BAU MBG BIO1003 General Biology Lecture 6 Energy and Life PDF

BAU MBG BIO1003 General Biology Lecture 6 Energy and Life Dr. Dilek ÇEVİK © 2021 Pearson Education, Inc. How do the laws of thermody...

BAU MBG BIO1003 General Biology Lecture 6 Energy and Life Dr. Dilek ÇEVİK © 2021 Pearson Education, Inc. How do the laws of thermodynamics relate to biological processes? Energy use by living things demonstrates the first law of thermodynamics – Energy can be transferred or transformed, but not created or destroyed The conversion of energy to thermal energy released as heat by living things demonstrates the second law of thermodynamics – Every energy transfer or transformation increases the entropy (disorder) of the universe © 2021 Pearson Education Ltd. CONCEPT 6.1: An organism’s metabolism transforms matter and energy Metabolism is the totality of an organism’s chemical reactions Bioenergetics is the study of how energy flows through living organisms © 2021 Pearson Education Ltd. Metabolic Pathways In a metabolic pathway, a specific molecule is altered in a series of steps to produce a product Each step is catalyzed by a specific enzyme, a macromolecule that speeds up a specific reaction © 2021 Pearson Education Ltd. Figure 6.UN01 © 2021 Pearson Education Ltd.  Catabolic pathways release energy by breaking down complex molecules into simpler compounds Cellular respiration, the breakdown of glucose in the presence of O2, is an example of a pathway of catabolism © 2021 Pearson Education Ltd.  Anabolic pathways consume energy to build complex molecules from simpler ones – For example, the synthesis of protein from amino acids is an anabolic pathway © 2021 Pearson Education Ltd.  Processes that increase the entropy of the universe can occur spontaneously Spontaneous processes occur without energy input; they can happen quickly or slowly Processes that decrease entropy are nonspontaneous; they require an input of energy © 2021 Pearson Education Ltd. CONCEPT 6.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously Biologists follow the energy and entropy changes during chemical reactions to determine whether they require an input of energy or occur spontaneously © 2021 Pearson Education Ltd. Free-Energy Change, G Gibbs free energy, G, can be simplified and referred to as free energy Free energy is the portion of a system’s energy that can do work when temperature and pressure are uniform throughout the system, as in a living cell © 2021 Pearson Education Ltd.  Equilibrium, the point at which forward and reverse reactions occur at the same rate, describes a state of maximum stability Systems never spontaneously move away from equilibrium A process is spontaneous and can perform work only when it is moving toward equilibrium © 2021 Pearson Education Ltd. Free Energy and Metabolism The concept of free energy can be applied to the chemistry of life’s processes © 2021 Pearson Education Ltd. Exergonic and Endergonic Reactions in Metabolism Chemical reactions can be classified based on their free-energy changes – An exergonic reaction (“energy outward”) proceeds with a net release of free energy to the surroundings – An endergonic reaction (“energy inward”) absorbs free energy from the surroundings © 2021 Pearson Education Ltd. Figure 6.6 © 2021 Pearson Education Ltd. Animation: Exergonic and Endergonic Reactions © 2021 Pearson Education Ltd.  The magnitude of ΔG determines the maximum amount of work an exergonic reaction can perform – For example, for each mole of glucose broken down during cellular respiration, 686 kcal of energy is available for work – The chemical products of respiration store 686 kcal less free energy per mole than the reactants © 2021 Pearson Education Ltd.  The magnitude of ΔG determines the quantity of energy required to drive an endergonic reaction – For example, to produce glucose and O2 from CO2 and H2O requires an input of 686 kcal/mol – The products of photosynthesis store 686 kcal more free energy per mole than the reactants – This reaction is powered by converting light energy to chemical energy © 2021 Pearson Education Ltd. Equilibrium and Metabolism Reactions in a closed system, such as an isolated hydroelectric system, eventually reach equilibrium and can then do no work © 2021 Pearson Education Ltd. CONCEPT 6.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work: – Chemical work—pushing endergonic reactions – Transport work—pumping substances across membranes against the direction of spontaneous movement – Mechanical work—such as beating cilia or contracting muscle cells © 2021 Pearson Education Ltd.  Cells manage energy resources to do work through energy coupling, the use of an exergonic process to drive an endergonic one Most energy coupling in cells is mediated by ATP © 2021 Pearson Education Ltd. The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups In addition to energy coupling, ATP functions as one of the nucleoside triphosphates used to make RNA © 2021 Pearson Education Ltd.  Energy is released from ATP when the terminal phosphate bond is broken by hydrolysis, the addition of a water molecule The energy does not come directly from the phosphate bonds, but from the chemical change to a state of lower free energy in the products © 2021 Pearson Education Ltd. Figure 6.9b © 2021 Pearson Education Ltd.  ATP releases more energy with the loss of a phosphate than most other molecules could deliver Repulsion between the negative charges of the three phosphate groups creates a lot of potential energy The triphosphate tail is the chemical equivalent of a compressed spring © 2021 Pearson Education Ltd. How ATP Provides Energy That Performs Work Cellular work (mechanical, transport, and chemical) is powered by ATP hydrolysis In the cell, energy from the exergonic hydrolysis of ATP is used to drive endergonic reactions Overall, the coupled reactions are exergonic © 2021 Pearson Education Ltd.  Phosphorylation, transfer of a phosphate group from ATP to another molecule, is typically used to power endergonic reactions The recipient molecule, a phosphorylated intermediate, is more reactive (less stable, with more free energy) that the original molecule © 2021 Pearson Education Ltd. Figure 6.10 © 2021 Pearson Education Ltd.  Transport and mechanical work in the cell are also nearly always powered by ATP hydrolysis ATP hydrolysis causes a change in protein shape and binding ability © 2021 Pearson Education Ltd. Figure 6.11 © 2021 Pearson Education Ltd. The Regeneration of ATP ATP is regenerated by addition of a phosphate group to adenosine diphosphate (ADP) Free energy needed to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) The shuttling of inorganic phosphate and energy is called the ATP cycle; it couples energy-yielding processes to energy-consuming ones © 2021 Pearson Education Ltd. Figure 6.12 © 2021 Pearson Education Ltd. Animation: Metabolism Overview © 2021 Pearson Education Ltd. CONCEPT 6.4: Enzymes speed up metabolic reactions by lowering energy barriers Spontaneous reactions do not need added energy, but they can be slow enough to be imperceptible – For example, the hydrolysis of sucrose to glucose and fructose is spontaneous – At room temperature, a solution of sucrose in sterile water would sit for years without appreciable hydrolysis © 2021 Pearson Education Ltd.  A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction An enzyme is a macromolecule (typically protein) that acts as a catalyst to speed up a specific reaction – For example, adding the enzyme sucrase to a sucrose solution at room temperature will catalyze the complete hydrolysis of sucrose within seconds © 2021 Pearson Education Ltd. Figure 6.UN02 © 2021 Pearson Education Ltd. The Activation Energy Barrier Every chemical reaction between molecules involves bond breaking and bond forming A molecule must be put into a highly unstable state before bonds can break to start the reaction To reach this state, the molecule must absorb energy from its surroundings © 2021 Pearson Education Ltd.  The initial energy needed to break the bonds of the reactants is called the activation energy (EA) Heat in the form of thermal energy absorbed from the surroundings often supplies activation energy Molecules become unstable when enough energy is absorbed to break bonds; this is the transition state © 2021 Pearson Education Ltd.  As atoms settle into new, more stable bonds, energy is released to the surroundings In an exergonic reaction, the formation of new bonds releases more energy than was invested in breaking the old bonds © 2021 Pearson Education Ltd. Figure 6.13 Energy profile of an exergonic reaction © 2021 Pearson Education Ltd. How Enzymes Speed Up Reactions An enzyme catalyzes a reaction by lowering the E A barrier enough for the reaction to occur at moderate temperatures An enzyme cannot change ΔG; it only speeds up a reaction that would eventually occur anyway © 2021 Pearson Education Ltd. Figure 6.14 © 2021 Pearson Education Ltd. Animation: How Enzymes Work © 2021 Pearson Education Ltd. 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 While bound, the catalytic activity of the enzyme converts substrate to product © 2021 Pearson Education Ltd.  Most enzyme names end in -ase – For example, the enzyme sucrase catalyzes the hydrolysis of sucrose into glucose and fructose Each enzyme catalyzes a specific reaction and can recognize its specific substrate among even closely related compounds © 2021 Pearson Education Ltd.  The active site is the region on the enzyme, often a pocket or groove, that binds to the substrate The complementary fit between the shape of the active site and the shape of the substrate is responsible for enzyme specificity © 2021 Pearson Education Ltd.  When the substrate enters the active site, the enzyme changes shape slightly, tightening around the substrate like a handshake This induced fit results from interactions between chemical groups on the substrate and the active site It brings the chemical groups of the active site into positions that enhance catalysis of the reaction © 2021 Pearson Education Ltd. Figure 6.15 © 2021 Pearson Education Ltd. Video: Closure of Hexokinase Via Induced Fit © 2021 Pearson Education Ltd. Catalysis in the Enzyme’s Active Site The substrate is typically held in the enzyme’s active site by weak bonds, such as hydrogen bonds The conversion of substrate to product happens rapidly, and product is released from the active site Because enzymes emerge from reactions in their original form, small amounts can have huge metabolic impacts © 2021 Pearson Education Ltd. Figure 6.16-1 © 2021 Pearson Education Ltd. Figure 6.16-2 © 2021 Pearson Education Ltd. Figure 6.16-3 © 2021 Pearson Education Ltd. Figure 6.16-4 © 2021 Pearson Education Ltd. Animation: Enzymes: Steps in a Reaction © 2021 Pearson Education Ltd.  Enzymes use a variety of mechanisms to lower EA – Substrates may be oriented to facilitate the reaction – Substrates may be stretched to make the bonds easier to break – The active site may provide a microenvironment that favors the reaction – Amino acids in the active site may participate in the reaction © 2021 Pearson Education Ltd.  The rate of an enzyme-catalyzed reaction can be sped up by increasing substrate concentration When all enzyme molecules have their active sites engaged, the enzyme is saturated If the enzyme is saturated, the reaction rate can only be sped up by adding more enzyme © 2021 Pearson Education Ltd. Effects of Local Conditions on Enzyme Activity Enzyme activity can be affected by general environmental factors, such as temperature and pH It can also be affected by chemicals that specifically influence the enzyme © 2021 Pearson Education Ltd. Effects of Temperature and pH Each enzyme has an optimal temperature at which it catalyzes its reaction at the maximum possible rate Up to this point, the reaction rate increases with increasing temperature; beyond this point the rate of reaction begins to drop Enzymes begin to denature at temperatures beyond their optimum © 2021 Pearson Education Ltd.  The optimal temperature of an enzyme is dependent on the environment in which it typically functions – For example, the optimal temperature for human enzymes is about 37°C, whereas the optimal temperature for thermophilic bacteria is about 75°C © 2021 Pearson Education Ltd. Figure 6.17a © 2021 Pearson Education Ltd.  Each enzyme has an optimal pH that is dependent on the environment in which it is typically active – For example, the optimal pH for pepsin—a human stomach enzyme—is 2, whereas the optimal pH for trypsin—an intestinal enzyme—is 8 © 2021 Pearson Education Ltd. Figure 6.17b © 2021 Pearson Education Ltd. Cofactors Cofactors are nonprotein helpers that bind to the enzyme permanently, or reversibly with the substrate Inorganic cofactors include metal atoms such as zinc, iron, and copper in ionic form Organic cofactors are called coenzymes Most vitamins either act as coenzymes or provide the raw materials needed to make them © 2021 Pearson Education Ltd. Enzyme Inhibitors Certain chemicals selectively inhibit the action of specific enzymes If an inhibitor forms covalent bonds with the enzyme, then the inhibition is usually irreversible Many inhibitors bind to the enzyme by weak interactions, resulting in reversible inhibition © 2021 Pearson Education Ltd.  Competitive inhibitors closely resemble the substrate, and can bind to the enzyme’s active site Enzyme productivity is reduced because the inhibitor blocks the substrate from entering the active site Increasing substrate concentration can overcome this type of inhibition © 2021 Pearson Education Ltd. Figure 6.18a © 2021 Pearson Education Ltd. Figure 6.18b © 2021 Pearson Education Ltd. Animation: Enzymes: Competitive Inhibition © 2021 Pearson Education Ltd.  Noncompetitive inhibitors bind to another part of the enzyme, away from the active site Binding of the inhibitor causes the enzyme to change shape, making the active site less effective at catalyzing the reaction © 2021 Pearson Education Ltd. Figure 6.18c © 2021 Pearson Education Ltd. Animation: Enzymes: Noncompetitive Inhibition © 2021 Pearson Education Ltd.  Toxins and poisons are often irreversible enzyme inhibitors – For example, sarin gas was used in a chemical attack in Syria in 2017, killing and injuring hundreds – Sarin binds covalently to the active site of acetylcholinesterase, an enzyme important in the nervous system Other examples include pesticides and antibiotics © 2021 Pearson Education Ltd. The Evolution of Enzymes Enzymes are proteins encoded by genes Changes in genes (mutations) lead to changes in the amino acid composition of the enzyme Altered amino acids, particularly at the active site, can result in novel enzyme activity or altered substrate specificity © 2021 Pearson Education Ltd.  If a mutation results in a new enzyme function that is beneficial to the organism, natural selection will favor the mutated allele – For example, repeated mutation and selection on the β-galactosidase enzyme in E. coli resulted in a change of sugar substrate under lab conditions © 2021 Pearson Education Ltd. Figure 6.19 © 2021 Pearson Education Ltd. CONCEPT 6.5: Regulation of enzyme activity helps control metabolism Chemical chaos would result if a cell’s metabolic pathways were operating simultaneously Cells can regulate metabolic pathways by switching on or off the genes that encode specific enzymes, or by regulating the activity of existing enzymes © 2021 Pearson Education Ltd. Allosteric Regulation of Enzymes Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site This type of regulation may either inhibit or stimulate enzyme activity © 2021 Pearson Education Ltd. Allosteric Activation and Inhibition Most allosterically regulated enzymes are made from polypeptide subunits, each with its own active site The complex oscillates between two shapes, one catalytically active and the other inactive © 2021 Pearson Education Ltd.  An activating or inhibiting molecule may bind to a regulatory site, often located where the subunits join The binding of an activator stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme © 2021 Pearson Education Ltd. Figure 6.20a © 2021 Pearson Education Ltd.  In cooperativity, substrate binding to one active site triggers a shape change in the enzyme that stabilizes the active form for all other sites This mechanism amplifies the response by priming the enzyme to act on additional substrate molecules more readily © 2021 Pearson Education Ltd. Figure 6.20b © 2021 Pearson Education Ltd. 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 © 2021 Pearson Education Ltd. Figure 6.21 © 2021 Pearson Education Ltd. Localization of Enzymes Within the Cell Compartmentalization of the cell helps to bring order to metabolic pathways In some cases, the enzymes for several steps in a metabolic pathway form a multienzyme complex Some enzymes have fixed locations and act as structural components of particular membranes © 2021 Pearson Education Ltd.  In eukaryotic cells, some enzymes reside within specific organelles – For example, enzymes for the second and third stages of cellular respiration are located within mitochondria © 2021 Pearson Education Ltd.