and stabilization. Therefore, it seems appropriate to consider them here along with the other basic elements making up three-dimensional protein structure. 

The development of technology for the isolation, fractionation, and purification of the principal polypeptides of VLDL, LDL, and HDL is undoubtedly a major achievement in the area of lipoprotein research. The availability of such polypeptides in pure form has permitted studies on their characterization and the definition of their chemical, physical, and immunological properties. The primary structure of many of these poly-... 

Originally, the caseins were defined as those phosphoproteins which precipitate from raw skim milk upon acidification to pH 4.6 at 20°C, and the individual families were identified by alkaline urea gel electrophoresis (Whitney et al 1976). With the resolution of their primary structure, it became possible to classify them according to their chemical structure, rather than on the basis of an operational definition. When one does this, it is apparent that not all of the caseins contain phosphorus (Table 3.1) some are also found in the acid whey after removal of the precipitated caseins. 

Peptides extracted from casein with N, N-dimethyl formamide have complex electrophoretic patterns identical to those of the fraction first prepared by Long and co-workers and called X-casein (El-Negoumy 1973). These peptides are identical electrophoretically to those released by the action of plasmin, which is present in fresh raw milk, upon asr casein (Aimutis and Eigel 1982). Two of these peptides have tryptic peptide maps and molecular weights identical to those of a pair of the peptides produced by plasmin degradation of asl-casein. These peptides appear to be fragments of a8l-casein which are present in milk as the result of plasmin proteolysis. More definitive information on their primary structure is needed before nomenclature for these fragments can be established. 

The ADSA Committee on Milk Protein Nomenclature (Eigel et al. 1984) presented a tentative nomenclature for the new enzyme membrane proteins. While the primary structures of these proteins have not been established, sufficient information exists to obtain an operational definition. The total protein complement of the membrane as observed is dependent upon the past history of the membrane from its formation to its analysis. Both the temperature and the time of storage before analysis can alter the membrane composition and physical state (Wooding 1971). In addition, plasmin has been shown to be associated with preparations of the membrane, and proteolytic products of the membrane protein have been observed in milk (Hoffman et al. 1979 Kanno and Yamauchi 1979). Therefore, one should use fresh warm raw milk for the study of the native MFGM protein. 

Using procedures such as those outlined in this section more than 100 proteins have been sequenced. This is an impressive accomplishment considering the complexity and size of many of these molecules (see, for example, Table 25-3). It has been little more than two decades since the first amino acid sequence of a protein was reported by F. Sanger, who determined the primary structure of insulin (1953). This work remains a landmark in the history of chemistry because it established for the first time that proteins have definite primary structures in the same way that other organic molecules do. Up until that time, the concept of definite primary structures for proteins was openly questioned. Sanger developed the method of analysis for N-terminal amino acids using 2,4-dinitrofluorobenzene and received a Nobel Prize in 1958 for his success in determining the amino-acid sequence of insulin. 

Proteins consist of a primary structure of amino acid residues connected in a definite sequence by peptide linkages to form polypeptide chains ... 

The definition of the primary structure of synaptotagmin-1, composed of an N-terminal transmembrane region and two C-terminal C2-domains (Figure 3), led... 

The complexity of quality control for proteins, as compared to small molecules, is most evident in the requirements for proof of structure. Many small molecules can be fully characterized using a few spectroscopic techniques (e.g., NMR, IR, mass spectrometry, and UV) in conjunction with an elemental analysis. However, proving the proper structure for a protein is much more complex because 1) the aforementioned spectroscopic techniques do not provide definitive structural data for proteins, and 2) protein structure includes not only molecular composition (primary structure) but additionally, secondary, tertiary, and, in some cases, quaternary features. Clearly, no single analytical test will address all of these structural aspects hence a large battery of tests is required. 

Up to now, we have discussed the primary structure of proteins. The primary structure is the covalently bonded structure of the molecule. This definition includes the sequence of amino acids, together with any disulfide bridges. All the properties of the protein are determined, directly or indirectly, by the primary structure. Any folding, hydrogen bonding, or catalytic activity depends on the proper primary structure. 

The most valuable confirmation of this view to date is, without doubt, to be found in the known structures of homologous proteins and peptide hormones, that is compounds of identical biological function isolated from different species. As is well known, the primary structures of the homologous insulins, corticotropins, hypertensins, posterior pituitary hormones, and heme peptide sequences from cytochromes c are closely similar and differ only at certain definite sites in the peptide chains. These can, in particular, serve as a useful point of departure in a search for more general principles governing protein structure, and in the comparison of different proteins. 

Gussow, D Rein, R., Ginjaar, I., Hochstenbach, F Seeman, G., Kottman, A., and Ploegh, H. L. (1987) The human beta2-microglobulin gene. Primary structure and definition of the transcriptional unit. J. Immunol. 139, 3132-3138. 

There are several other points of view regarding the definition of the nucleus of zeolite. For example, it was suggested that some primary structural units of the framework, such as rings and basic cages, could be defined as the nucleus of zeolites and other microporous crystals. It was also proposed that the nucleus of zeolite could be defined as particles with critical size. These particles should be stable under crystallization conditions. Compared with the classical theory of nucleation from homogeneous solution, the theory developed by Pope could well explain the significant decrease of the free-energy barrier of nucleation for zeolites and other microporous compounds.[43] This... 

In conclusion, it can be seen that the primary structure of the unusual oligosaccharides of the cell envelope of mycobacteria is reasonably well understood, although a number of questions need to be resolved. The biosynthesis of these polymers is much less well defined but current studies are rapidly closing the gap. Oddly, it is the definition of the ultrastructure of the mycobacterial cell envelope and reconciling the data with the known chemistry that seems to present the greatest challenge in understanding the mycobacterial cell envelope. 

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