An Introduction to Metabolism

Transcription

1 An Introduction to Metabolism The living cell is a microscopic factory where life s giant processes can be performed: -sugars to amino acids to proteins and vise versa -reactions to dismantle polymers (hydrolysis) -reactions to assemble polymers (dehydration and condensation) -cellular respiration: extracting energy stored in sugars and other fuels to perform another work (e.g. transportation of solutes across the plasma membrane) Concept 1: The metabolism of an organism that transforms matter and energy is subjected to the laws of thermodynamics The Chemistry of Life is Organized into Metabolic Pathways - Metabolism: the total of chemical reactions carried out by an organism; thousands of intersecting metabolic pathways. - A metabolic pathway begins with a specific molecule and ends with another specific molecule (or product) through a series of steps, each step is catalyzed by a specific enzyme. - Enzymes: regulate/balance metabolic supply and demand; averting/preventing deficits or surpluses of important cellular molecules. - Catabolic pathways (breakdown pathways or degradative processes): release energy by breaking down complex molecules to simpler compounds, e.g. cellular respiration is a major catabolic pathway. - Anabolic pathways (biosynthetic pathways): consume energy to build complicated molecules from simpler ones, e.g. synthesis of a protein from amino acids. - Metabolism is, thus, about management of the material and energy resources of the cell; energy released from the catabolic reactions can be stored and then used to drive the anabolic reactions. - Bioenergetics: the study of how organisms manage their energy resources (studying of mechanisms common to metabolic pathways) Forms of Energy - Energy, in general, is the capacity to do work. The life s work depends on the ability of cells to transform energy from one type to another. Cells or organisms are energy transformers (not energy producers). - Light energy - Chemical energy - Kinetic energy - Potential energy - Thermal energy (heat) The Laws of Energy Transformation Thermodynamics is the study of the energy transformation that occur in a system (a system refers to the matter under study) -A closed system, an open system, surroundings, and the universe. 1

2 The First Law of Thermodynamics - Energy can be transferred and transformed but it cannot be created or destroyed ---the energy of the universe is constant. The Second Law of Thermodynamics - Every energy transfer or transformation increases the entropy of the universe --- entropy is a measure of disorder or randomness due to loss of usable/available energy during energy transfer or transformation---the more randomly arranged a system (a collection of matter) is the greater its entropy. -The second low in other statement For a process to occur spontaneously, it must increase the entropy of the universe ---a spontaneous process (a process occur without input of energy, like flow of water down hills or like breakdown of complex molecules to simpler ones) releases energy with partial loss of usable (chemical) energy into unusable (heat) energy. Biological Order and Disorder---organisms are islands of low entropy in an increasingly random universe---explain. Concept 2: The free- energy change of a reaction tells us whether the reaction occurs spontaneously Biologists want to understand the chemical reactions of life---they want to know which reactions occur spontaneously and which ones require some input of energy from outside- --spontaneous reactions are those that can supply energy to do work in the living cell, and, therefore, they are of metabolic importance. Free-Energy Change ( G) - Free energy G is (or measures) the energy portion of a system that can perform work when temperature and pressure are uniform throughout the system, as in living cell--- when a system changes during chemical reactions its free energy changes as well---how a change in free energy of a system can be determined: For any chemical reaction: G = H - T S G: the free energy of a system G: the change in free energy of a system H: the total energy of a system (system s enthalpy) H: the change in system s enthalpy S: the system s entropy (the amount of randomness or disorder of a system) S: the change in the system s entropy T: the absolute temperature in Kelvin (K) units - The value of G indicates/predicts whether the process will be spontaneous (i.e. the process will run without input of energy from outside). - For a process to occur spontaneously: - G must be negative ( G<0) - H of the system must decrease (i.e. the system gives up enthalpy) or - TS must increase (the system gives up order, i.e. becomes disordered) or - both (decrease in the system s enthalpy and increase in the system s entropy) - Processes that have a positive or zero G are never spontaneous. 2

3 - Why this information is immensely interesting to biologists? Free Energy, Stability, and Equilibrium - G represents the difference between the free energy of the final state and the free energy of the initial state: G = G final state G initial state - G can only be negative when the process involves a loss of free energy during the change from initial state to final state. The system in its final state is more stable than it was in the initial state because it has less free energy which is less likely to change. - Free energy can be a measure of system s instability---unstable systems (higher G) tend to change in such a way that they become more stable (lower G)---example: a sugar molecule is less stable than the simpler molecules into which it can be broken. - Equilibrium = a state of maximum stability = forward and backward chemical reactions occur at the same rate. - For a system at equilibrium, the free energy (G) is at its lowest possible value in the system---a system at equilibrium can not be spontaneously changed and, therefore,. it can do no work. - A process is spontaneous and can perform work only when it is moving toward equilibrium. -For the relationship of free energy to stability, work capacity, and spontaneous change, see figure 8.5, page 146. Free Energy and Metabolism - Chemical reactions can be classified as either exergonic (energy outward) or endergonic (energy inward). - In an exergonic (spontaneous) chemical reaction, the products have less free energy (G) than the reactants ( ΔG ).---the reaction proceeds with a net release of free energy. -The magnitude of ΔG for an exergonic reaction represents the maximum amount of work the reaction can perform. - The overall reaction for cellular respiration is an example of exergonic reaction: i.e. for each mole (180 g) of glucose broken down by respiration under standard condition, 686 kcal (2,870 kj) of energy are made available for work.---the chemical products of respiration store 686 kcal less free energy per mole than the reactants. 3

4 - Endergonic (nonspontaneous) reactions require an input of energy (+ΔG). i.e. absorbs free energy from its surroundings. - In an endergonic (nonspontaneous) chemical reaction, the products have higher free energy (G) than the reactants (+ΔG ).---the reaction cannot proceed by itself. -The magnitude of ΔG for an endergonic reaction represents the amount or quantity of energy required to drive the reaction. -Plants get the required energy (686 kcal to make a mole of sugar) from the environment by capturing light and converting its energy to chemical energy. Next, in a long series of exergonic steps, they gradually spend that chemical energy to assemble sugar molecules. - See figure 8.6, page 147, for free energy changes (ΔG) in exergonic and endergonic reactions. Equilibrium and Metabolism - A cell that has reached metabolic equilibrium is dead! That is because systems at equilibrium are at a minimum of G and can do no work. - A cell in our body is not in equilibrium; the constant flow of materials in and out of the cell keeps the metabolic pathway from ever reaching equilibrium. The key to maintaining this lack of equilibrium is that the product of one reaction does not accumulate, but instead becomes a reactant in the next step; finally, waste products are expelled from the cell. In brief, the addition of starting materials and the removal of end products prevent metabolism from reaching equilibrium. Concept 3: 8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work: - Mechanical work (e.g. beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction) - Transport work (e.g. pumping of substances across membranes against the direction of spontaneous movemen) - Chemical work (e.g. pushing of endergonic reactions, the synthesis of polymers from monomers). How cells manage their energy resources to do work? - Energy coupling: the use of an exergonic process (ATP hydrolysis) to drive an endergonic one (the synthesis of the amino acid glutamine from glutamic acid and ammonia) - ATP is responsible for mediating most energy coupling in cells. 4

5 The Structure and Hydrolysis of ATP - ATP contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups bonded to it - The ATP-hydrolysis reaction is exergonic and under standard conditions releases 7.3 kcal of energy per mole of ATP hydrolyzed. - The release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves. Why does the hydrolysis of ATP release so much energy? - The three phosphate groups of the ATP molecule are negatively charged and their mutual repulsion contributes to the instability of the triphosphate tail (region) of the ATP molecule. Example of an Energy coupling using ATP hydrolysis - The exergonic process (ATP hydrolysis) is used to drive an endergonic process (the synthesis of the amino acid glutamine from glutamic acid and ammonia). How ATP Performs Work (Phosphate group transfer) - The key to coupling exergonic and endergonic reactions is the formation of a phosphorylated intermediate, which is more reactive (less stable) than the original unphosphorylated molecule. - With the help of specific enzymes, the cell is able to couple the energy of ATP hydrolysis directly to endergonic processes by transferring a phosphate group from ATP to other molecule (the reactant). How ATP drives the three types of cellular work mechanical, transport, and chemical - ATP drives mechanical work by phosphorylating motor proteins, such as the ones that move organelles along cytoskeletal tracks in the cell. - ATP drives active transport by phosphorylating certain membrane proteins. - ATP drives chemical work by phosphorylating key reactants, for example glutamic acid that is then converted to glutamine. - The phosphorylated molecules lose the phosphate groups as work is performed, leaving ADP and inorganic phosphate (P i ) as products. - Cellular respiration regenerate the ATP supply by powering the phosphorylation of ADP. The Regeneration of ATP The free energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in the cell. The ATP cycle - Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. - Energy stored in ATP drives most cellular work. 5

6 Concept 4: 8.3 Enzymes speed up metabolic reactions by lowering energy barriers - The laws of thermodynamics tell us what will and will not happen under given conditions but say nothing about the rate of these processes. - A solution of sucrose dissolved in sterile water will sit for years at room temperature with no appreciable hydrolysis. - However, if we add a small amount of a catalyst, such as the enzyme sucrase, to the solution, then all the sucrose may be hydrolyzed within seconds. - How does an enzyme do this? - What impedes a spontaneous reaction from occurring faster and how an enzyme changes the situation? The Activation Energy Barrier - Every chemical reaction between molecules involves both bond breaking and bond forming. - Changing one molecule into another generally involves contorting the starting molecule into a highly unstable state before the reaction can proceed. - To reach the contorted state where bonds can change, reactant molecules must absorb energy from their surroundings. - When the new bonds of the product molecules form, energy is released as heat, and the molecules return to stable shapes with lower energy. - The initial investment of energy for starting a reaction the energy required to contort the reactant molecules so the bonds can change is known as the free energy of activation, or activation energy, abbreviated E A. - Activation energy is often supplied in the form of heat that the reactant molecules absorb from the surroundings. - (The bonds of the reactants break only when the molecules have absorbed enough energy to become unstable and are therefore more reactive (in the transition state) - The absorption of thermal energy increases the speed of the reactant molecules - For some reactions, E A is modest enough that even at room temperature there is sufficient thermal energy for many of the reactants to reach the transition state in a short time. - In most cases, however, E A is so high and the transition state is reached so rarely that the reaction will hardly proceed at all. How Enzymes Lower the E A Barrier - Proteins, DNA, and other complex molecules of the cell are rich in free energy and have the potential to decompose spontaneously. - However, the barriers for selected reactions must occasionally be overcome for cells to carry out the processes necessary for life. - Heat speeds a reaction by allowing reactants to attain the transition state more often, but this solution would be inappropriate for biological systems. - Organisms use an alternative: catalysis - An enzyme catalyzes a reaction by lowering the E A barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures. 6

7 Enzymes affect the reaction rate not the free-energy change - An enzyme speeds the reaction by reducing its activation energy (E A )without affecting the free energy change (ΔG) for a reaction. Substrate Specificity of Enzymes - The enzyme binds to its substrate (or substrates) forming an enzyme substrate complex. - The reaction catalyzed by each enzyme is very specific; an enzyme can recognize its specific substrate even among closely related compounds, such as isomers. - The specificity of an enzyme is attributed to a compatible fit between the shape of its active site and the shape of the substrate. - When the substrate enters the active site, it induces a change in the shape of the protein. - This change allows more weak bonds to form, causing the active site to embrace the substrate and hold it in place. Catalysis in the Enzyme s Active Site - Very small amounts of enzyme can have a huge metabolic impact by functioning over and over again in catalytic cycles. - The enzyme always catalyzes the reaction in the direction of equilibrium. - When an enzyme population is saturated, the only way to increase the rate of product formation is to add more enzyme molecules. - Cells sometimes do this by making more enzyme molecules. Effects of Local Environmental Conditions on Enzyme Activity Effects of Temperature and ph - Each enzyme has an optimal temperature at which its reaction rate is greatest. - Without denaturing the enzyme, this temperature allows the greatest number of molecular collisions and the fastest conversion of the reactants to product molecules. - Most human enzymes have optimal temperatures of about C (close to human body temperature). - Bacteria that live in hot springs contain enzymes with optimal temperatures of 70 C or higher. - Each enzyme has a ph at which it is most active. - The optimal ph values for most enzymes fall in the range of ph 6 8, but there are exceptions. - For example, pepsin, a digestive enzyme in the stomach, works best at ph 2. - In contrast, trypsin, a digestive enzyme residing in the alkaline environment of the intestine, has an optimal ph of 8. Cofactors - A cofactor is any non-protein molecule or ion that is required for the proper functioning of an enzyme. - Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis. 7

8 - A Coenzym is an organic molecule serving as a cofactor. Most vitamins function as coenzymes in important metabolic reactions. Enzyme Inhibitors - Certain chemicals selectively inhibit the action of specific enzymes. - If the inhibitor attaches to the enzyme by covalent bonds, inhibition is usually irreversible. - Competitive inhibitors: Chemical substances Enzyme mimics reduce the productivity of enzymes by blocking substrates from entering active sites. - This kind of inhibition can be overcome by increasing the concentration of substrate. - Noncompetitive inhibitor: A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate. 8