NationMaster - Encyclopedia: Hydrophobic core

The hydrophobic effect is the property that nonpolar molecules like to self-associate in the presence of aqueous solution. In the most extreme case, oils will pool together and fail to be miscible with water; detergents forming micelles and bilayers (as in soap bubbles) are another dramatic consequence of the hydrophobic effect. Soap bubbles can easily merge A soap bubble A soap bubble is a very thin film of soap water that forms a hollow spherical shape with an iridescent surface. ...

The hydrophobic effect is usually described in the context of protein folding, protein-protein interactions, nucleic acid structure, and protein-small molecule interactions. A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Schematic diagram of a double-stranded nucleic acid. ...

In the case of protein folding, it is used to explain why many proteins have a hydrophobic core which consists of hydrophobic amino acids, such as alanine, valine, leucine, isoleucine, phenylalanine, and methionine grouped together; often coiled-coil structures form around a central hydrophobic axis. An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ... Alanine is one of the 20 most common natural amino acids. ... Valine is one of the 20 natural amino acids, and is coded for in DNA. Nutritionally, valine is also an essential amino acid. ... Leucine is one of the 20 most common amino acids and coded for by DNA. It is isomeric with isoleucine. ... Isoleucine is one of the 20 natural amino acids, and is coded for in DNA. Its chemical composition is identical to that of leucine, but the arrangement of its atoms is slightly different, resulting in different properties. ... It has been suggested that DL-Phenylalanine be merged into this article or section. ... Methionine (Met, M. C5H11NO2S) is an essential nonpolar amino acid, and a lipotropic. ... A coiled coil is a structural motif found in many proteins. ...

The energetics of DNA tertiary structure assembly were determined by Eric Kool to be mostly caused by the hydrophobic effect, as opposed to Watson-crick base pairing. The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid â€” usually in the form of a double helix â€” that contains the genetic instructions or genocode monitoring the biological development of all cellular forms of life, and many viruses. ...

The hydrophobic effect can be nullified to a certain extent by lowering the temperature of the solution to near zero degrees; at such temperatures, water "prefers" to be in an ordered structure and the order generated by hydrophobic patches is no longer as energetically unfavorable. This is neatly demonstrated by the increased solubility of benzene in water at temperatures lower than room temperature. Benzene, also known as C6H6, PhH, and benzol, is an organic chemical compound that is a colorless and flammable liquid with a pleasant, sweet smell. ...

The transfer free energy of nonpolar molecule from nonpolar solvent to aqueous solvent is often used to quantify the hydrophobic effect. The transfer free energy of hydrophobic molecule, $Δ G t$ , is positive. The $Δ G t$ can be decomposed to the enthalpy component $Δ H t$ and entropy component $- T Δ S t$ by the thermodynamic relation $G = H - T S$ . In room temerature, $Δ H t$ is approximately zero, and $Δ S t$ is negative. In other word, the hydrophobic effect is entropy driven in room temperature. The other characteristic thermodynamic quantity of the hydophobic effect is heat chapacity change in transfer, $Δ C p,t$ . $Δ C p,t$ has a positive value as contrasted to a negative value in transferring of hydrophilic molecule.