Enzymology Lesson 5 PDF

ENZYMOLOGY LESSON 5 Enzymology • Concept • Importance of enzymes in the development of biological reactions. • Water-soluble vitamins as coenzymes. • Regulation of enzyme activity Structure of enzymes Enzyme: A protein that catalyzes a specific chemical reaction Active site: The region of an enz...

ENZYMOLOGY LESSON 5 Enzymology • Concept • Importance of enzymes in the development of biological reactions. • Water-soluble vitamins as coenzymes. • Regulation of enzyme activity Structure of enzymes Enzyme: A protein that catalyzes a specific chemical reaction Active site: The region of an enzyme surface that binds the substrate molecule and catalytically transforms it; also known as the catalytic site. • Their catalytic activity depends on the integrity of their native protein conformation • The surface of the active site is lined with amino acid residues with substituent groups that bind the substrate and catalyze its chemical transformation • Increase the speed of the reaction Enzymes properties • High specificity: Substrate specificity: They can bind only one substrate Reaction: They always catalyze the same reaction • Efficiency: proximity creates tension between the substrate and catalytic residues. • Increase the reaction rate in mild conditions: Compatible with life • Enzymatic reactions occur in specialized pockets called active sites • Under regulation: Some agents can modulate their activity by modifying the active site. How do enzymes work? CHEMICAL REACTION Initial compound Intermediate Initial energy state Transition state (higher energy) Final compound Final state (less energy than the initial compound) To reach the intermediate compound, a lot of activation energy needs to be given to the substrate. How do enzymes work? ENZYMATIC REACTION Enzymes increase reaction rates, lowering reaction activation barriers Steps in an enzymatic reaction: 1. E-S complex is formed 2. E-S complex is transformed into a transition complex. 3. Formation of the E-P complex 4. Separation of the E-P complex into enzyme and product. Enzymatic kinetics • The study of the rate of a reaction and how it changes in response to changes in experimental parameters V0 = 𝑑𝑑𝑑𝑑 − 𝑑𝑑𝑑𝑑 = 𝑑𝑑𝑑𝑑 𝑑𝑑𝑑𝑑 = Slope Product concentration will increase as substrate concentration declines Rate or velocity of a reaction (V0): number of substrate molecules converted to product per unit time Enzymatic kinetics (EXTERNAL) FACTORS AFFECTING REACTION RATE • Enzyme concentration • Substrate concentration [E] • pH • Temperature V0 Each enzyme has an optimal pH and temperature for its activity [S] V0 *Until maximum velocity is reached Maximum velocity (Vmax): Maximum rate of a reaction when the enzyme is saturated with substrate (all the enzymes are attached to substrate) Metabolic pathway Metabolic pathway: Sequences of consecutive enzymatic reactions in which the product of one reaction becomes the substrate in the next one • Each metabolic pathway consists of several reactions with several enzymes. • Each pathway includes one or more enzymes that have a greater effect on the rate (velocity) of the overall sequence. Regulatory enzyme: An enzyme with a regulatory function, through its capacity to undergo a change in catalytic activity by allosteric mechanisms or by covalent modification. • Changes in the rate of a metabolic pathway occur because at least one enzyme in that pathway, the regulatory enzyme, has been activated or inhibited, or the amount of enzyme has increased or decreased. Regulators of enzyme activity ALLOSTERIC REGULATION Allosteric enzyme: A regulatory enzyme with catalytic activity modulated by the noncovalent binding of a specific metabolite at a site other than the active site. Allosteric inhibitor Allosteric site: The specific site on the surface of an allosteric protein molecule to which the modulator or effector molecule binds.. Allosteric activator Allosteric modulators or effectors: small metabolites or cofactors that bind to the allosteric site of an allosteric enzyme and modify its catalytic activity Regulators of enzyme activity REVERSIBLE COVALENT MODIFICATION • The activity is modulated by covalent modification of one or more of the amino acid residues in the enzyme molecule • Charasteristic in hormonal signal  adrenaline, glucagon or insulin • The most common covalent modification  Phosphorylation REVERSIBLE COVALENT MODIFICATION Regulators of enzyme activity Coenzymes PARTS IN AN ENZYME • Apoenzyme: The protein portion of an enzyme • Prosthetic group: A metal ion or organic compound (other than an amino acid) covalently bound to a protein and essential to its activity. Cofactor  inorganic ions Coenzyme  complex organic or metalloorganic molecule Vitamins • Group transports  Coenzyme A • Electron transfer  NADH, FADH2 Derive from hydrosoluble vitamins (C and all the B group). Non-vitamins • Coenzyme Q • NTP