Chapter 8 Notes - The Energy of Life Lecture Notes

Overview: The energy of Life ● The living cell is a miniature chemical factory where thousands of reactions occur ● The cell extracts energy and applies energy to perform work ● Some organisms even convert energy to light, as in bioluminescence Concept 8.1: An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics ● Metabolism is the totality of an organism’s chemical reactions ● Metabolism is an emergent property of life that arises from interactions between molecules within the cell Organization of the Chemistry of Life into Metabolic Pathways ● A metabolic pathway begins with a specific molecule and ends with a product ● Each step is catalyzed by a specific enzyme ● Catabolic pathways release energy by breaking down complex molecules into simpler compounds ● Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism ● Anabolic pathways consume energy to build complex molecules from simpler ones ● The synthesis of protein from amino acids is an example of anabolism ● Bioenergetics is the study of how organisms manage their energy resources Forms of Energy ● Energy is the capacity to cause change ● Energy exists in various forms, some of which can perform work ● Kinetic energy is energy associated with motion ● Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules ● Potential energy is energy that matter possesses because of its location or structure ● Chemical energy is potential energy available for release in a chemical reaction ● Energy can be converted from one form to another The Laws of Energy Transformation ● Thermodynamics is the study of energy transformations ● A isolated system, such as that approximated by liquid in a thermos, is isolated from its surroundings ● In an open system, energy and matter can be transferred between the system and its surroundings ● Organisms are open systems The First Law of Thermodynamics ● According to the first law of thermodynamics, the energy of the universe is constant ● Energy can be transferred and transformed, but it cannot be created or destroyed ● The first law is also called the principle of conservation of energy The Second Law of Thermodynamics ● During every energy transfer or transformation, some energy is unusable, and is often lost as heat ● According to the second law of thermodynamics ● Every energy transfer or transformation increases the entropy (disorder) of the universe ● Living cells unavoidably convert organized forms of energy to heat ● Spontaneous processes occur without energy input; they can happen quickly or slowly ● For a process to occur without energy input, it must increase the entropy of the universe Biological Order and Disorder ● Cells create ordered structures from less ordered materials ● Energy flows into an ecosystem in the form of light and exits in the form of heat ● The evolution of more complex organisms does not violate the second law of thermodynamics ● Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases Concept 8.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously ● Biologists want to know which reactions occur spontaneously and which require input of energy ● To do so, they need to determine energy changes that occur in chemical reactions Free-Energy Change, ΔG ● A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell ● The change in free energy (∆G) during a process is related to the change in enthalpy, or change in total energy (∆H), change in entropy which is the energy that it lost (∆S), and temperature in Kelvin (T) ∆G = ∆H – T∆S ● Only processes with a negative ∆G are spontaneous ● Spontaneous processes can be harnessed to perform work ● Delta G will be negative in EXERGONIC ● Delta G will be positive in ENDERGONIC Free Energy, Stability, and Equilibrium ● Free energy is a measure of a system’s instability, its tendency to change to a more stable state ● During a spontaneous change, free energy decreases and the stability of a system increases ● Equilibrium is a state of maximum stability ● A process is spontaneous and can perform work only when it is moving toward equilibrium Free Energy and Metabolism ● The concept of free energy can be applied to the chemistry of life’s processes Exergonic and Endergonic Reactions in Metabolism ● An exergonic reaction proceeds with a net release of free energy and is spontaneous ● An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous Equilibrium and Metabolism ● Reactions in a closed system eventually reach equilibrium and then do no work ● Cells are not in equilibrium; they are open systems experiencing a constant flow of materials ● A defining feature of life is that metabolism is never at equilibrium ● A catabolic pathway in a cell releases free energy in a series of reactions Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions ● A cell does three main kinds of work ● Chemical (converting) ● Transport (diffusion or active transport) ● Mechanical (moving substances within cell or moving cells) ● To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one ● Most energy coupling in cells is mediated by ATP The Structure and Hydrolysis of ATP ● ATP (adenosine triphosphate) is the cell’s energy shuttle ● ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups (negatively charged) ● The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis ● Energy is released from ATP when the terminal phosphate bond is broken ● This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves How the Hydrolysis of ATP Performs Work ● The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP ● In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction ● Overall, the coupled reactions are exergonic ● ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant ● The recipient molecule is now called a phosphorylated intermediate The Regeneration of ATP ● ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP) ● The energy to phosphorylate ADP comes from catabolic reactions in the cell ● The ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways Concept 8.4: Enzymes speed up metabolic reactions by lowering energy barriers ● A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction ● An enzyme is a catalytic protein ● Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction The Activation Energy Barrier ● Every chemical reaction between molecules involves bond breaking and bond forming ● The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA) ○ Even in exergonic reactions, you still need to have a minimum amount of energy to carry out the reaction ● Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings How Enzymes Lower the EA Barrier ● Enzymes catalyze reactions by lowering the EA barrier ● Enzymes do not affect the change in free energy (∆G); instead, they hasten reactions that would occur eventually Substrate Specificity of Enzymes ● The reactant that an enzyme acts on is called the enzyme’s substrate ● The enzyme binds to its substrate, forming an enzyme-substrate complex ○ Enzyme is a protein ● The active site is the region on the enzyme where the substrate binds ● Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction Catalysis in the Enzyme’s Active Site ● In an enzymatic reaction, the substrate binds to the active site of the enzyme ● The active site can lower an EA barrier by ○ Orienting substrates correctly ○ Straining substrate bonds ○ Providing a favorable microenvironment ○ Covalently bonding to the substrate Effects of Local Conditions on Enzyme Activity ● An enzyme’s activity can be affected by ○ General environmental factors, such as temperature and pH ○ Chemicals that specifically influence the enzyme Effects of Temperature and pH ● Each enzyme has an optimal temperature in which it can function ● Each enzyme has an optimal pH in which it can function ● Optimal conditions favor the most active shape for the enzyme molecule Cofactors ● Cofactors are non-protein enzyme helpers ● Cofactors may be inorganic (such as a metal in ionic form) or organic ● An organic cofactor is called a coenzyme ● Coenzymes include vitamins Enzyme Inhibitors ● Competitive inhibitors bind to the active site of an enzyme, competing with the substrate ● Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective ● Examples of inhibitors include toxins, poisons, pesticides, and antibiotics The Evolution of Enzymes ● Enzymes are proteins encoded by genes ● Changes (mutations) in genes lead to changes in amino acid composition of an enzyme ● Altered amino acids in enzymes may alter their substrate specificity ● Under new environmental conditions a novel form of an enzyme might be favored Concept 8.5: Regulation of enzyme activity helps control metabolism ● Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated ● A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes Allosteric Regulation of Enzymes ● Allosteric regulation may either inhibit or stimulate an enzyme’s activity ● Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site Allosteric Activation and Inhibition ● Most allosterically regulated enzymes are made from polypeptide subunits ● Each enzyme has active and inactive forms ● The binding of an activator stabilizes the active form of the enzyme ● The binding of an inhibitor stabilizes the inactive form of the enzyme ● Cooperativity is a form of allosteric regulation that can amplify enzyme activity ● One substrate molecule primes an enzyme to act on additional substrate molecules more readily ● Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site Identification of Allosteric Regulators ● Allosteric regulators are attractive drug candidates for enzyme regulation because of their specificity ● Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses Feedback Inhibition ● In feedback inhibition, the end product of a metabolic pathway shuts down the pathway ● Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed Specific Localization of Enzymes Within the Cell ● Structures within the cell help bring order to metabolic pathways ● Some enzymes act as structural components of membranes ● In eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondria