Chemical system. Chemical reaction A rearrangement of bonds one or more molecules becomes one or more different molecules A + B C.

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1 Chemical system a group of molecules that can react with one another. Chemical reaction A rearrangement of bonds one or more molecules becomes one or more different molecules A + B C Reactant(s) Product(s) Metabolism Collectively, all of the chemical reactions that go on inside of organisms. Thousands of different chemical reactions controlled by catalysts (enzymes) Each kind of molecule potentially participates in many different reactions Metabolic pathways are series of reactions Partial diagram of the metabolic pathways related to ATP production in cells Each dot represents a particular kind of molecule Each line is a chemical reaction that converts one kind of molecule to another (rearranges the atoms) 1

2 ENERGY What makes matter move and change Kinetic energy- associated with a mass in motion. Heat- energy of random movements of atoms and molecules Potential energy- gravitational, electrical, chemical, other Potential energy The potential of objects (including atoms and molecules) to move and change. Depends upon: 1) arrangement of objects in space, relative to other objects, and 2) forces that result in attraction or repulsion among objects, e.g. gravity, electrostatic forces, tendency to form bonds, etc Gravitational potential energy Gravity + altitude = potential for movement! 2

3 Chemical potential energy Describes molecules in a system and their tendency to move and react with one another Relates to 1) concentration (number of particles per unit volume) and 2) The tendency of the molecules to undergo chemical reactions (form bonds) Diffusion Diffusion is spontaneous net movement of particles toward a region of lower concentration. Each particle moves randomly (heat) and the arrangement of the particles in space becomes more random. This link provides an animation. ` Box of marblesanalogy for diffusion ` ` link 3

4 Order, energy and entropy The non-random arrangement of particles in a volume of solution (a concentration gradient) is a form of energy. So, order is a form of energy some say that information is too. The opposite of order is called entropy Chemical equilibrium The arrangement of a chemical system at which there is no tendency to change. Concentrations of products and reactants such that forward and reverse reaction rates are equal. A chemical system that is not at equilibrium has potential energy. Equilibrium depends on the system Some systems go all the way: O 2 + C 6 H 12 O 6 CO 2 + H 2 O Other systems reach equilibrium with similar concentrations of products and reactants. Some systems head for equilibrium immediately- others are stuck unless a catalyst is present 4

5 First Law of Thermodynamics Conservation of energy Energy is neither created or destroyed, but can change form and location Free energy Energy that is available in a system to do do work = useful energy Depends on the system glucose and O 2 useful for energy in cells but not in your gas tank. Heat from combustion is expands gases in cylinders of car engine. But, heat is not useful energy in cells why not? 5

6 Second Law of Thermodynamics All real processes (chemical reactions, etc) involve loss free energy. Whenever anything changes, the capacity for further change is reduced. Overall, energy is conserved, but useful energy is either converted to heat, or entropy increases. Entropy A measure of disorder Orderly (non-random) arrangements of matter tend to get less orderly, not more so. Diffusion as an example. Chemical reactions may convert free energy to heat, or increase entropy or both. Chemical reactions and heat All net reactions are exergonic (there is a net loss of free energy). Endergonic processes can only happen as part of a larger exergonic process. Many reactions are exothermic (convert energy to heat) e.g. combustion, respiration Some are endothermic take up heat. How can that be? Examples: melting of ice, dissolution of NH 4 NO 3 6

7 The Laws, restated First Law: No new energy is being created, so you can't win. Second Law: You can't break even, either. Eventually everything will get where its going and no more change will occur (maximum entropy). What about Life? Life decreases entropy- creates order. Does life violate the Second Law? Energy equation: G = H - TS G = free energy (available for work) H = enthalpy, the total energy of the system, including heat S = entropy (energy not available for work, multiplied by temperature) T= absolute temperature (Kelvin) 7

8 Why TS? The energy associated with entropy is proportionate to temperature (greater at higher temperature) Diffusion is faster at higher temperatures. Chemical reactions also proceed faster at higher temperature Gibbe's free energy equation: ΔG = ΔH - TΔS Δ = change ΔG is negative (free energy decreases) for any real process in a closed system ( closed = no inputs or outputs) This is the 2nd Law. Endergonic processes exist only as part of a net exergonic process Endergonic ΔG positive 8

9 Endergonic ΔG positive Exergonic ΔG negative Metabolic rate The free energy that is used in organisms becomes heat. Therefore, metabolic rate can be measured as rate of heat production Of course, free energy can also be stored by growth. 9

10 How can ATP provide energy? An endergonic reaction can only happen as net result of an exergonic pathway. Example: glutamine synthesis Glu + NH 3 Glu-NH 3 ΔG = +3.4 kcal/mole (won t happen) A metabolic pathway using ATP Net reactions Glu + NH 3 Glu-NH 2 ATP ADP + P i ΔG = +3.4 kcal/mole ΔG = -7.3 kcal/mole ΔG = -3.9 kcal/mole Actual reactions Glu + ATP Glu-P + ADP ΔG = -1.8 kcal/mole Glu-P + NH 3 Glu-NH 2 + P i ΔG = -2.1 kcal/mole 10

11 Energy transitions and chemical reactions Energy profile of an exergonic reaction Temperature and catalysts increase reaction rates "Activation energy" = minimum kinetic energy of reactants necessary for reaction Higher temperature- more molecules exceed the activation energy. If catalyst present, activation energy lowered, more molecules exceed the activation energy. 11

12 Atoms and molecules vary in their kinetic energy Temperature is the average heat energy per molecule, but individual molecules are moving at different speeds- some fast and some slow At higher temperature, more of them are moving fast enough to react. More exceed the E A Boltzmann energy distribution 12

13 Enzymes lower the activation energy Catalyst lowers activation energy by providing a binding site does not change reactants, products or equilibrium of the reaction enzymes and ribozymes enzyme activity is controlled by concentration, inhibitors, and effectors 13

14 Inhibition of enzyme activity The catalytic cycle of an enzyme The induced fit between an enzyme and its substrate 14