Covalent phosphate structure

AIPO4 is a classic example of the Si02 type covalent phosphate structure. In this structure, A1 and P atoms share one bond with each oxygen and each of them forms a tetrahedron. Through the common oxygen atom, the tetrahedra are linked to each other and form a three-dimensional covalent structure that is similar to silica... 

Bonding in the silica-type covalent phosphate structure is illustrated in Fig. 8.5. Because this bonding is covalent, the resulting minerals are very hard and their aqueous solubility is extremely low. These properties make them attractive for the disposal of radioactive barium and strontium isotopes formed during nuclear reactions. These two isotopes may be converted to their covalent phosphate structures as Sr3(P04)2 and Ba3(P04)2 and can be disposed or stored in repositories safely. 

There is little motion of the protein, the main movement being closure of a loop over the active site after binding phosphate and substrate analogue. There are indications that when an acceptor maltooligosaccharide and glucose-1-phosphate are both bound, the phosphate is forced down and in an unfavourable torsional angle however there is no indication of any direct covalent interaction between the nucleophilic phosphate and the phosphate attached to the pyridoxal moiety, which had been proposed on the basis on NMR studies on glycogen phosphorylase. There is also no indication of any covalent intermediate. Structurally, the S i mechanism is plausible whereas the doubledisplacement mechanism would create difficulties. 

As we have previously stated, most starch granules are composed of amylose and amylopectin in a ratio of 1 4 or 1 3. Tuber starches in addition contain covalently linked phosphate potato starch has 0.06%, and shoti starch has 0.18% covalent phosphate [30a]. The cereal starches are devoid of phosphate but contain 1-5% lipid [30b], which is believed to be complexed with the amylose component in a helical structure. 

The contractile apparatus may be thought of as the sum of those intracellular components which constitute the machinery of chemomechanical transduction. It is the set of proteins which convert the chemical energy of the terminal phosphate ester bond of ATP into mechanical work. The structure of the contractile apparatus is determined by the connections between the various protein molecules via specific binding sites or, in a minority of cases, via labile covalent linkages. The kinetics of the contractile machinery are determined by the regulation of changes in these connections. 

In terms of their molecular structures, the nucleotide and protein realms are usually considered to be rather independent of each other. However, these two families of molecules are covalently linked in the translational aminoacyl- RNAs and ribonucleoproteins as well as in the nucleoproteins involved in cellular and viral replication. In these hybrid biomolecules, a (deoxy)ribose phosphate moiety serves as the structural connection between the nucleoside and peptide moieties. 

This is illustrated in Scheme VI. The protected glyceryl derivatives are insoluble in aqueous media and appear to be hydrolytically stable. The deprotected species (structure 27) is water-soluble and hydrolyzes in aqueous media at neutral pH at 37°C to give glycerol, phosphate, and ammonia. The free hydroxyl units of the deprotected polymer provide sites for the covalent attachment of drug molecules. Water insolubility can be imparted by the use of appropriate hydro-phobic cosubstituent groups to generate solid, erodible materials. 

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

Based on a series of studies of the effect of organic solvent on the reaction of Ca-ATPase with Pj and ATP synthesis, De Meis et al. proposed that a different solvent structure in the phosphate microenvironment in Ej and E2 forms the basis for existence of high- and low-energy forms of the aspartyl phosphate [93]. Acyl phosphates have relatively low free energy of hydrolysis when the activity of water is reduced, due to the change of solvation energy. The covalently bound phosphate may also reside in a hydrophobic environment in E2P of Na,K-ATPase since increased partition of Pj into the site is observed in presence of organic solvent [6] in the same manner as in Ca-ATPase. 

The change in the conformation of the control enzyme brought about by covalent modification alters the activity of the control enzyme and so regulates substrate flux through that step. This fact underlines the importance of the three-dimensional structure of an enzyme. The inclusion of phosphates may bring about quite a small architectural change to the protein structure but it is sufficient to affect substrate binding and therefore enzyme activity. 

DNA is a structurally polymorphic macromolecule which, depending on nucleotide sequence and environmental conditions, can adopt a variety of conformations. The double helical structure of DNA (dsDNA) consists of two strands, each of them on the outside of the double helix and formed by alternating phosphate and pentose groups in which phosphodiester bridges provide the covalent continuity. The two chains of the double helix are held... 

Figure 4.4 Structure of the oxyanion hole of cutinase, with a covalently bound transition state analog, diethyl phosphate (PDB 2CUT).

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