ENERGY, CATALYSIS, and BIOSYNTHESIS Chapter 3 p83-115

1. ENERGY, CATALYSIS, and BIOSYNTHESIS Chapter 3 p83-115

2. The living cell is a chemical industry in miniature, where thousands of reactions occur within a microscopic space. Metabolism is an emergent property of life that arises from specific interactions between molecules within the orderly environment of the cell. Sugars are converted into amino acids, and vice versa. Small molecules are assembled into polymers, which may later be hydrolyzed as the needs of cell change.

3. Two Laws of Thermodynamics According to the first law of thermodynamics, the energy of universe is constant. Energy can be transferred and transformed, but it cannot be created or destroyed. This is also known as conservation energy. The second law of thermodynamics can be stated in several ways. Every energy transfer or transformation makes universe more disordered. There is a quantitative measure of disorder, called entropy, whose value increases as disorder increases. Therefore, second law of thermodynamics states that every energy transfer or transformation makes universe more disordered.

5. One of the unique property living things is to create and maintain the order. In order to create and maintain order cells perform many different chemical reactions, which are small organic molecules like sugars, fatty acids, nucleotides are taken up and modified within cells by chemical reactions through a series of reactions. The chemical reactions occur in every cells require boost in reactivity and precise chemical control. These are achieved by specialized protein called enzymes. Each enzyme accelerates or catalyzes a specific reaction. Enzyme-catalyzed reactions are usually under connected in a series, so that the product of one reaction becomes the starting material or substrate for the next.

6. How a set of enzyme-catalyzed reactions generates a metabolic pathway. Each enzyme catalyzes a particular chemical reaction, leaving the enzyme unchanged. In this example, a set of enzymes acting in series converts molecule A to molecule F, forming a metabolic pathway.

7. As a whole, metabolism is concerned with managing the material and energy • resources of the cell. • Some metabolic pathways release energy by breaking down complex molecules into simpler compounds. These degradative processes are called catabolic pathways. A major example of catabolism is cellular respiration, in which sugar glucose and other and other organic fuels are broken down to carbon dioxide and water. • There are also anabolic pathways or biosynthesis, which consumes energy to build complicated molecules from simpler ones. An example of anabolism is the synthesis of protein from amino acids.

8. Schematic representation of the relationship between catabolic and anabolic pathways in metabolism. As suggested here, since a major portion of the energy stored in the chemical bonds of food molecules is dissipated as heat, the mass of food required by any organism that derives all of its energy from catabolism is much greater than the mass of the molecules that can be produced by anabolism.

9. The Metabolic Map Metabolism is the totality of an organism’s chemical processes. We can think of a cell’s metabolism as an elaborate road map of the thousands of reactions in that cell. These longer linear reaction pathways, or metabolic pathways, are in turn linked to one another, forming a complex web interconnected reactions that enable to the cell to survive, grow, and reproduce

10. Some of the metabolic pathways and their interconnections in a typical cell. About 500 common metabolic reactions are shown diagrammatically, with each molecule in a metabolic pathway represented by a filled circle

11. Biological Order Is Made Possible by the Release of Heat Energy from Cells Living cells-by surviving, growing, and forming complex organisms-are generating order and thus might appear to defy the second low of thermodynamics. But this is not the case. A cell is not isolated system. It takes energy form as food or photons from the sun and it then use this energy to generate order within itself. In the course of performing the chemical reactions that generate order, chemical and bond energy is converted into heat.

12. A simple thermodynamic analysis of a living cell. In the diagram on the left the molecules of both the cell and the rest of the universe (the sea of matter) are depicted in a relatively disordered state. In the diagram on the right the cell has taken in energy from food molecules and released heat by a reaction that orders the molecules the cell contains. Because the heat increases the disorder in the environment around the cell (depicted by the jagged arrows and distorted molecules, indicating increased molecular motions), the second law of thermodynamics, which states that the amount of disorder in the universe must always increase, is satisfied as the cell grows and divides.

13. Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules All animals live on energy stored in the chemical bonds of organic molecules made by other organisms. Solar energy enters the living world through photosynthesis carried out by plants and photosynthetic bacteria. Photosynthesis allows the electromagnetic energy in sunlight to be converted into chemical energy into cell. Plants needs inorganic source to make its food Carbon dioxide from atmosphere Oxygen and hydrogen from water Nitrogen from ammonia and nitrates And other elements from the soil

14. The reactions of photosynthesis take place in two stages 1. Light -dependent stage: in this stage light captured and transiently stored as chemical bond energy in specialized small molecules that carry energy in their reactive chemical group. 2. Carbon fixation: in this stage, sugars are formed from carbon dioxide and oxygen. The net result of the entire process of photosynthesis Light energy+ CO2+H2O ------ Sugars +O2 + heat energy

16. Cells Obtain Energy by the Oxidation of Organic Compound All animal and plant cells are powered by chemical energy stored in the chemical bonds organic molecules. Sugars+ O2 ------ CO2+H2O This process is known as cellular respiration.

17. Photosynthesis and respiration are complementary processes

18. Oxidation and Reduction Involve Electron Transfer In oxidation reaction electrons are transferred to from one atom to another. Oxidation, in this sense, refers to removal of electrons. However, in reduction reaction addition of electrons occursOxidation and reduction reactions always occur simultaneously: i.e. if one molecule gains an electron in a reaction (reduction), second molecules loses the electron (oxidation).

19. When molecule in a cell picks up an electron, it often picks up a proton H+ at the same time. The net effect in this case is to add a hydrogen atom to the molecule. Although a proton plus electron is involved, such hydrogenation reactions are reductions, and the reverse, dehydrogenation reactions, are oxidants. Reduction is occurring if its number of C-H increases, whereas oxidation is occurring if its number of C-H bonds decreases.

20. Enzymes Lower the Barriers That Block Chemical Reactions A chemical reaction involves bond breaking and bond forming. When a reaction rearranges the atoms of molecules, existing bonds in the reactants must be broken and the new bonds of products formed. These processes require exchanges of energy between the mixture of molecules and surrounding environment. The reactant molecules must absorb energy for their bonds to break, and energy is released when the bonds of product molecules are formed. The initial investment of energy for starting of a reaction –the energy required to break bonds in the reactant molecules- is known as activation energy or free energy of activation.

22. The success of living organisms is attributable to the cell’s ability to make enzymes of many types, each with precisely specified properties. Each enzyme has unique shape containing an active site where a particular substrate will fit.

23. The Free-Energy Change for a Reaction Determines Whether It Can Occur Although enzymes speed up reactions, they cannot by themselves force energetically unfavorable reactions to occur. According to the second law of thermodynamics, a chemical reaction can proceed only if it results in net increase in disorder of the universe. Disorder is increased when useful energy that could be harnessed to do work is dissipated as heat. This disorder can be measured by free energy, G, of a system. Energetically favorable reactions are those create disorder by decreasing the free energy of system to which they belong, in other words, they have negative ΔG. On the other hand, energetically unfavorable reactions which have positive ΔG create order in the universe.

25. Rapid diffusion Allows Enzymes to Find Their Substrates

26. Rapid binding of an enzyme to its substrate is possible because motions are enormously fast at molecular level. Because of heat energy, molecules are in constant motion and consequently will explore the space inside cell very efficiently by wandering randomly through it-a process called diffusion. In this way, every molecule in a cell collides with a huge number of molecules every second.

29. Vmax and Km Measure Enzyme Performance To catalyze a reaction, an enzyme first binds its substrate. The substrate then undergoes a reaction to form a product, which initially remains bound to the enzyme. Finally, the product is released and diffuses away, leaving the enzyme free to bind to another substrate molecule and catalyze another reaction.

30. The rates of these different steps vary widely from one enzyme to another, and they can be measured by mixing purified enzymes and substrate under the defined conditions. Enzyme molecules become occupied by substrate until very high concentration of substrate reaches a maximum value, termed Vmax. At this point all active sites of all enzymes are occupied with substrate. And product formation will depend on how fast enzymes are. The concentration of substrate needed to make an enzyme work efficiently is often measured by Michaelis constant, Km. An enzyme’s Km is the concentration of substrate at which enzymes works at half of its maximum speed.

32. Activated Carrier Molecules and Biosynthesis The energy is released during break down of food into small molecules. This energy is usually stored as a chemical bond in small sets of activated “carrier molecules”. These molecules rapidly diffuse within the cell and moves to sites where energy is required. Activated carriers store energy in an easily exchangeable form. The most important activated carriers are ATP, NADH, and NADPH.

33. ATP Is the Most Widely Used Activated Carrier Molecule The most important and versatile of the activated carriers in cells is ATP. ATP serves as a convenient and versatile store, or currency, of energy to drive a variety of chemical reactions in the cell

34. The energetically favorable reaction of ATP hydrolysis is coupled to many other unfavorable reactions through which other molecules are synthesized. Hydrolysis reaction often involve the transfer of a phosphate group to a molecule is termed a phosphorylation. Phosphorylation reactions are involved in many important cellular functions: -activation of substrate -facilitate the exchange of chemical energy -help to control of the cell signaling process

35. ATP is used for many important cellular processes: 1.to supply energy for many of the pumps 2.to power molecular motors 3.transport of organelles or vesicle

36. Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together A frequent type of reaction that is needed for biosynthesis (anabolic) is one in which two molecules, A and B, are joined together to produce A-B in the energetically unfavorable condensation reaction.

37. NADH and NAPDH Are Important Electron Carriers There are other important activated carriers involved in biosynthesis of molecules. These activated carriers are involved in oxidation-reduction reactions and involved in coupling reactions. The most important of these carriers are NAD+ (nicotinamide adenine dinucleotide) and closely related molecule NADP+ (nicotinamide adenine dinucleotide phosphate). NADPH is produced in the reactions in which two hydrogen atoms are removed from substarte. Oxidized form of NADP+ receives one hydrogen atom plus an electron, and the proton (H+) from other H atom is released into the solution. Because NADPH holds it hydride ion in a high-energy linkage, the added hydride ion can easily be transferred to other molecules.