BCHM
Module 1 Part 1.docx

Bond resulting in planar geometry typically occurs in

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bond, resulting in planar geometry) Typically occurs in molecules that undergo resonance (i.e. a phenomenon where molecules that contain single and double bonds adjacent to each other can exist as an average of multiple structures) o e.g. the molecular structure around the peptide bond (i.e. as a result of resonance, the chemical groups that make up the peptide bond must be located in the same plane due to the partial double-bond character of the carbonyl and amino bonds that restricts rotation about these positions) o e.g. resonance exists in the bases and the phosphate group of the phosphodiester bond, giving the phosphodiester bond a tetrahedral geometry The negative charge on the phosphate group can shift between the two oxygen atoms that are not bound to sugars in the backbone The bases themselves are conjugated ring systems (i.e. they have alternating double and single bonds, giving rise to shared electrons around the ring(s)); the accuracy of base pairing (i.e. A and T; C and G) results from the dominance of particular resonance structures of the bases Resonance hybrid: a molecule that exists in an average of two possible forms Electric dipole moment: combination of separated positive and negative charges Polar and nonpolar regions can exist within the same molecule; the outer surfaces of proteins that function in the aqueous environment tend to be polar (thereby favouring interactions with polar water molecules) and proteins that function in the nonpolar environment of cellular membranes tend to have nonpolar surfaces (thus fostering contacts with the nonpolar fatty acid chains of the membrane).
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Ionic interactions can occur between pairs of oppositely charged amino acid side chains; the amino acids with side chains that most often form salt bridges are arginine, lysine, aspartic acid, and glutamic acid . Salt bridge: a link between electrically charged acidic and basic groups, especially on different parts of a large molecule such as a protein (e.g. negative charges on the oxygen atoms in the glutamic acid side chain attract the positive charges on the nitrogen atoms in the arginine side chain, forming a salt bridge) o Involves a combination of two weak interactions: hydrogen bonding and electrostatic interactions Chemical Properties: Weak Chemical Bonds Three kinds of weak chemical interactions are important in biological systems: 1 van der Waals forces o Non-specific contacts between atoms; as two atoms get closer, induced fluctuating charges between them cause a weak, nonspecific attractive interaction that heavily depends on the distance between the interacting atoms o As the distance decreases below a certain point, a more powerful van der Waals repulsive force is caused by overlap of the atoms' outer electron shells o van der Waals radius: distance at which attractive and repulsive forces are balanced; characteristic for each atom o For atoms to interact effectively using van der Waals forces, the intermolecular fit
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  • Winter '13
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