Energy Basics Metabolism and Enzymes Chapter 5 Pgs. 77 86 Chapter 8 Pgs. 142 162 Energy is the capacity to cause change, and is required to do work. Very difficult to define quantity. Two types of energy: Potential energy (PE): stored energy as a result of its position or structure Chemical energy is PE available for release in a chemical reaction. Kinetic energy (KE): energy associated with motion Heat (thermal energy) is associated with random movement of atoms or molecules. Energy can be converted from one form to another, as in chemical mechanical electrical. Gravitational Elastic Nuclear Electrical (separation of charges) Chemical (energy stored in chemical bonds) Potential Energy Kinetic Energy Moving objects Radiation (movement of light particles/waves) Thermal (heat, movement of particles) Electrical (movement of electrons) Thermodynamics How energy works follows the laws of thermodynamics. Thermodynamics is the study of energy transformations that occur in nature. First law: the total amount of energy in the universe remains constant energy cannot be created or destroyed, but is converted from one form to another. Also called the principle of Conservation of Energy. Second law: when energy is converted form one form to another, some energy is lost not gone, but becomes unusable or unable to do work (usually heat). As additional energy conversions occur, more energy becomes unusable, and things become disorganized disorder or randomness increases (entropy). Because energy is constantly moving from one form to another, a consequence is that entropy increases in the universe. Energy Conversions Energy conversions are usually discussed within the context of a system, like a chemical reaction, cell, organism, or a planet like Earth. Closed systems are those in which energy transfers among specific items are considered. They are isolated from their surroundings, as liquid in a furnace. Open systems are those in which exchanges of energy with the surroundings are included. Living things and the earth are open systems because they receive energy from sunlight. As energy is converted, a lot of it is lost as heat. Energy is also spread from areas of high energy to low energy. 1
Gibbs Free Energy Gibbs free energy: energy in a system that is available for conversions Not all of this energy is actually available for chemical reactions because during the reaction, some energy will be lost as heat as entropy increases. Change in free energy as a result of conversion is represented by ΔG. ΔG = ΔH - T ΔS H = total energy, S = entropy, T = temperature The value of ΔG can be negative or positive. ΔG When ΔG is negative for a reaction, there is a net release of free energy. This reaction is exergonic and can occur spontaneously (without the input of energy). Respiration: the breakdown of glucose into CO 2 and H 2 O. ΔG is -686 kcal/mol When ΔG is positive for a reaction, free energy must be added to the reaction for it to occur. This reaction is endergonic. Photosynthesis: the making of glucose from CO 2 and H 2 O. ΔG is +686 kcal/mol These reactions cannot occur spontaneously. More about Free Energy Most metabolic reactions are endergonic (positive ΔG) and require an input of energy. Usually comes from hydrolysis of ATP to ADP (ΔG = -7.3 kcal/mol) This hydrolysis of ATP (an exergonic reaction, negative ΔG ) occurs in tandem, or coupled, with the endergonic metabolic reaction. This coupling usually involves the transfer of energy with one of the inorganic phosphates (P i ) from ATP to one of the reactants. Coupled reactions with ATP (and with the help of specific enzymes) are typical of most endergonic metabolic reactions Adenosine Triphosphate (ATP) ATP is the cell s main energy source in energy coupling, where exergonic reactions drive endergonic ones. ATP = adenine + ribose + 3 phosphates Hydrolysis breaks the bonds between the phosphate groups to release energy. Phosphorylation makes bonds between phosphate groups to store energy. Enzymes responsible for this are called kinases. 2
Generating ATP Phosphorylation is the process of adding energy and an inorganic phosphate to ADP to make ATP: Energy + P i + ADP ATP Two basic mechanisms: Substrate-level phosphorylation: substrate donates the phosphate group and associated energy are to convert ADP to ATP. Oxidative phosphorylation: the phosphate group used to convert ADP to ATP comes from electrons transported through a chain of reactions Protein Review Categories Structural proteins Storage proteins Transport proteins Defensive proteins Enzymes Monomer: amino acids Structure, structure, structure! Levels of protein folding Hydrogen bonding, ionic bonding, and disulfide bonds Metabolism The sum of all chemical reactions that occur in biological systems. Metabolic pathway: begins with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product; each step is catalyzed by a specific enzyme. Includes Catabolism: break-down of substances, releases energy Anabolism: synthesis; formation of new products, requires energy Transferring of energy from one substance to another Requires sufficient activation energy (E A ) to trigger the formation of new bonds Catalysts accelerate the rate of reaction without being consumed themselves by the reaction Common Characteristics of Metabolism The net direction of metabolic reactions is determined by the concentration of the reactants and the end products. Will the overall reaction proceed in the forward or reverse direction? Chemical equilibrium: the rate of reaction in the forward and reverse directions are equal; there is no net production of reactants or products. A + B C + D Enzymes are globular proteins with tertiary structure that act as catalysts for metabolic reactions. They have the following characteristics: Substrate is the substance(s) that the enzyme acts on. Enzymes are substrate-specific and form an enzymesubstrate complex. An enzyme is unchanged as the result of a reaction. An enzyme catalyzes a reaction in both the forward and reverse directions. The efficiency of an enzyme is affected by temperature, ph, chemicals, and salt concentration. Optimum temperature, ph Denaturation The standard suffix for enzymes is -ase and enzymes are typically named after their substrate. The induced-fit model describes how enzymes work. 3
Activators Cofactors are nonprotein molecules that assist enzymes by binding to them. Coenzymes are organic cofactors that usually function to donate or accept some component of a reaction, often electrons. Include vitamins. Inorganic cofactors are often metal ions, like Fe 2+ and Mg 2+. Include most minerals. ATP (adenosine triphosphate) is a common source of activation energy for metabolic reactions. Essentially an RNA adenine nucleotide with two additional phosphate groups. When it releases its energy, a hydrolysis reaction breaks the last phosphate bond of the ATP molecule to form ADP (adenosine diphosphate) and an inorganic phosphate group (P i ). ATP + H 2 O ADP + P i + energy In the reverse dehydration reaction, new ATP molecules are assembled by phosphorylation when ADP combines with a phosphate group using energy obtained from an energy-rich molecule (like glucose) Regulating Chemical Reactions Enzymes have two kinds of binding sites one is an active site for the substrate and the other is an allosteric site for an allosteric effector. Two types: Allosteric activator: binds to enzyme and induces the active form. Stabilizes the active site. Allosteric inhibitor: binds to enzyme and induces the inactive form. Stabilizes the inactive form. Some inhibitors bind irreversibly and permanently change the enzyme structure. Others are weakly bonded and their effects are reversible. Feedback inhibition: end product of a series of reactions acts as an allosteric inhibitor, shutting down one of the enzymes catalyzing the reaction series. Prevents wasting chemical resources. Competitive inhibition: a substance mimicking the substrate inhibits an enzyme by occupying the active site; this displaces the substrate and prevents the enzyme from catalyzing the substrate. Noncompetitive inhibition: substance that inhibits an enzyme by binding at a location other than the active site (i.e. allosteric site). This changes the shape of the enzyme, disabling its activity. Many toxins and antibiotics are noncompetitive inhibitors. Cooperativity: enzyme becomes more receptive to additional substrate molecules after one substrate molecule attaches to an active site Occurs in enzymes that consist of two or more subunits, each with its own active site. Common example: though not an enzyme, hemoglobin has increased binding capacity for oxygen molecules after the first oxygen binds to an active site Specific Localization of Enzymes Within the Cell Cell is compartmentalized and cellular structures help bring order to metabolic pathways Some enzymes are on particular membranes (mitochondria) Some enzymes are on fixed locations within the cell 4
Why Do Biologists Care About This Physics Stuff? Because living things obey these laws! Living things need an energy input to remain whole. They are also always losing energy to their surroundings. Energy and Living Things Order and organization require energy. Things naturally break down to keep them from breaking down or to put them together requires energy input. Maintain body temperature. Endotherms regulate body temperature using metabolic reactions. Ecotherms use external sources to maintain body temperature. Reproduction requires lots of energy! Many species only reproduce when energy is available. Growth. Extra free energy not needed for cellular processes like movement and reproduction can be put into growth. Movement. Energy Deprivation Mass is broken down to provide energy. Eventually death will occur if there is no energy input. Smaller Organisms Require More Food Per Body Mass Smaller organisms have more surface area relative to volume, so they lose more heat. They must replenish that energy loss by eating more (relative to their body size) than larger animals do. The Trophic Levels Energy works its way up the food chain. BUT at every level energy is being lost due to entropy. So there is less energy available for higher levels of the food chain. The more energy available for a population, the more it will grow. There is rarely enough energy to support more than 3 4 steps on a food chain. There is very little energy left for top level carnivores this is part of the reason these animals are so often endangered. 5