Hydrogen bonds tertiary protein structure

The duplex is a right-handed double helix with 10 bases per turn. The diameter of the helix is 20 A (2 nm) and the pitch is 34 A (3.4 nm). The sugar-phosphate backbone is on the outside of the helix, and the two antiparallel chains are connected by the hydrogen-bonded bases. The DNA in prokaryotes and eukaryotes is generally found in the duplex form, although there are some single-stranded DNA viruses. DNA is a very robust molecule in comparison with many proteins. The simple double-helical secondary structure is readily reassembled after denaturation, unlike the complex tertiary protein structures that can denature... 

While it is clear that the action of F on plant metabolism is complex and involves a variety of enzymes, the mode of action of F- ion on these enzymes is not so clear. The principal mechanisms that have been suggested include (1) formation of complexes with metalloenzymes, (2) removal of a metal cofactor from an enzyme system, and (3) binding to the free enzyme or to the enzyme substrate complex (Miller et al. 1983). Studies using a model system indicate that F can disrupt the hydrogen bonding of protein molecules (Edwards et al. 1984). Because hydrogen bonding is important in the maintenance of the tertiary structure of a protein molecule, disruption of an enzyme protein by F would result in enzyme inhibition. 

It must also be remembered that enzymes have structures that depend on pH. Under excessively acid or alkaline conditions, denaturation of the tertiary protein structure will occur due to disruption of the normal hydrogen bonding modes, and this denaturation will have dramatic effects on enzyme activity. 

Chemical immobilization methods may alter the local and net charges of enzymes, through covalent modification of charged residues such as lysine (NH4), aspartate, and glutamate (COO-). Conformational changes in secondary and tertiary protein structure may occur as a result of this covalent modification, or as a result of electrostatic, hydrogen-bonding or hydrophobic interactions with the support material. Finally, activity losses may occur as a result of the chemical transformation of catalytically essential amino acid residues. 

The data indicate that penetration of the monolayer occurs when the polyoxyethylene nonionic surfactants are injected into the substrate. Polar portions of surfactant molecules interact with their counterparts on the protein film through permanent dipole attraction and dipole-induced-dipole (van der Waals) interaction, and electrostatic attraction. The nature of this adsorption disrupts hydrogen bonding which partially stabilizes the tertiary protein structure. This makes the macromolecules more amenable to unfolding, and this has been observed with proteins in the presence of ionic surfactants (22) as well. 

Surface-active materials consist of molecules containing both polar and nonpolar portions, i.e., amphiphilic molecules. The proteins are typically amphiphilic, polymeric substances made of amino acid residues combined in definite sequences by peptide bonds (primary structure). In many cases polypeptide chains are present in helical or /3-sheet configuration (secondary structure) which are stabilized by intramolecular (S-S and hydrogen) bonding. The next structural level, the tertiary structure, is determined by the folding of the polypeptide chains to more or less compact globules, maintained by hy-... 

Protein tertiary structure. Protein tertiary stmctures are the result of weak interactions. When a protein folds, either as it is being made on ribosomes or refolded after it is purified, the first step involves the formation of hydrogen bonds within the structure to nucleate secondary structural (alpha and beta) regions. For example, amide hydrogen atoms can form H-bonds with nearby carbonyl oxygens an alpha helix or beta sheet can zip up, prompted by these small local structures. 

The native state of a single-domain protein is its tertiary structure, and it is estimated that approximately 1000 different shapes or folds exist in nature. The native state generally adopts a globular three-dimensional shape, stabilized by both covalent (peptide bonds, disulfide bridges) and noncovalent (electrostatic, hydrophobic and hydrogen bonds) interactions. Local structures within the native fold are known as secondary structures, with common motifs including alpha heHces and beta sheets. The classic experiments of Anfinsen et al. su ested a Thermodynamic Hypothesis for folding, in which the... 

How do hydrogen bonds involved in tertiary protein structures differ from those involved in secondary structures ... 

To a physical chemist an idealized picture of rigid protein molecules always did appear improbable. Secondary and tertiary protein structure is maintained by a system of hydrogen bonds, complementary charge pairs and non-polar interactions. The equilibria between intramolecular and intermolecular (with water) pairing of the first and second of these are not far from unity and are, therefore, readily perturbed. Two types of flexibility with consequences for the reaction profile of protein molecules were to be expected, and indeed have been found to occur. These have already been... 

Hydrogen bonding stabilizes some protein molecules in helical forms, and disulfide cross-links stabilize some protein molecules in globular forms. We shall consider helical structures in Sec. 1.11 and shall learn more about ellipsoidal globular proteins in the chapters concerned with the solution properties of polymers, especially Chap. 9. Both secondary and tertiary levels of structure are also influenced by the distribution of polar and nonpolar amino acid molecules relative to the aqueous environment of the protein molecules. Nonpolar amino acids are designated in Table 1.3. 

Equation (8.97) shows that the second virial coefficient is a measure of the excluded volume of the solute according to the model we have considered. From the assumption that solute molecules come into surface contact in defining the excluded volume, it is apparent that this concept is easier to apply to, say, compact protein molecules in which hydrogen bonding and disulfide bridges maintain the tertiary structure (see Sec. 1.4) than to random coils. We shall return to the latter presently, but for now let us consider the application of Eq. (8.97) to a globular protein. This is the objective of the following example. 

The three-dimensional conformation of a protein is called its tertiary structure. An a-helix can be either twisted, folded, or folded and twisted into a definite geometric pattern. These structures are stabilized by dispersion forces, hydrogen bonding, and other intermo-lecular forces. 

Name the amino acids in Table 19.4 that contain side groups capable of forming hydrogen bonds. This interaction contributes to the tertiary structure of a protein. 

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