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580.221 BME Molecules and Cells L02 Molecular Forces p 1 Lecture Two – Molecular forces: Chemical basis of specificity and affinity Outline: chemical foundations (covalent, noncovalent) 4 weak forces importance of pH, pK a , Henderson-Hasselbach equation Molecular Binding The “ lock and key ” explanation (unique matching, rigid shapes fit each other) is overly simplistic polymer – chain of repeated subunits that are covalently attached. Examples – proteins, DNA, RNA (see below). The subunits are called monomers and need not all be identical (e.g. amino acids in a protein) chirality – specific 3D arrangement of an atom’s shared bonds (more when considering protein structure) Water-Related Reactions condensation – reaction in which the release of a water molecule results in the formation of a covalent bond (i.e., making a polymer). Repeated condensation of amino acids results in a chain (polypeptide). hydrolysis – reaction in which a water molecule joins another molecule, sometimes breaking up a pre-existing covalent bond (i.e., breaking a polymer). Non-covalent Bonds These are weak forces in cells – why? Because in water (cells are mostly water), these forces are weaker than covalent bonds. This is not necessarily true in a different environment. You should
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