m5 - Protein Function:Protein Binding Introduction Ch2 Page...

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Protein Function:Protein Binding Introduction Ch2, Page 36 Ch3, Page 73-79, 82-86
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Enzymes Protein Function Proteins are very versatile…they can perform a variety of “jobs” in the cell How do proteins accomplish their function?
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Protein Function: Protein binding
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Protein Function: Protein binding • The function of nearly all proteins depends on their ability to bind to molecules, called ligands or substrates , with a high degree of specificity. Ex. Binding molecules: –Ions –Sugars, –Fatty acids –Proteins, –DNA, etc -Surfaces of molecules A and D form stable interaction
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Protein binding: Affinity and Specificity • Protein-ligand interaction can be transient, stable, or permanent, but they must be specific . • Protein-ligand interaction can be measured by the affinity (binding strength) and specificity (binding preference). • Level of affinity and specificity depends upon molecular complementarities –The complementation between the shape and chemical surface of the binding site of the protein and the ligand molecule –“lock and key”
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Weak non-covalent bonds Protein binding: Non-covalent interactions • Protein-ligand interaction is mediated by non-covalent bonds
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Amino acid side chains Bound ligand Protein binding to its ligand Binding site: region of a protein that associates with a ligand. Protein Function: Protein binding
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Antigen (Ag): Foreign substance that elicits production of an antibody Antigen Antigen antibodies Antibody -In some cases, antibody can distinguish between proteins that differ by a single amino acid. Antibodies (immunoglobulin) : Proteins produced by the immune system Antibodies: example of protein binding specificity
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Antigen binding site Antigen binding site Antibodies: example of protein binding specificity • An antibody has 4 subunits (polypeptides): -2 heavy chains -2 light chains • Chains are held together by S-S bonds
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Antibodies: example of protein binding specificity • Each polypeptide chain can be divided into 2 domains: –Variable domain VL & VH –Constant domain CL & CH • The variable domains interact with the antigen
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CDR Antigen-binding site Antibodies: example of protein binding specificity • The variable domains contain the complementarity- determining region (CDR) • CDR contains 6 highly variable loops that form the antigen-binding sites which interacts with antigen
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Antibodies: example of protein binding specificity Epitope What do you think is stabilizing this interaction between the antibody and the antigen? • Interaction between antibody and epitope of antigen is complementary… Epitope : region of antigen that is recognized by the antibody • “fits like a glove”
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Antibodies are useful tools in molecular biology • Purify proteins : -Immunoaffinity column chromatography • Detect specific proteins -ELISA, Immunoblot, etc.
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