Lecture_9_EnzymesConcepts.pptx

Enzymes: Concepts Lecture 9 BCMB 401 Spring 24 Reading: Chapter 5.1-3 Enzymes – Biological catalysts  Catalyst – accelerates the reaction rate without being consumed in the reaction  Almost all enzymes are proteins (A few RNA molecules, ribozymes, can catalyze reactions)  10 - 20% of proteins in...

Enzymes: Concepts Lecture 9 BCMB 401 Spring 24 Reading: Chapter 5.1-3 Enzymes – Biological catalysts  Catalyst – accelerates the reaction rate without being consumed in the reaction  Almost all enzymes are proteins (A few RNA molecules, ribozymes, can catalyze reactions)  10 - 20% of proteins in a typical cell are enzymes.  Reaction catalyzed by carbonic anhydrase  Enzymes increase the rate of reaction in both directions Enzyme specificity  Enzymes can display a high degree of specificity in both reaction type and substrates.  The specificity is due to the precise interaction of the enzyme and its substrate.  Example: The proteolytic enzymes trypsin (digestion) and thrombin (blood clotting) have different degrees of specificity. (A) Trypsin cleaves on the carboxyl side of arginine and lysine residues, whereas (B) Thrombin cleaves Arg–Gly bonds in particular sequences only (LVPRGS) Enzyme Cofactors Cofactors: small molecules that many enzymes require for catalytic activity Coenzymes (small organic molecules often derived from vitamins) Can be prosthetic groups Metals Thermodynamics of biological reactions  Whether a reaction will occur spontaneously depends on ΔG [C][D] G G  RT ln [A][B] o'  The spontaneity of the reaction depends on two parameters: 1. The standard biological free energy ΔGo′ (inherent, ΔG° = ΔH°- TΔS°) 2. The relative concentrations of substrates [A] and [B] and products [C] and [D] -ΔG : exergonic reaction (spontaneous) +ΔG : endergonic reaction (requires energy input) ΔG = 0 : reaction at equilibrium R = gas constant T = temperature in kelvin Thermodynamics of biological reactions [C][D] o' G G  RT ln [A][B]  The standard free energy change is related to the equilibrium constant [C][D] 0 G  RT ln [A][B] o' [C][D] G  RT ln [A][B] o' [C][D] K eq  [A][B]  G   RT ln K eq 𝐾 ′ 𝑒𝑞=𝑒 ′ − ∆ 𝐺° / 𝑅𝑇 Enzymes do not affect ΔG°ʹ  Enzymes alter only the reaction rate and not the reaction equilibrium  The same equilibrium point is reached but much more quickly in the presence of an enzyme.  The reaction equilibrium is determined only by the freeenergy difference between the products and reactants (ΔG°′). Enzymes cannot alter this difference.  ΔG (and ΔG°′) is path independent. Even reactions that have a very favorable ΔG will proceed very slowly if there is an energetically unfavorable step in the reaction  ΔG (or ΔG°′) does not determine the rate of the reaction Enzymes: Biological catalysts ΔG‡ = activation energy  The energy input needed to attain the transition state  transition state, X‡ = a transitory molecular structure that is no longer substrate but not yet product  is the species along the reaction pathway with the highest (most unfavorable) free energy v ∝ [X‡]  The overall rate of the reaction (v) depends on the amount of molecules that reach X‡  The amount of molecules that reach X‡ depends on ΔG‡ ENZYMES: Biological catalysts that stabilize the transition state Enzymes can lower the activation energy in several ways:  Enzymes can make favorable interactions with the transition state  Enzymes can distort the substrate to make the reaction easier  Enzymes can bring substrates together in a way that facilitates the reaction  Enzymes can change the reaction mechanism (pathway) Enzyme Specificity: the Active Site lysozyme, an enzyme that breaks down bacterial cell walls  Enzymes are globular proteins with a specific 3-D fold (tertiary structure)  In the native fold, they contain a small pocket (the Active Site) which binds reversibly to substrate molecules  Active site may include residues distant in primary structure (sequence) Enzyme-substrate interaction at the active site: Chemical Complementarity cytochrome P450 enzyme bound to a substrate (camphor) Properties of the active site:  Non-aqueous environment  Substrate binding involves multiple noncovalent interactions  High specificity due to chemical complementarity  High binding affinity for substrate  Even higher affinity for the transition state Hydrogen bonds between an enzyme and substrate  An example of multiple noncovalent interactions: Hydrogen bonds from the enzyme Ribonuclease (Rnase) to uridine (part of substrate  In the non-aqueous environment of the active site of RNase, these hydrogen bonds are stronger Enzyme-substrate interaction at the active site: Chemical Complementarity  Enzyme active sites have chemical complementarity with substrates  Active site residues have the proper shape and stereochemistry that allows binding of substrate and stabilization by noncovalent interactions with key amino acid side chains and other cofactors  There are different models that explain how chemical complementarity is achieved Enzyme-substrate interaction at the active site: Conformational Selection  In a population of enzymes: some have chemical complementarity with substrate, while some enzyme molecules do not.  Substrate preferentially binds to complementary enzyme molecules.  To maintain equilibrium: non-complementary enzyme molecules shift to complementary conformation Enzyme-substrate interaction at the active site: Chemical Complementarity In a population of enzymes: some have chemical complementarity with substrate, while some enzyme molecules do not. Substrate preferentially binds to complementary enzyme molecules. Conformational Selection To maintain equilibrium – non-complementary enzyme molecules shift to complementary conformation  Conformational selection – conformational change before substrate binds  Induced fit – conformational change after substrate binds