BIO 281- Week 6 Notes: Capturing and Using Energy
BIO 281- Week 6 Notes: Capturing and Using Energy BIO 281
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Date Created: 09/24/16
Week 5 Chapter 6: Capturing and Using Energy Monday, September 12, 2016 7:28 PM 6.1 An overview of Metabolism When considering a cell's use of energy, it is helpful to consider the cell's sources of carbon. Carbon-based compounds are stable forms of energy storage. There are four ways in which organisms acquire the energy and materials needed to grow, function, and reproduce. Metabolism is the set of chemical reactions that sustain life. The term metabolism encompasses the entire set of these chemical reactions that convert molecules into other molecules and transfer energy in living organisms. Metabolism is divided into two branches: catabolism is the set of chemical reactions that break down molecules into smaller units and, in process, produce ATP, andanabolism is the set of chemical reactions that build molecules from smaller units and require an input of energy, usually in the form of ATP. Carbohydrates can be catabolized into sugars which release energy stored in the chemical bonds. The synthesis of macromolecules such as carbohydrates by contrast is anabolic. 6.2 Kinetic and Potential Energy Energy can be defined as the capacity to do work. While there are many different sources of energy, energy comes in just two major forms. Kinetic energy and potential energy are two forms of energy Kinetic energy is the energy of motion, and it is perhaps the most familiar form of energy. Energy is not always associated with motion. An immobile object can still possess a form of energy called potential energy or stored energy. Potential energy depends on the structure of the object or its position relative to its surroundings, and it is released by a change in the object's structure or position. Energy can be converted from one form to another. Chemical energy is a form of potential energy Chemical energy is a form of potential energy held in the chemical bonds between pairs of atoms in a molecule. Some bonds are stronger than others. A strong bond is hard to break because the arrangement of orbitals in these molecules is much more stable than the two atoms would be on their own. As a result, strong bonds do not contain very much energy. Some covalent bonds are relatively weak, and these bonds are easily broken because the arrangement of orbitals in these molecules is somewhat more stable than if the two atoms did not share any electrons. Bio 281 Lecture Page 1 Some covalent bonds are relatively weak, and these bonds are easily broken because the arrangement of orbitals in these molecules is somewhat more stable than if the two atoms did not share any electrons. These weak covalent bonds require a lot of energy to stay intact and contain a lot of chemical energy, similar to the potential energy of a ball at the top of the stairs. ATP is a readily accessible form of cellular energy 6.3 The Laws of Thermodynamics The first law of thermodynamics: Energy is conserved The first law of thermodynamics is the law of conservation of energy which states the universe contains a constant amount of energy. Therefore, energy is neither created nor destroyed. The second law of thermodynamics: Energy transformations always result in an increase in disorder in the universe In going from one form of energy to another, the energy available to do workdecreases. Energy transformations are never 100% efficient since the amount of energy available to do work decreases every time energy changes forms. When kinetic energy is changed into potential energy, the amount of disorder always increases. This principle is summarized by the second law of thermodynamics, which states that the transformation of energy is associated with an increase in disorder of the universe. The degree of disorder is called entropy. The higher the temperature, the more rapidly molecules move and the higher the disorder. In organisms, catabolic reactions result in an increase of entropy as a single ordered biomolecules is broken down into several smaller ones with more freedom to move around. Anabolic reactions decrease entropy because they use individual building blocks to synthesize more ordered biomolecules. 6.4 Chemical Reactions Chemical reactions are central to life processes due to the fact that organisms break down food molecules, such as glucose, storing energy in the bonds of ATP, which powers these reactions. A chemical reaction is the process by which molecules, called reactants, are transformed into other molecules, called products. During a chemical reaction, atoms keep their identity, but the bonds linking the atoms change. Most reactions are readily reversible: The products can react to form the reactants. The way a reaction is written defines forward and reverse reactions. A forward reaction proceeds from left to right and the reactants are located on the left side of the arrow; a reverse reactions proceeds right to left and the reactants are located on the right side of the arrow. Direction of a reaction can be influenced by the concentrations of reactants and products. Increasing the concentration of the reactants or decreasing the concentration of the products favors forwards reaction. This effect explains how many reactions in metabolic pathways proceed: The products of many reactions are quickly consumed by the next reaction, helping to drive the first reaction forward. The laws of thermodynamics determine whether a chemical reaction requires or releases energy available to do work. The amount of energy available to do work is called the Gibbs free energy (G). Bio 281 Lecture Page 2 The amount of energy available to do work is called the Gibbs free energy (G). In a chemical reaction, we can compare the free energy of the reactants and products to determine whether the reaction releases energy that is available to do work. The difference between the two values is denoted by the Greek letter delta (Δ). If the products of a reaction have more free energy than the reactants, thenΔG is positive and a net input of energy is required to drive the reaction forward. By contrast, if the products of a reaction have less free energy than the reactants,ΔG is negative and energy is released and available to do work. Reactions with a negative ΔG that release energy and proceed spontaneously are called exergonic and reactions with a positive ΔG that require an input of energy and are not spontaneous are called endergonic. Negative G = lots of energy + spontaneous + exergonic-catabolic Positive G=little to no energy + not spontaneous + endergonic-anabolicx Spontaneous in this context means that a reaction releases energy. The total amount of energy is equal to the energy available to do work plus the energy that is not available to do work because of the increase in entropy. This relationship can be shown as an equation in which the total amount of energy is enthalpy (H), the energy available to do work is Gibbs free energy (G), and the degree of disorder is entropy (S) multiplied by the absolute temperature (T) (measured in degrees Kelvin). Total amount of energy (H)= energy available to do work (G) + energy lost to entropy (TS) If we want to find energy available for a cell to do work, or G the equation is: G=H-TS We can compare the total energy and entropy of the reactants with the total energy and entropy of the products to see if there is energy available to do work. Shown by the equation: ΔG =ΔH - TΔS This is useful way to see if a chemical reaction takes place spontaneously, what direction the reaction proceeds in and whether net energy is required or released. Catabolic reactions are those which the products have less energy (lower enthalpy) in their bonds than the reactants have, and the products have more disordered (higher entropy) than the reactants are. In other words, such reactions have a negative value ofΔH and a positive value of ΔS. Therefore these ractions proceed spontaneously. If ΔG is positive or negative determines whether a reaction is spontaneous or not. The hydrolysis of ATP is an exergonic reaction A hydrolysis reaction breaks down polymers into their subunits, and in the process one product gains a proton and the other gains a hydroxyl group. The reaction of ATP with water is an exergonic reaction because there is less free energy in the products compared to the reactants. ADP has two energy groups while ATP has three therefore, ADP is more stable than ATP, resulting in a negative value of ΔH. A single molecule of ATP is broken down into two molecules, ADP and P. Therifore, the reaction is also associated with an increase in entropy, or a positive value of ΔS. The free energy difference for ATP hydrolysis is approximately-7.3 kcal per mole (kcal/mol) of ATP. This is influenced by several factors including concentration of reactants and product, pH of the solution and temperature and pressure. -7.3 kcal/mol is the value under standard lab conditions. In the cell, it is likely -12 kcal/mol. Non-spontaneous reactions are often coupled to spontaneous reactions If the conversion reactant A into product B is spontaneous, the reverse reaction reactant B into product A is not. The ΔG's for the forward and reverse reactions have the same absolute value but opposite signs. Bio 281 Lecture Page 3 Non-spontaneous reactions are often coupled to spontaneous reactions If the conversion reactant A into product B is spontaneous, the reverse reaction reactant B into product A is not. The ΔG's for the forward and reverse reactions have the same absolute value but opposite signs. Energetic coupling is a process in which a spontaneous reaction (negativeΔG) drives a non- spontaneous reaction (positive ΔG). It requires that the net ΔG of the two reactions be negative. In addition, the two reactions must occur together. In some cases, this coupling can be achieved if the two reactions share an intermediate. ATP hydrolysis can be used to drive a non-spontaneous reaction. The phosphate group is released during ATP hydrolysis is transferred to glucose to produce glucose 6-phosphate. The net ΔG for the two reactions is negative. So ATP hydrolysis provides the thermodynamic driving force for the non- spontaneous reaction, and the shared phosphate group couples the two reactions together. Following ATP hydrolysis, the cell needs to replenish its ATP. 6.5 Enzymes and the Rate of Chemical Reactions Catalysts increase the rate of chemical reactions without themselves being consumed. In biological systems, these catalysts are usually proteins called enzymes. Enzymes reduce the activation energy of a chemical reaction All chemical reactions require an input of energy to proceed, even exergonic reactions that release energy. The intermediate stage between reactants and products is called thetransition state. It is highly unstable and therefore has a large amount of free energy. In all reactions, reactants adopt at least one transition state before their conversion into products. To reach the transition state, the reactant must absorb energy from its surroundings. As a result, all chemical reactions require an input of energy. The energy input necessary to reach the transition state is called the activation energy (EA). There is an inverse correlation between the rate of a reaction and the height of the energy barrier: the lower the energy barrier, the faster the reaction; the higher the barrier, the slower the reaction. Enzymes reduce the activation energy, however the difference in free energy between reactants and products does not change. Enzymes form a complex with reactants and products In a chemical reaction catalyzed by an enzyme, the reactant is often referred to as thesubstrate. In such a reaction, the Substrate (S) is converted to a product (P): In the presence of an enzyme, the substrate first forms a complex with the enzyme (ES). While still part of the complex, the substrate is converted to product. Finally the product dissociates, releasing the enzyme and product. The formation of this complex is critical for accelerating the rate of a chemical reaction. Enzymes are folded into three-dimensional shapes that bring particular amino acids into close proximity to form an active site. The active site is the part that binds to a substrate. In the active site, the enzyme and substrate form transient covalent bonds and/or weak noncovalent interactions. Enzymes also reduce the energy of activation by positioning two substrates to react. The formation of the enzyme-substrate complex promotes the reaction between two substrates by aligning their reactive chemical groups and limiting their motion to each other. The large size of many enzymes is required at least in part to bring the catalytic amino acids into very specific positions in the active site of the folded enzyme. Enzymes are highly specific Bio 281 Lecture Page 4 The large size of many enzymes is required at least in part to bring the catalytic amino acids into very specific positions in the active site of the folded enzyme. Enzymes are highly specific The specificity of enzymes can be attributed to the structure of their active sites. The enzyme active site only interacts with substrates having a precise three-dimensional structure. Enzyme activity can be influenced by inhibitors and activators Inhibitors decrease the activity of enzymes whereas activators increase the activity of enzymes. Inhibitors are synthesized naturally by many plants and animals as a defense against predators. There are two classes of inhibitors. Irreversible inhibitors usually form covalent bonds with enzymes and irreversibly inactivate them. Reversible inhibitors form weak bonds with enzymes and therefore easily dissociate from them. Some inhibitors prevent the binding of the substrate. Other inhibitors bind to a site other than the active site but still inhibit activity of the enzyme. In this case, changing the shape and activity of the enzyme. Enzymes are regulated by molecules that bind at sites other than their active sites are calledallosteric enzymes. Allosteric enzymes regulate key metabolic pathways A bacteria produces isoleucine from threonine. Once it has enough isoleucine, it needs to shut down the pathway via an enzyme inhibitor, isoleucine. The final product of five reactions. This binds to the first enzyme in the pathway, threonine dehydratase at a site distinct from the active site. The isoleucine pathway also provides an example of negative feedback, in which the final product inhibits the first step of the reaction. This is used to maintain homeostasis. At a low concentration of threonine, the reaction is very slow. As the concentration of threonine increases, the activity of the enzyme increases. At a particular threshold, a small increase in threonine concentration results in a large increase in reaction rate. When there is excess substrate, the reaction slows down. Bio 281 Lecture Page 5
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