Test 2 Theme E - combination of my notes, khan academy and class notes PDF

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combination of my notes, khan academy and class notes...

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Theme E1 Binding of ligands to proteins, examples - enzymes to substrates - Inhibitors and activators - Hormone receptors to hormones - Immunoglobulin and myoglobin to O2 and CO2 Binding Site Most of the polypeptide ensures formation and stabilisation Non polar nature- water excluded, facilitates ligand binding Polar residue lends specificity and is involved in catalysis non -polar residue is involved in binding

Function of lysozyme is the hydrolyses peptidoglycans in bacterial cell wall (ligands=peptidoglycans) Active site residue-close together in 3D structure May be far apart in the primary structure Ligand binding is highly specific precise arrangement of amino acid residues in binding site → specificity ligand binds only if binding site is complementary − lock-and-key

Hexokinase Binding site changes upon ligand binding. Sites form complementary to ligands Haemoglobin Binding of o2 to haemoglobin Conformational charge Ionic interactions between a and B subunits a/b subunit rotates and shifts upon O2 vinding Forces involved in ligand binding weak non-covalent forces specific H-bonds − Trp, Arg, Lys – donors − Ser, Thr, Tyr, Asn, Gln, Cys – donors/acceptors − Asp, Glu – donors if protonated/acceptors if charged electrostatic forces − + charged groups: N-terminal, Arg, Lys, His (sometimes) − – charged groups: C-terminal, Asp, Glu, Cys (sometimes Tyr) − dipoles: -OH, -SH, C=O containing residues van der Waals and hydrophobic interactions − non-polar residues Key concepts 1. Biological specificity depends on the non-covalent binding of small molecules (ligands) to proteins. 2. Ligands bind to specific sites on proteins. 3. The structures of binding sites are complementary to those of ligands. Theme E2

The binding equation Key concepts 1. Binding of ligands to protein shows the principle of saturation. 2. The degree of saturation of the protein is dependent on the concentration of the ligand. 3. The concentration-dependency of ligand binding to monomeric proteins can mathematically be described by a hyperbolic equation.

Theme E3 Binding of Ligands to Proteins Key concepts Binding of ligands to oligomeric proteins is mostly cooperative with a sigmoidal relationship between the amount of binding and ligand concentration....