Chapter 8 Bio. Lecture Notes PDF

Chapter 8 An Introduction to Metabolism 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 C...

Chapter 8 An Introduction to Metabolism 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 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 starting molecule and ends with a product Each step is catalyzed by a specific enzyme Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1 Reaction 2 Reaction 3 Starting Product molecule  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 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 Figure 8.2 A diver has more potential Diving converts energy on the platform potential energy to than in the water. kinetic energy. Climbing up converts the kinetic A diver has less potential energy of muscle movement energy in the water to potential energy. than on the platform. 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 Organisms areareopen open systems 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, * The overall amount of energy in the entire but it cannot be created or destroyed universe remains constant 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 With each change, some energy will always be lost to an unusable form as HEAT!!  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 Organisms also replace ordered forms of matter and energy with less ordered forms Energy flows into an ecosystem in the form of light and exits in the form of heat 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, G 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 (∆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 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 At total equilibrium, there is Equilibrium is a state of maximum stability no more free energy to do work— A process is spontaneous and can perform work This is why cells/organisms only when it is moving toward equilibrium can never reach that state, and concentration gradients must be maintained. Figure 8.5 The Relationship of Free Energy to Stability, Work Capacity, and Spontaneous Change More free energy (higher G) Less stable Greater work capacity In a spontaneous change The free energy of the system decreases (G  0) The system becomes more stable The released free energy can be harnessed to do work Less free energy (lower G) More stable Less work capacity (a) Gravitational motion (b) Diffusion (c) Chemical reaction 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 Figure 8.6 (a) Exergonic reaction: energy released, spontaneous Reactants Amount of energy released Free energy (G  0) Energy Products Progress of the reaction (b) Endergonic reaction: energy required, nonspontaneous Products Amount of energy required Free energy (G  0) Energy Reactants Progress of the reaction 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 – Transport – Mechanical To do work, cells manage energy resources by energy coupling, the use of an exergonic process Energy lost in exergonic process goes to the to drive an endergonic one energy needed for an endergonic process 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 Figure 8.8b Adenosine triphosphate (ATP) Energy Inorganic Adenosine diphosphate (ADP) phosphate (b) The hydrolysis of ATP  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 Figure 8.10 Transport protein Solute Transport and mechanical work in the cell are also powered by ATP ATP ADP Pi hydrolysis P Pi ATP hydrolysis leads to a change in Solute transported protein shape and binding ability (a) Transport work: ATP phosphorylates transport proteins. Vesicle Cytoskeletal track ATP ADP Pi ATP Motor protein Protein and vesicle moved (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed. 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) Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings Figure 8.12 A B C D Transition state A B Free energy EA C D Reactants A B G  O C D Products Progress of the reaction 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 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 Figure 8.14 Substrate Active site Enzyme Enzyme-substrate complex (a) (b) 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 Figure 8.15-1 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex Active site Enzyme Figure 8.15-2 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex 3 Active site can lower EA and speed up a reaction. Active site Enzyme 4 Substrates are converted to products. Figure 8.15-3 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex 3 Active site can lower EA and speed up a reaction. 6 Active site is available for two new substrate molecules. Enzyme 5 Products are 4 Substrates are released. converted to products. Products 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 nonprotein 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 Figure 8.18 Evolution of Beta-Galactosidase Two changed amino acids were Active site found near the active site. Two changed amino acids Two changed amino acids were found in the active site. were found on the surface. 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 Figure 8.19a (a) Allosteric activators and inhibitors Allosteric enzyme Active site with four subunits (one of four) Regulatory site (one of four) Activator Active form Stabilized active form Oscillation Nonfunctional active site Inhibitor Inactive form Stabilized inactive form  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 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 Figure 8.21 Initial substrate Active site (threonine) available Threonine in active site Enzyme 1 (threonine Isoleucine deaminase) used up by cell Intermediate A Active site of Feedback enzyme 1 is inhibition Enzyme 2 no longer able to catalyze the Intermediate B conversion of threonine to Enzyme 3 intermediate A; pathway is Intermediate C switched off. Isoleucine binds to Enzyme 4 allosteric site. Intermediate D Enzyme 5 End product (isoleucine)