BI110 Lecture 8 - Wed Oct. 2 PDF

BI110 Lecture 8 – Wed Oct. 2 Dr. Leonard Reminders: SI sessions Sunday, Monday and Metabolic Pathways and Reactions Two groups of reactions: Exergonic reaction where ΔG is negative because products contain less free energy than reactants Spontaneous process...

BI110 Lecture 8 – Wed Oct. 2 Dr. Leonard Reminders: SI sessions Sunday, Monday and Metabolic Pathways and Reactions Two groups of reactions: Exergonic reaction where ΔG is negative because products contain less free energy than reactants Spontaneous process Endergonic reaction where ΔG is positive because products contain more free energy than reactants Nonspontaneous process Exergonic and Endergonic Reactions Notice that both types of reactions require an initial input of energy called Activation Energy Fig. 3.7,  Diffusion across a Membrane [Insert Fig. 3.8 on p. 59] Molecules move Diffusion is driven by an spontaneously from increase in entropy and the higher concentration to energy associated with the lower concentration. molecules is spread out. Fig. 3.8 Equilibrium Equilibrium is maximum stability. The equilibrium point is reached when reactants are converted to products and products are converted back to reactants at equal rates. Or, when the concentration of a molecule is the same on both sides of a membrane, and rate of movement is the same in both directions At equilibrium, a system has no capacity to do work.  Chemical Reactions and Equilibrium Equilibrium is a state of maximum stability Equilibrium point is reached when reactants are converted to products and Example: conversion of glucose 1- products are phosphate (blue) to glucose 6-phosphate converted back to (pink) reactants at equal rates  ΔG = 0 Fig. 3.9  Equilibrium At the point of equilibrium, molecules do not stop reacting At equilibrium the rate of the forward reaction equals the rate of the backward reaction As a system moves toward equilibrium, the free energy change (energy available to do work, ΔG) of the system becomes lower At equilibrium, there is no drive for change in the forward or reverse directions, G=0 3.3 Thermodynamics and Life Questions to Consider: Are living systems counter to the laws of thermodynamics? How does energy flow through the biosphere? Equilibrium in Living Systems Living systems are highly organized (maintain low entropy) Living systems are Open, which means they bring in both energy and matter from surroundings and use them to do work and maintain an organized state. They release energy and disordered molecules into the environment (surroundings); therefore, the second law of thermodynamics is upheld, as the entropy of the system and surroundings  Cells Are Open Systems Open systems give off heat and waste byproducts, that are used to increase entropy of surroundings [Insert Fig. 3.10 on p. 60] Open systems bring in both energy and matter from Increased Increased surroundings and use order disorder them to maintain an organized state Fig. 3.10  Why Do We Need to Eat? Organisms never reach equilibrium (ΔG = 0); life requires a constant supply of energy A significant portion of the energy we consume in food is used to maintain a low entropy, highly organized state for our cells Fig. 3.11  Flow of Energy through the Biosphere Heat Heat Heat H2O, CO2, O2 H2O, CO2, O2 Localized energy Localized energy (photons of light) (e.g., carbohydrates) Fig. 3.12  Flow of Energy through the Biosphere Photosynthesis Cellular captures light respiration breaks energy and uses it down carbohydrates to convert carbon and transforms the dioxide into energy into ATP carbohydrates  Metabolic Pathways and Reactions Metabolic pathway: Series of sequential reactions in which products of one reaction are used immediately as reactants for the next reaction in the series Catabolic pathway: Energy is released by breakdown of complex molecules to simpler compounds Anabolic pathway: Consumes energy to build complicated molecules from simpler ones  Catabolism Breakdown of molecules into smaller units, releasing energy Sugars Energy Fatty Amino acids acids  Anabolism Building of more complex molecules/macromolecules from smaller units, requiring an input of energy Energy Amino Acids Proteins  Metabolism Collection of all chemical reactions present within a cell or organism [Insert Fig. 3.13 on p. 61] Fig. 3.13  Metabolism hemical structure of ATP (adenosine triphosphate) Hydrolysis of the phosphate bonds, which includes formation of new bonds in products, results in the net release of free energy that can be used by a cell Fig. 3.14a  Adenine Phosphate groups Ribose Adenosine Adenosine–monophosphate (AMP) Adenosine–diphosphate (ADP) Adenosine–triphosphate (ATP)  See also ATP Hydrolysis Fig. 3.14b Free energy ATP + H 2O ADP + Pi Adenosine Water Adenosine Inorganic triphosphate diphosphate phosphate Exergonic ATP hydrolysis Spontaneous reaction releases free energy Releases energy (-ΔG) that can be used as a source of energy for ΔG = -7.3 kcal/mol the cell  ATP Hydrolysis ATP hydrolysis releases free energy that can be used as a source of energy for the cell Exergonic Spontaneous reaction Releases energy (-ΔG) ΔG = -7.3 kcal/mol Fig. 3.14b, p. 68 ATP and Energy Coupling Energy coupling—the coupling of an endergonic reaction to an exergonic reaction Hydrolysis of ATP is an exergonic reaction that can be coupled to make otherwise endergonic reactions proceed spontaneously. Coupling reactions require enzymes.  ATP and Energy Coupling Spontaneous reactions can drive non- spontaneous reactions Requires that the net ΔG of the two reactions is negative Energy coupling links the energy of exergonic ATP breakdown to endergonic reactions Reaction 1: ΔG > 0 (energy is required) Reaction 2: ΔG < 0 (energy is released) Overall Reaction : ΔG < 0  ATP and Energy Coupling Hydrolysis of ATP is an exergonic reaction that can be coupled to make otherwise endergonic reactions proceed spontaneously Coupling reactions require enzymes Fig. 3.15  ATP/ADP Cycle ATP cycle: Continuous breakdown and resynthesis of ATP [Insert Fig. 3.16 on p. 63] ATP used in coupling reactions is replenished. Reactions replenishing ATP link ATP synthesis to Fig. 3.16  Section 3.5 - Enzymes Just because a reaction is spontaneous does not mean that it proceeds rapidly Enzymes are a special group of proteins that can increase the rate of chemical reactions Catalysts  Enzyme-Catalyzed Reactions Enzymes bind to a reactant (substrate) After binding to reactant, and ultimately releasing the product(s), the enzyme is unchanged Highly specific, recognizing a unique substrate or a class of similar substrates  Activation Energy Initial input of energy to start a reaction, even if it is spontaneous Activation energy, EA: Initial energy investment required to start a reaction Molecules that gain necessary activation energy occupy the transition state Fig. 3.17  Biological Catalysts Catalyst: Chemical agent that speeds up the rate of reaction without itself being chemically altered Enzymes are biological catalysts Increase the rate of a reaction by lowering activation energy of a reaction  Rate of a Reaction All reactions require an input of energy, (EA) to begin An enzyme accelerates the Transition reaction by state reducing EA. ΔG is the same with and without Uncatalyzed reaction an enzyme. Catalyzed reaction Fig. 3.19  Enzyme Specificit y Active site of enzyme combines briefly with reactants (substrates) After releasing the product, the enzyme is unchanged Fig. 3.20 Catalytic Cycle of Enzymes [Insert Fig. 3.21 on p. 67] Fig. 3.21  Enzyme Cofactors Enzyme cofactors Nonprotein groups necessary for catalysis to occur Cofactors: Metallic ions (Mg2+, Fe2+, Cu2+, Zn2+) Example: Mg2+ is a cofactor for GTPases Coenzymes: Organic cofactors such as vitamins  Transition State During catalysis, the substrate and active site of the enzyme form an intermediate transition state Enzymes facilitate the formation of the transition state via 3 major mechanisms: 1. Bringing the reacting molecules into close proximity 2. Exposing the reactant molecules to altered environments that promote their interactions 3. Changing the shape of a substrate Formation of the Transition State [Insert Fig. 3.22 on p. 67] Fig. 3.22, p. 67 Formation of the Transition State [Insert Fig. 3.22 on p. 67] Fig. 3.22, p. 67 Formation of the Transition State [Insert Fig. 3.22 on p. 67] Fig. 3.22, p. 67  Enzyme and Substrate Concentrations In presence of excess substrate, rate of catalysis is proportional to amount of enzyme When substrate concentration is low: Enzymes and substrates collide infrequently Reaction rate slows When substrate concentration is high: Enzymes become saturated with reactants Rate of reaction levels off Enzyme and Substrate Concentrations Excess substrate Enzyme concentration is kept constant [Insert Fig. 3.23 on p. 68] Enzyme and substrate concentrations can change the rate of catalysis Fig. 3.23  Enzyme Inhibition Enzyme inhibitors are nonsubstrate molecules that can bind to an enzyme and decrease its activity Competitive inhibition: Inhibitor competes with normal substrate for active site Noncompetitive inhibition: Inhibitor does not compete with normal substrate for active site, but combines with sites elsewhere on enzyme Inhibitor  Competitive Inhibition of Enzyme Activity Competitive inhibitors differ in how strongly they bind to the active site.  Reversible: weak  Irreversible: strong, covalent bonds, highly toxic (cyanide) Fig. 3.24  Enzyme Regulation Allosteric regulation occurs with reversible binding of a regulatory molecule to an allosteric site, a location on the enzyme that is different from the active site High-affinity state (active form); enzyme binds substrate strongly Low-affinity state (inactive form); enzyme binds substrate weakly or not at all  Noncompetitive/ Allosteric Activator Allosteric activators convert an enzyme from the low to the high affinity state Fig. 3.25  Noncompetitive/ Allosteric Inhibitor Allosteric inhibitors convert an enzyme from the high to the low affinity state Fig. 3.25  Feedback Inhibition Product of enzyme-catalyzed pathway acts as a regulator of the reaction Helps conserve cellular resources Mechanism is allosteric regulation Fig. 3.26  Temperature and pH Effects Typically, each enzyme has an optimal temperature and pH where it operates at peak efficiency At temperature and pH values above or below optimum, reaction rates fall off Most enzymes have a pH optimum near pH of cellular contents, about pH 7 Enzymes secreted from cells may have pH optima farther from neutrality Enzyme Activity and pH [Insert Fig. 3.27 on p. 71] Changes in pH affect the charged groups in the amino acids of the enzyme Fig. 3.27  Effects of Temperature Two distinct effects:  As temperature rises toward the optimum, the rate of reactions increases  High temperatures affect proteins, including enzymes, by denaturing them, and reducing the rate of reactions Fig. 3.28  Enzyme Activity and Temperature Visible effects of environmental temperature on enzyme activity in Siamese cats A heat-sensitive enzyme controlling melanin production is denatured in warmer body regions Fig. 3.28