Lecture 7: Enzymes and Energetics I. Biological Background A. Biological work requires energy 1. Energy is the capacity to do work a. Energy is expressed in units of work (kilojoules) or heat energy (kilocalories) 2. Organisms convert potential energy and kinetic energy a. Potential energy is stored energy b. Kinetic energy is energy of motion II. Laws of thermodynamics governing energy transformations A. Total energy in the universe does not change 1. First law of thermodynamics: Conservation of energy a. The total energy of a closed system remains constant b. Biological systems are open systems c. Organisms can only convert energy to other forms B. Entropy of the universe is increasing 1. In most energy conversions, energy is lost as heat 2. Entropy may be defined as an increase in disorder or randomness 3. Second law of thermodynamics a. Total amount of entropy (S) increases in the universe as energy is converted from one form to another III. Energy Transformations during Metabolic Reactions A. Types of metabolism 1. Anabolic and catabolic pathways a. Anabolism includes synthetic pathways b. Catabolism includes reactions in which molecules are degraded B. Enthalpy is the total potential energy of a system 1. Bond energy is the amount of energy required to break a molecular bond 2. Enthalpy (H) is the total bond energy C. Free energy is energy that is available to do cellular work 1. Free energy is the total energy available to do work a. Expressed in kilojoules or kilocalories as G 2. G is inversely related to entropy 3. H = G + TS a. H is enthalpy b. T is the absolute temperature ( K) c. S is entropy d. When T is constant, E = free energy + entropy (unusable energy) e. As the temperature increases, entropy increases
D. Chemical reactions involve changes in free energy 1. The Greek letter delta ( ) is used to refer to changes between initial and final states 2. G = H T S E. Free energy decreases during an exergonic reaction 1. The total free energy of a system in the final state is less than the total free energy in the original state 2. Exergonic reactions have a G a. Exergonic reactions release energy and are spontaneous reactions b. These reactions still require activation energies F. Free energy increases during an endergonic reaction 1. An endergonic reaction is one in which there is a gain of free energy G. Free energy changes depend on the concentrations of reactants and products 1. Reactions proceed to a state of dynamic equilibrium 2. Cellular reactions are typically never at equilibrium H. Cells drive endergonic reactions by coupling them to exergonic reactions 1. Coupled reactions may drive thermodynamically unfavorable endergonic reactions 2. In energy coupling, one must look at the total G of both reactions 3. Endergonic reactions are coupled with exergonic reactions a. Beakdown of ATP
IV. Adenosine triphosphate (ATP) A. ATP molecule has three main parts 1. Nitrogen-containing base (adenine) 2. Ribose, a pentose 3. 3 phosphate groups in a series
B. ATP donates energy through the transfer of a phosphate group 1. The bonds linking the 3 phosphate groups may be broken by hydrolysis a. These reactions have a large G ( 7.6 kcal/mole) b. ATP is hydrolyzed to form ADP + Pi c. This reaction may be coupled with an endergonic reaction d. Phosphorylation reactions occur when the phosphate group is transferred to another molecule C. ATP links exergonic and endergonic reactions 1. Phosphorylation is coupled to endergonic processes D. The cell maintains a very high ratio of ATP to ADP 1. The actual free energy of ATP under cellular conditions is -10 to -12 kcal/mole 2. The ratio of ATP to ADP is about 10:1 3. ATP cannot be stockpiled 4. A resting human uses about 450 kg (100 lbs.) per day of ATP a. Amount present at any given time in the entire body is less than 1 gram (0.03 oz.) 5. Approximately 10 million molecules of ATP are made and recycled in every cell each second
V. Redox Reactions A. Oxidation 1. Loss of electrons a. Oxidation involves the loss of energy B. Reduction 1. Gain of electrons a. Gain of energy 2. These processes occur simultaneously, called redox reactions B. Most electron carriers carry hydrogen atoms 1. Electron carriers transfer energy to an acceptor 2. Electrons lose energy as they are transferred between acceptors 3. Nicotinamide adenine dinucleotide (NAD+) is a common hydrogen acceptor in respiratory and photosynthetic pathways 4. Nicotine adenine dinucleotide phosphate (NADP+) is involved in photosynthesis 5. Flavin adenine dinucleotide (FAD) is involved in cellular respiration 6. Cytochromes are proteins containing iron and are also electron carriers VI. Enzymes are chemical regulators A. Most enzymes are protein catalysts 1. Increase the rate of chemical reactions 2. Some organic catalysts are enzymes Nucleotide-based molecules 3. Enzymes are targets for cellular control B. All reactions have a required energy of activation (EA)
C. An enzyme lowers the activation energy needed to initiate a chemical reaction 1. Enzymatic action has no effect on the overall free energy D. An enzyme works by forming an enzyme-substrate (ES) complex 1. Enzymes have at least one 3-dimensional area active site 2. The current model of enzymatic action is the induced-fit model a. Active site is not rigid b. Binding of the substrate to the active site involves conformational changes in both the enzyme and (typically) the substrate c. The enzyme and substrate form an ES or enzyme-substrate complex d. After binding to the substrate, the product is released, and the enzyme can be reused E. Naming enzymes 1. Named for substrate a. Names end in -ase b. E.g. Sucrase is an enzyme that reacts with sucrose 2. Other enzymes have older names ending in zyme a. Do not reflect function b. E.g. Pepsin and trypsin give F. Enzyme specificity 1. Because of the binding at the active site, the substrate is very specific to the enzyme 2. Not all enzymes are specific (e.g. lipases react with a variety of fats)
G. Many enzymes require cofactors 1. Many enzymes are composed of a protein (an apoenzyme) and a cofactor 2. Inorganic cofactors include elements such as Mg, Ca, Fe, Cu, Zn, and Mn 3. Organic non-protein cofactors bind with the enzyme, forming a coenzyme a. Coenzymes are typically transfer agents i. NADH, NADPH, and FADH2 b. ATP is a coenzyme c. Coenzyme A is important in the transfer of groups derived from organic acids 4. Most vitamins are coenzymes or are parts of coenzymes H. Enzymes are most effective at optimal conditions 1. Each enzyme has an optimal temperature a. In the human body, the optimal temperature for enzymes is near body temperature b. High temperatures denature protein enzymes 2. Each enzyme has an optimal ph a. In the human body, the optimal ph for most enzymes is between 6 and 8 b. A suboptimal ph denatures protein enzymes I. Enzymes are organized into teams in metabolic pathways 1. Enzymes often work in sequences J. The cell regulates enzymatic activity 1. Amount of enzyme produced can control the rate of a reaction a. Typically by feedback mechanisms 2. Allosteric enzymes have a receptor site to which allosteric regulators bind a. Some allosteric regulators are inhibitors of the enzyme; others are activators of the enzyme K. Enzymes can be inhibited by certain chemical agents 1. Reversible inhibition may be competitive or noncompetitive a. Reversible competitive inhibition involves a molecule that is structurally similar to the normal substrate i. The inhibitor binds to the active site temporarily ii. Reversible noncompetitive inhibition involves binding at a site other than the active site temporarily (similar to allosteric inhibition) 2. Irreversible inhibitors permanently inactivate the enzyme a. E.g. Nerve gases (cyanide), heavy metals (Hg, Pb)