Proteins biological functions

Structures of Prenylated Proteins Biological Functions of Protein Prenyl Groups... 

If we consider that the role played by an amino acid inside a folded protein is equivalent to its interaction degree, then these plots show that despite a functional diversity between the 4 SCOP classes, there are globally the same amino acids which interact most, namely the Ala, Cys, Gly, Leu, Val. Therefore, the amino adds having a high connectivity interact independently of the protein biological function, we will explain this behavior further. Thus, the figure shows dearly that the amino add Ala plays a central role in the studied proteins independently of the classification of their secondary structure. 

A dipeptide is a molecule consisting of two ammo acids joined by a peptide bond A tnpeptide has three ammo acids joined by two peptide bonds a tetrapeptide has four ammo acids and so on Peptides with more than 30-50 ammo acids are polypeptides Proteins are polypeptides that have some biological function... 

Coagulation Factors II, III, VII, IX, X, XI, and Xlla fragments, thrombin, and plasmin are classified as serine proteases because each possesses a serine residue with neighboring histidine and asparagine residues at its enzymatically active site (Table 3). Factors II, VII, IX, and X, Protein C, Protein S, and Protein Z are dependent on the presence of vitamin K [84-80-0] for their formation as biologically functionally active procoagulant glycoproteins. 

Copper is required for all forms of aerobic and most forms of anaerobic life. In humans, the biological function of copper is related to the enzymatic action of specific essential copper proteins (66). Lack of these copper enzymes is considered a primary factor in cerebral degeneration, depigmentation, and arterial changes. Because of the abundance of copper in most human diets, chemically significant copper deficiency is extremely rare (67). 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

To understand the biological function of proteins we would therefore like to be able to deduce or predict the three-dimensional structure from the amino acid sequence. This we cannot do. In spite of considerable efforts over the past 25 years, this folding problem is still unsolved and remains one of the most basic intellectual challenges in molecular biology. 

The side chains of the 20 different amino acids listed in Panel 1.1 (pp. 6-7) have very different chemical properties and are utilized for a wide variety of biological functions. However, their chemical versatility is not unlimited, and for some functions metal atoms are more suitable and more efficient. Electron-transfer reactions are an important example. Fortunately the side chains of histidine, cysteine, aspartic acid, and glutamic acid are excellent metal ligands, and a fairly large number of proteins have recruited metal atoms as intrinsic parts of their structures among the frequently used metals are iron, zinc, magnesium, and calcium. Several metallo proteins are discussed in detail in later chapters and it suffices here to mention briefly a few examples of iron and zinc proteins. 

Simple combinations of a few secondary strucfure elements with a specific geometric arrangement have been found to occur frequently in protein structures. These units have been called either supersecondary structures or motifs. We will use the term "motif" throughout this book. Some of these motifs can be associated with a particular function such as DNA binding others have no specific biological function alone but are part of larger strucfural and functional assemblies. 

We have already discussed one envelope protein of influenza virus, neuraminidase, as an example of an up-and-down antiparallel p motif. In the second envelope protein, hemagglutinin, one domain of the polypeptide chain is folded into a jelly roll motif. We shall now look at some other features of hemagglutinin that are important for its biological function. 

Important novel information has thus been obtained for the specific biological function of those molecules, but disappointingly few general lessons have been learned that are relevant for other membrane-bound proteins with different biological functions. In that respect the situation is similar to the failure of the structure of myoglobin to provide general principles for the construction of soluble protein molecules as described in Chapter 2. 

Protein (Chapter 27) A naturally occurring polypeptide that has a biological function. 

Proteins are the indispensable agents of biological function, and amino acids are the building blocks of proteins. The stunning diversity of the thousands of proteins found in nature arises from the intrinsic properties of only 20 commonly occurring amino acids. These features include (1) the capacity to polymerize, (2) novel acid-base properties, (3) varied structure and chemical functionality in the amino acid side chains, and (4) chirality. This chapter describes each of these properties, laying a foundation for discussions of protein structure (Chapters 5 and 6), enzyme function (Chapters 14-16), and many other subjects in later chapters. 

FIGURE 4.5 The structures of some ammo acids that are not normally found in proteins but that perform other important biological functions. Epinephrine, histamine, and serotonin, although not amino acids, are derived from and closely related to amino acids. 

Proteins Their Biological Functions and Primary Structure... 

Each such segment of encoded information defines a gene, and expression of the gene leads to synthesis of the specific protein encoded by it, endowing the cell with the functions unique to that particular protein. Proteins are the agents of biological function they are also the expressions of genetic information. 

Proteins are the agents of biolo ealfunction. Virtually every cellular activity is dependent on one or more particular proteins. Thus, a convenient way to classify the enormous number of proteins is by the biological roles they fill. Table 5.3 summarizes the classification of proteins by function and gives examples of representative members of each class. 

Biological Functions of Proteins and Some Representative Examples ... 

HEMOPROTEINS. These proteins are actually a subclass of metalloproteins because their prosthetic group is heme, the name given to iron protoporphyrin IX (Figure 5.15). Because heme-containing proteins enjoy so many prominent biological functions, they are considered a class by themselves. 

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