Proteins, structure primary

Proteins are built from a-amino acid monomer units of the type H2N CH. (R) COOH which are linked together by an amide (peptide) bond. They are formed by elimination of water from adjacent 

Form Glucose Units Outer Diameter (A) Cavity Volume mw (A ) Solubility g/cm RT mw (A) Torus Height (A) 

Although almost any a-amino acid might be used, natural proteins are constructed from only about 20 different amino acids, and the group R is never very large (Table 10.7). The nature and sequence of these amino acids determines the primary (chemical) structure of the protein. A shorthand notation is frequently used to portray this primary structure as, for example, in 

In addition to the 20 amino acids in Table 10.7, which are widely distributed in all natural proteins, a few other amino acids occur, often in significant concentration, but only in a few varieties. These include hydroxylysine (10.39a) and hydroxyproUne (10.39b). 

Apart from glycine, the amino acids in Table 10.7 all contain an asymmetric C atom and can exist in left-handed and right-handed forms. Natural amino acids almost always exist in the left- 

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Fi.sieh, Y. L., et al., 1996. Automated analytical. sy.stem for the examination of protein primary. structure. Analytical Chemistry 68 455-462. An analyti-... 

Protein primary structure databases include the following ExPASy Molecular Biology Server (Swiss-Prot) expasy.ch/ Protein Information resources (PIR) pir.georgetown.edu Protein Research Foundation (PRF) prf.or.jp/en/os.html. 

While these stages I-IV represent generic processes applying to all food proteins, it is significant to note that even small differences in the protein primary structure can sometimes cause major changes in functionality (Wilde, 2000). For example, the genetic variants A and B of P-... 

The differences in primary structure can be especially informative. Each protein has a distinctive number and sequence of amino acid residues. As we shall see in Chapter 4, the primary structure of a protein determines how it folds up into a unique three-dimensional structure, and this in turn determines the function of the protein. Primary structure is the focus of the remainder of this chapter. We first consider empirical clues that amino acid sequence and protein function are closely linked, then describe how amino acid sequence is determined finally, we outline the many uses to which this information can be put. 

Various procedures are used to analyze protein primary structure. Several protocols are available to label and identify the amino-terminal amino acid residue (Fig. 3-25a). Sanger developed the reagent l-fluoro-2,4-dinitrobenzene (FDNB) for this purpose other reagents used to label the amino-terminal residue, dansyl chloride and dabsyl chloride, yield derivatives that are more easily detectable than the dinitrophenyl derivatives. After the amino-terminal residue is labeled with one of these reagents, the polypeptide is hydrolyzed to its constituent amino acids and the labeled amino acid is identified. Because the hydrolysis stage destroys the polypeptide, this procedure cannot be used to sequence a polypeptide beyond its amino-terminal residue. However, it can help determine the number of chemically distinct polypeptides in a protein, provided each has a different amino-terminal residue. For example, two residues—Phe and Gly—would be labeled if insulin (Fig. 3-24) were subjected to this procedure. 

The primary structure of a peptide or protein is defined by the sequence of amino acids. In this experiment the procedures that are in common use to determine protein primary structure are applied to an unknown dipeptide. Amino acid composition of the peptide will be determined by acid hydrolysis followed by HPLC, CE, or paper chromatography. The identity of the NH2-terminal amino acid will be achieved by the dansyl method followed by thin-layer chromatography. 

R Garrett and C Grisham, Biochemistry, 2nd ed (1999), W B Saunders (Orlando, FL), pp 107-152 Protein primary structure... 

A major problem, until recently, was the determination of the protein primary structure, but with the advent of modern analysis of DNA this has become comparatively easy. One of the first structures to be described was that of insulin which contains 60 amino-acids and has a molecular weight of 12,000. Once the primary structure is known, it is possible to predict the secondary and tertiary structures using additional information obtained through X-ray crystallography of the crystallised protein. 

Fig. 5.A2. Protein primary structure. The amino-acid sequence of ox insulin...

National Biomedical Research Foundation specializes in providing a database for protein primary structure. This database contains all the information from the Atlas of Protein Sequence and Structure edited by M.O. Dayhoff. In this database proteins are categorized according to their super family grouping. In addition to the primary structure information, detailed descriptions of proteins, including active site, prosthetic group, etc., are included. 

Direct protein sequencing, by the methods discussed above (Sects. 5.1.5 and 5.1.6), is the preferred route to primary structure. It is now widely accepted that an indirect approach, via the sequence of cloned cDNA is also appropriate, and possibly easier. It does need to be established, however, that the protein primary structure is not affected by tissue specific mRNA processing (splicing or editing) or by post-translational modification such as N- or C-terminal processing or protein splicing. 

Y. L. Hsieh, H. Wang, C. Ehcone, J. Mark, S. A. Martin, and E. Regnier, Automated analytical system for the examination of protein primary structure, Anal. Chem. 68(3) 455 (1996). 

Biochemists have distinguished several levels of the structural organization of proteins. Primary structure, the amino acid sequence, is specified by genetic information. As the polypeptide chain folds, it forms certain localized arrangements of adjacent amino acids that constitute secondary structure. The overall three-dimensional shape that a polypeptide assumes is called the tertiary structure. Proteins that consist of two or more polypeptide chains (or subunits) are said to have a quaternary structure. 

The polypeptide chain of a protein folds systematically into a specific three-dimensional structure (72). There are various levels of structure in such a folded protein. Primary structure refers to the amino acid sequence, secondary structure is any regular local structure of a segment of a polypeptide chain, while tertiary structure is the overall topology of the folded polypeptide chain. Quaternary structure describes the aggregation of folded polypeptides with each other by means of specific interactions, such as the aggregation of subunits to give a complete protein molecule. 

Protein Primary Structure Can Be Determined by Chemical Methods and from Gene Sequences... 

Figure 1.84 Schematic of translation. The mRNA codons are read and converted from nucleoside sequences to protein primary structure by means of cognate aminoacyl-tRNAs. All mRNA codons are translated at a ribosome (prepared from rRNA) that has two cognate aminoacyl-tRNA binding sites P (peptidyl) and A (aminoacyl). All tRNAs are "adaptors" that can bind a particular mRNA codon through their anticodon loop, using Watson-Crick base pairing, and also associate covalently with the appropriate amino acid residue coded for by the corresponding mRNA codon When two cognate aminoacyl-tRNA molecules bind mRNA in P and A sites (a), then both are close enough for peptide link formation to take place with the emergence of a peptide chain (b). As amino acyl tRNA molecules continue to dock sequentially onto mRNA codons (in the direction 5 (c), and amino acid residues continue to be added (W —> C ) (d),...

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