BIOLOGY 2B03 Lecture Notes - Lecture 2: Ionic Bonding, Protein A, The Sequence

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Ligand or substrate is the molecule which the protein binds to. Examples: antigens (molecules which antibodies target), enzymes binding to a substrate, dna-binding proteins associating with. Dna, or receptors on the surface of a cell binding to signalling molecules. Liganding must have both high affinity and specificity. High affinity: this is the strength of binding. A strong interaction means the ligand is associated with the protein for a long time since the interaction is powerful. Specificity: the ability for the protein to preferentially bind to a unique ligand or sometimes to 2 or 3 very similar ligands. Both specificity and affinity are dependent on the concept called molecular complementarity. Molecular complementarity is dependent on the abundance of non-covalent interactions. The more complementary the shapes of the ligand and the protein, the greater the number of non-covalent interactions and the stronger the affinity and specificity. It will be unlikely for the interaction to break from thermal motion and vibrations.

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