The primary structure of proteins

Proteins are biopolymers composed of many amino acids connected to one another through amide (peptide) bonds. They play numerous roles in biological systems. Some proteins are major components of structural tissue (muscle, skin, nails, and hair). Others transport molecules from one part of a living system to another. Yet others serve as catalysts for the many biological reactions needed to sustain life. 

In the remainder of this chapter, we will describe the main features of peptide and protein structure. We will first examine what is called the primary structure of peptides and proteins that is, how many amino acids are present and what their sequence is in the peptide or protein chain. We will then examine three-dimensional aspects of peptide and protein structure, usually referred to as their secondary, tertiary, and quaternary structures. 

The backbone of proteins is a repeating sequence of one nitrogen and two carbon atoms. 

Things we must know about a peptide or protein, if we are to write down its structure, are (1) which amino acids are present and how many of each there are and (2) the sequence of the amino acids in the chain. In this section, we will briefly describe ways to 

The primary structure is quite simply the order in which the individual amino acids making up the protein are linked together through peptide bonds (Fig. 3.1). 

The 20 common amino acids found in man are listed below and the structures are shown in Appendix 1. 

The primary structure of Met-enkephalin (one of the body s own painkillers) is shown in Fig. 3.2. 

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FIGURE 5.8 Two structural motifs that arrange the primary structure of proteins into a higher level of organization predominate in proteins the a-helix and the /3-pleated strand. Atomic representations of these secondary structures are shown here, along with the symbols used by structural chemists to represent them the flat, helical ribbon for the a-helix and the flat, wide arrow for /3-structures. Both of these structures owe their stability to the formation of hydrogen bonds between N—H and 0=C functions along the polypeptide backbone (see Chapter 6). 

A new chapter on the primary structure of proteins, which provides coverage of both classic and newly emerging proteomic and genomic methods for identifying proteins. A new section on the appHcation of mass spectrometry to the analysis of protein structure has been added, including comments on the identification of covalent modifications. 

The primary structure of proteins is not the whole story. To really understand how proteins work, we have got to understand them as three-dimensional objects. So on to higher dimensions in the next chapter. But first, a few paragraphs about another role for the protein amino acids biosynthesis. 

The primary structure of proteins determines the three-dimensional or tertiary structure. 

In all living cells, DNA serves to store genetic information. Specific segments of DNA ( genes ) are transcribed as needed into RNAs, which either carry out structural or catalytic tasks themselves or provide the basis for synthesizing proteins (see p.82). In the latter case, the DNA codes for the primary structure of proteins. The language used in this process has four letters (A, G, C, and T). All of the words ( codons ) contain three letters ( triplets ), and each triplet stands for one of the 20 proteinogenic amino acids. 

Like all fats, milk fat provides lubrication. They impart a creamy-mouth feel as opposed to a dry texture. Fat globules produce a shortening effect in cheese by keeping the protein matrix extended to give a soft texture. Milk proteins are one of the most important constituents. The primary structure of proteins consists of... 

The sequence of amino acids in a protein is called the primary struc ture of the protein. Understanding the primary structure of proteins is important because many genetic diseases result in proteins with abnor mal amino acid sequences, which cause improper folding and loss or impairment of normal function. If the primary structures of the normal and the mutated proteins are known, this information may be used to diagnose or study the disease. 

W. A. Schroeder, The Primary Structures of Proteins, Harper and Row, New York, 1968. 

The amino-acids that make up the primary structure of proteins will change their charge when the pH of the solution is altered due to their acid-base properties (Section 5.3 and Appendix 5.1). The effects of pH on enzyme-catalysed reactions can be complex since both Km and may be affected. Here, only the effects on Kmax are considered, as this usually reflects a single constant rather than several that may be associated within the constant Km (see Section 5.4.4.). It is assumed that pH does not change the limiting step in a multi-step process and that the substrate is saturating at all times. 

The a-aminocarboxylic acids are of particular importance as the result of their involvement in the primary structure of protein molecules. Although customarily represented by the general formula NHj CHR-CC H amino acids are... 

While the primary structure of proteins and nucleic acids can be experimentally determined in a straight-forward manner, their higher-order structures are much more difficult to elucidate. In general, computational methods dealing with primary structure focus on interpretation of the structure-function, as in promoter analysis. By contrast computational methods working on higher-order structure instead focus on the prediction of structural details. Further, most techniques are limited to the prediction of RNA and protein structures—sugar-, fatty-add-, and DNA-structural prediction methods are in their infancy. 

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. 

Endopeptidases. Our expanding understanding of the relationship between structure and functionality of food proteins presents the opportunity for designing functionality into proteins by selective, specific proteolytic modification. Control of reaction and prevention of autolysis offered by immobilization are essential to establish the conditions for a highly selective modification. Hydrolysis at specific positions in the primary structure of proteins could be coupled with resynthesis of peptide bonds by selection of conditions, for example, as in the plastein reaction. By careful choice of enzymes and conditions according to the characteristics of the substrate proteins, it may be possible to design new structures from known food proteins. 

Amino acids joined together by peptide bonds form the primary structure of proteins. The amino acid composition establishes the nature of secondary and tertiary structures. These, in turn, significantly influence the functional properties of food proteins and their behavior during processing. Of the 20 amino acids, only about half are essential for human nutrition. The amounts of these essential amino acids present in a protein and their availability determine the nutritional quality of the protein. In general, animal proteins are of higher quality than plant proteins. Plant... 

Proteins are macromolecules with different levels of structural organization. The primary structure of proteins relates to the peptide bonds between component amino acids and also to the amino acid sequence in the molecule. Researchers have elucidated the amino acid sequence in many proteins. For example, the amino acid composition and sequence for several milk proteins is now well established (Swaisgood 1982). 

The genetic information of living organisms is coded in DNA in the form of base pair sequences. There are four types of nucleotides, which are linked to a polynucleotide with a sugar-phosphate backbone. The arrangement of nucleotides along the one-dimensional chain is called the primary structure of DNA, which directly encodes the primary structure of proteins by means of... 

The advent of both ESI and MALDI revolutionized the analysis of large biomolecules of low volatility such as peptides and proteins by their capability to form stable ions with little excess energy, enabling the determination of molecular weights even in protein mixtures. To obtain information specific to the primary structure of proteins, however, principles such as the activation of molecules via collisions with small neutral molecules, which have been used in the study of gaseous ion chemistry for decades, had to be adapted and helped to propel mass spectrometry to being of the most important tools in the field of proteomics. 

Proteins are biopolymers consisting of amino acids linked together through peptide bonds arranged in a certain sequence. This sequence of amino acids constitutes the primary structure of protein molecules. 

B. Development of Theories Concerning the Primary Structures of Proteins. 169... 

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