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Department
Biochemistry
Course
Biochemistry 3381A
Professor
Stanley Dunn
Semester
Fall

Description
Water Water is a Polar Molecule - O-H bond distance is 0.958 A (1A = 10^-10 m) and the angle formed by the 3 atoms is 104.5 degrees - Oxygen contains 4 sp3 orbitals, which 2 are occupied by hydrogen and pairs of electrons occupy the other 2 - Water molecules form hydrogen bonds: water is polar in which the oxygen atom with its unshared electrons carries a partial negative charge of -0.66e and the hydrogen atom carries a partial positive charge of 0.33e (e is the charge of the electron). Neighboring water molecules orient themselves so that the O-H bond of one water molecule (+’ve end) points towards the electron pair of another water molecule (- ‘ve end). This intermolecular association is called a hydrogen bond. H-bonds are characterized by an H - - - A distance that is at least 0.5A shorter than the calculated van der Waals distance (distance of closest approach between two nonbonded atoms). For ex. H- bonds = 1.8A, VDW = 2.6A). The energy of individual H- bond is small (around 20KJ/mol). - Ice is a Crystal of Hydrogen-Bonded Water Molecules: Each water molecule is tetrahedrally is surrounded by 4 nearest neighbors to which it is H- bonded. This causes water to have an open structure that expands from freezing (ice is less dense than water at 0 degrees). Ice has a larger volume than water but the mass stays the same when it’s in liquid form or solid. When water freezes the volume increases thus its density decrease and vice versa. The melting of ice represents the collapse of the tetrahedral orientation of H-bonded water molecules. The structure of Liquid Water is Irregular - Liquid water reorients itself many times. The H-bonds are distorted, so the networks of linked molecules are irregular and varied. These networks continually break up and re-form. Liquid water consists of a rapidly fluctuating, 3D network of H-bonded water molecules. The number of H-bonds depends on temperature, where liquid water at 0 degrees has approximately 85% as many H-bonds as water in ice. Water doesn’t not exist as individual molecules but as oligomers – trimers, tetramers and etc. The oligomers are highly transient or dynamic as the H-bonds break and form on the timescale of 10^-11 seconds. This is a very high entropy situation. -Effects of oligomeric nature on properties of water: It behaves like it has a higher molecular weight (high melting points and boiling points). It is more viscous than liquids than lack H-bonds. The effects of water on the conformation of macromolecules - Macromolecules are synthesized in a linear form, but biological function requires that they assume the proper conformation. The folding structure must be stable must be the most energetically favorable. The number of possible conformations for a polypeptide or nucleic acid is virtually limitless. Many biochemists study structure and the “folding” process- these occur largely in aqueous medium. Folding is complicated, but must be driven energetically favourable nature of the folded structure-usually this is taken as the lowest energy conformation and depends on non-covalent forces and effects, many involving water. Solubility and molecular interactions/recognition will also depend on these factors. What are these forces or effects, and what is water’s role? Bond Energies and Electrostatic Interactions -Covalent bonds are quite stable. The non-covalent interactions fall into a couple of classes. -Ionic interactions are between molecules that have opposite charges. Ionic interactions can be quantified by Coulomb’s Law: the force (F) between any two charged particles will be: q1 2 F  2 4r  where: q1and q2are the charges on the particles r is the distance between the particles e (epsilon) is the “dielectric constant” of the medium; it is related to its polarity but is, in fact, defined by Coulomb’s law. Note: effect of dielectric constant, e - - a high dielectric constant reduces the  strength of the interaction - The medium can reduce the strength between charged particles. Vacuum has no medium gives a dielectric constant of 1. Water has a very high dielectric constant. This means that an interaction between these two charged groups on the surface of a protein where it is totally aqueous It’s going to be less energetic. Ion Solvation by H2O - Why is water so effective at reducing the force between ions? Polar water molecules orient around ions to make favourable charged-dipole interactions. Water basically shields’ the charge interaction between other charged molecules. These hydration sh
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