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9 Enzymes.pdf

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Boris Zhorov

9 Enzymes Fermentation: process by which people produce alcohol from yeast. •Unable to reproduce using pure reagents •Enzyme: (greek for yeast) was proposed to hint at something that catalyzes the reactions of fermentation •Catalysts are substances that increase the rate of a chemical reaction without being consumed in the chemical process. •Most enzymes are proteins, but there are some RNA structures with catalytic properties. Properties of enzymes: Cells avoid a chemical mess of functional groups that otherwise are reactive because the rates of uncatalyzed reactions are very low. Enzymes increase rate of reactions by 10 to 10 12 times, and can occur at much milder conditions. Have a great specificity for their substrates and products. Regulation: Enzymatically catalyzed reactions arer egulated by allosteric mechanisms, covalent modification and variation of the amount of synthesized enzymes •Allosteric regulators: inhibitors or activators that bind to enzyme to cause conformational changes. Covalent modification: phosphorylation/dephosphorylation, • particularly for receptor sensitivity. •Gene expression of enzymes Summary of Properties 1. Faster rate 2. Milder conditions 3. High specificity 4. Capacity for regulation Lysase:Group elimination to form double bonds Ligase: Bond formation coupled with ATP hydrolysis. ! Binding site for a substrate is usually located in a cleft - pockets, gorges or crevices on the protein surface. The shape of a substrate has a geometric complementary to the shape of the binding site. Amino acid residues in the active site of an enzyme are arranged to maximize favorable electrostatic interactions with H-bonds with the corresponding substrate, this is known as electronic compementarity. ! Enzymes may undergo certain conformational changes upon binding of a substrate in a model known as an induced fit. Enzymes are highly specific to the configuration of their substrates, and are often stereo or regiospecific/selective. ! Certain chemical reactions are catalyzed by corresponding enzymes only in the presents of cofactors (metal ions) or coenzymes (organic molecules). 9 Enzymes Catalysts reduce the activation energy of the reaction. For a 10-fold rate enhancement, a change in free energy requires at least 5.7kJ/mol. Curved Arrows indicate electron pair rearrangements during a chemical reaction. Arrows start at the reactant’s electron pairs and point to the electron-deficient centers that attract the electron pairs. Catalytic Mechanism - Keto-enol tautomerization. •Can be catalyzed by acids or bases, or left uncatalyzed. 9 Enzymes Catalytic Mechanisms Metal ion Catalysis •Metal ion ensures proper orientation of substrate •Reversible changes in oxidation state of metal ion occur •Electron stabilization occurs, such as shielding of negative charges •About (1/3) of all known enzymes require the presence of metal ions in order to elicit their catalytic activity. Covalent Catalysis: transient covalent bonds are formed with substrate Electrostatic catalysis: Charges on the enzyme lower the free energy of the transient intermediate state of the substrate Proximity and orientation effects: Substrates are brought into contact with their catalytic groups, they are properly oriented and enzymes freeze the translational and rotational motions of substrates in order to keep the active groups in proximity. Preferential binding of the transition state complex: En
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