Alberts Chapter 3 2024 Bio PDF

https://youtu.be/UhCmt1dCtXY https://youtu.be/-6VyMFQ7rRo https://youtu.be/nDCxIpiI7-Y  Some properties of life (b) Evolutionary adaptation...

https://youtu.be/UhCmt1dCtXY https://youtu.be/-6VyMFQ7rRo https://youtu.be/nDCxIpiI7-Y  Some properties of life (b) Evolutionary adaptation (a) Order (c) Response to the environment Organisms regulate their internal environment to maintain a steady state, even in the face of fluctuating external environment. For example, a jackrabbit can adjust its body temperature by Organisms reproduce, life regulating the amount of blood comes only from life flowing through its ears (e) Energy (biogenesis). processing (d) Regulation (f) Growth and (g) Reproduction development Figure 1.2 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings One property above all makes living things seem almost miraculously different from nonliving matter: they create and maintain order in a universe that is tending always toward greater disorder. To accomplish this remarkable feat, the cells in a living organism must carry out a never ending stream of chemical reactions that produce the molecules the organism requires to meet its metabolic needs. To carry out the tremendous number of chemical reactions needed to sustain it, a living organism requires both a source of atoms in the form of food molecules and a source of energy. Most of the chemical reactions that cells perform would normally occur only at temperatures that are much higher than those inside a cell. Each reaction therefore requires a major boost in chemical reactivity to enable it to proceed rapidly within the cell. This boost is provided by specialized proteins called enzymes, each of which accelerates, or catalyzes chemical reactions. These enzyme-catalyzed reactions are usually connected in series, so that the product of one reaction becomes the starting material for the next. The long linear reaction pathways, or metabolic pathways, that result are in turn linked to one another, forming a complex web of interconnected reactions. Metabolism—the sum total of all the chemical reactions it needs to carry out to survive, grow, and reproduce. This control is central to the chemistry of life. Two opposing streams of chemical reactions occur in cells, the catabolic pathways and the anabolic pathways. The catabolic pathways (catabolism) break down foodstuffs into smaller molecules, thereby generating both a useful form of energy for the cell and some of the small molecules that the cell needs as building blocks. The anabolic, or biosynthetic, pathways (anabolism) use the energy harnessed by catabolism to drive the synthesis of the many molecules that form the cell. Nonliving things left to themselves eventually become disordered: buildings crumble and dead organisms decay. Living cells, by contrast, not only maintain, but actually generate order at every level, from the largescale structure of a butterfly or a flower down to the organization of the molecules that make up these organisms. This property of life is made possible by elaborate molecular mechanisms that extract energy from the environment and convert it into the energy stored in chemical bonds. THE USE OF ENERGY BY CELLS  Biological Order Is Made Possible by the Release of Heat Energy from Cells The universal tendency of things to become disordered is expressed in a fundamental law of physics, the second law of thermodynamics. This law states that, in the universe or in any isolated system (a collection of matter that is completely isolated from the rest of the universe), the degree of disorder can only increase.  ENTROPY The measure of a system’s disorder is called the entropy of the system, and the greater the disorder, the greater the entropy. Thus another way to express the second law of thermodynamics is to say that systems will change spontaneously toward arrangements with greater entropy. Movement toward disorder is a spontaneous process, requiring a periodic input of energy to reverse it.  Biological Order Is Made Possible by the Release of Heat Energy from Cells Living cells—by surviving, growing, and forming complex communities and even whole organisms—generate order and thus might appear to defy the second law of thermodynamics.  Biological Order Is Made Possible by the Release of Heat Energy from Cells A cell is not an isolated system. It takes in energy from its environment—in the form of food, inorganic molecules, or photons of light from the sun—and it then uses this energy to generate order within itself, forging new chemical bonds and building large macromolecules. In the course of performing the chemical reactions that generate order, some energy is lost in the form of heat. Because the cell is not an isolated system, the heat energy that its reactions generate is quickly dispersed into the cell’s surroundings. There, the heat increases the intensity of the thermal motions of nearby molecules, thereby increasing the entropy of the environment. Cells Can Convert Energy from One Form to Another Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules All animals live on energy stored in the chemical bonds of organic molecules, which they take in as food. Cells Obtain Energy by the Oxidation of Organic Molecules Oxidation and Reduction Involve Electron Transfers The terms oxidation and reduction apply even when there is only a partial shift of electrons between atoms linked by a covalent bond  Chemical Reactions Proceed in the Direction that Causes a Loss of Free Energy Paper burns readily, releasing into the atmosphere water and carbon dioxide as gases, while simultaneously releasing energy as heat: paper + O2 → smoke + ashes + heat + CO2 + H2O This reaction occurs in only one direction: smoke and ashes never spontaneously gather carbon dioxide and water from the heated atmosphere and reconstitute themselves into paper. When paper burns, much of its chemical energy is dissipated as heat: it is not lost from the universe, since energy can never be created or destroyed; instead, it is irretrievably dispersed in the chaotic random thermal motions of molecules. At the same time, the atoms and molecules of the paper become dispersed and disordered.  Chemical Reactions Proceed in the Direction that Causes a Loss of Free Energy  Real-Life Applications of Gibbs Free Energy Biological Processes: ATP hydrolysis has a negative ΔG, making it a key energy source for cells. Batteries: Gibbs Free Energy determines the maximum work that can be extracted from electrochemical cells.  Chemical Reactions Proceed in the Direction that Causes a Loss of Free Energy The useful energy in a system is known as its free energy, or G. And because chemical reactions involve a transition from one molecular state to another, the term that is of most interest to chemists and cell biologists is the free-energy change, denoted ΔG (“Delta G). A reaction can occur spontaneously only if ΔG is negative. On a macroscopic scale, an energetically favorable reaction with a negative ΔG is the relaxation of a compressed spring into an expanded state, which releases its stored elastic energy as heat to its surroundings. On a microscopic scale, an energetically favorable reaction—one with a negative ΔG—occurs when salt (NaCl) dissolves in water. ΔG measures the amount of disorder created in the universe when a reaction involving these molecules takes place. Energetically favorable reactions, by definition, are those that create disorder in the universe by decreasing the free energy of the system to which they belong; in other words, they have a negative ΔG (Figure 3–16).  Gibbs Free Energy (G) is a thermodynamic potential that helps predict whether a chemical reaction will occur spontaneously. Spontaneity of Reactions ΔG = ΔH - TΔS Key Points: If ΔG < 0, the reaction is spontaneous (exergonic). If ΔG > 0, the reaction is non-spontaneous (endergonic). If ΔG = 0, the system is at equilibrium. The useful energy in a system is known as its free energy, or G. And because chemical reactions involve a transition from one molecular state to another, the term that is of most interest to chemists and cell biologists is the free-energy change, denoted ΔG (“Delta G). The Free-Energy Change for a Reaction Determines Whether It Can Occur According to the second law of thermodynamics, a chemical reaction can proceed only if it results in a net (overall) increase in the disorder of the universe. Disorder increases when useful energy that could be harnessed to do work is dissipated as heat. ΔG measures the amount of disorder created in the universe when a reaction involving these molecules takes place. Energetically favorable reactions, by definition, are those that create disorder in the universe by decreasing the free energy of the system to which they belong; in other words, they have a negative ΔG (Figure 3–16). A reaction can occur spontaneously only if ΔG is negative. On a macroscopic scale, an energetically favorable reaction with a negative ΔG is the relaxation of a compressed spring into an expanded state, which releases its stored elastic energy as heat to its surroundings. On a microscopic scale, an energetically favorable reaction—one with a negative ΔG—occurs when salt (NaCl) dissolves in water.  Gibbs Free Energy (G) is a thermodynamic potential that helps predict whether a chemical reaction will occur spontaneously. Spontaneity of Reactions ΔG = ΔH - TΔS Key Points: If ΔG < 0, the reaction is spontaneous (exergonic). If ΔG > 0, the reaction is non-spontaneous (endergonic). If ΔG = 0, the system is at equilibrium.  Exergonic and Endergonic Reactions in Metabolism An exergonic reaction – Proceeds with a net release of free energy and is spontaneous Reactants Amount of energy released Free energy (∆G 0) Energy Reactants Progress of the reaction Figure 8.6 (b) Endergonic reaction: energy required  Enzymes Reduce the Energy Needed to Initiate Spontaneous Reactions Although the most energetically favorable form of carbon under ordinary conditions is CO2, and that of hydrogen is H2O, a living organism will not disappear in a puff of smoke, and the book in your hands will not burst spontaneously into flames. This is because the molecules in both the living organism and the book are in a relatively stable state, and they cannot be changed to lower-energy states without an initial input of energy. In other words, a molecule requires a boost over an energy barrier before it can undergo a chemical reaction that moves it to a lower energy (more stable) state. Enzymes Reduce the Energy Needed to Initiate Spontaneous Reactions The Free-Energy Change for a Reaction Determines Whether It Can Occur According to the second law of thermodynamics, a chemical reaction can proceed only if it results in a net (overall) increase in the disorder of the universe. Disorder increases when useful energy that could be harnessed to do work is dissipated as heat.  ATP hydrolysis – Can be coupled to other reactions Endergonic reaction: ∆G is positive, reaction is not spontaneous NH2 + NH3 ∆G = +3.4 kcal/mol Glu Glu Glutamic Ammonia Glutamine acid Exergonic reaction: ∆ G is negative, reaction is spontaneous ATP + H2O ADP + P ∆G = -7.3 kcal/mol Coupled reactions: Overall ∆G is negative; Figure 8.10 together, reactions are spontaneous ∆G = –3.9 kcal/mol Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Exercise 6 1. In generating order within the cell and biological systems, explain on why does the cell does not defy the law of entropy. 2. Discuss how energy flows and chemicals recycle during the complementary processes of photosynthesis and respiration. 3. Give an example of a coupled reaction showing an overall change in free energy. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Answer 1. A cell is not an isolated system. It takes in energy from its environment—in the form of food, inorganic molecules, or photons of light from the sun. In the course of performing the chemical reactions that generate order, some energy is lost in the form of heat that is quickly dispersed into the cell’s surroundings. There, the heat increases the intensity of the thermal motions of nearby molecules, thereby increasing the entropy of the environment. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Activated Carriers and Biosynthesis The Formation of an Activated Carrier Is Coupled to an Energetically Favorable Reaction ATP Is the Most Widely Used Activated Carrier Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together Cells Make Use of Many Other Activated Carriers NADPH operates chiefly with enzymes that catalyze anabolic reactions, supplying the high-energy electrons needed to synthesize energy-rich biological molecules. NADH, by contrast, has a special role as an intermediate in the catabolic system of reactions that generate ATP through the oxidation of food molecules. The Synthesis of Biological Polymers Requires an Energy Input