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BIOL 130 Study Notes Unit III Thermodynamics & Kinematics

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University of Waterloo
BIOL 130
Richard Ennis

Bio 130 Study Notes Unit III Thermodynamics: Specifically in biology, we are concerned with the first two laws of thermodynamics: The First Law: Energy can be transformed and transferred, but it cannot be destroyed or created • Energy = the capacity to do work o Moves matter against opposing forces o Rearranges matter • Kinetic Energy = energy caused by motion • Potential Energy = Stored energy as a result of: o location (e.g. a ball on top of a hill) o structure (e.g. the atoms in the arrangement of a molecule)  Chemical bonds in particular store potential energy and are therefore a source of useful cellular energy • Energy, Electrons, and Electron Shells: o Electrons participating in chemical bonds are a source of potential energy o The formation of new bonds can sometimes release more energy than was required to initially break those bonds  Therefore, the overall net excess of energy can be used by the cell to fuel a variety of cellular processes (e.g. the breaking of ATP into ADP + energy) The Second Law: Energy spontaneously disperses from being localized/ordered to becoming spread out/disordered (i.e. entropy = disorder) • Reactions cause disorder in two ways: o Heat is released during biological reactions, causing disorder in the outward environment  Note: While the release of heat outward into the environment causes the environment to be disordered, the inside of the cell is conversely more ordered when the reaction is completed o Reacting molecules becoming disordered because of the reaction  E.g. breaking a long chain of molecules causes them to disperse and be disordered because bond rotation is prevented o Chemical reactions are considered “spontaneous” if they occur on their own without input of energy o Thus, there are 2 types of chemical reactions:  Exergonic Reactions (spontaneous) • Products less ordered and have lower potential energy than reactants • A good way to remember this is: simple reactions = simple products with less energy potential  Endergonic Reactions (Not spontaneous) • Products are more ordered and have higher potential energy than reactants • Complex reactions = complex products with more energy potential Measuring Work in a System: Gibbs Free Energy (G): • Quantitatively measures the “useful” work obtained from a system at CONSTANT TEMPERATURE and PRESSURE o Predicts the spontaneity of reactions o Predicts chemical equilibria (whether a reaction lies left or right) o DOES NOT predict rate of chemical reactions o It is also additive for coupled reactions  This property allows energetically unfavourable (i.e. endergonic reactions) to occur b/c a spontaneous chemical reaction can be used to fuel the non-spontaneous one Free energy: • ΔG is negative if disorder of the universe increases (i.e. a reaction would occur spontaneously) o This makes sense because if a reaction has a ΔG that is negative, then that infers that it is a spontaneous reaction • Exergonic reactions o Are energetically favourable o ΔG < 0 (negative) o Disorder of universe increases during reaction • Endergonic reactions o Are energetically unfavourable o ΔG > 0 (positive) o Universe would become more ordered o These reactions can only occur if coupled with a second energetically favourable reaction Standard Free Energy (ΔG⁰): • Standard free energy represents the loss or gain of free energy as one mole of reactant is converted to one mole of product under standard conditions o Useful to compare different reactions and their spontaneity o Assume “standard” or ideal conditions  concentration of all reactants is 1M  pH = 7 • Depends only on the characteristics of molecules • The magnitude of ΔG⁰ indicates the equilibrium position of a reaction o If it’s positive then it’s to the left; if it’s negative then it’s to the right Chemical Reactants & Biological Systems: • Eventually, organisms must build more complex molecules out of simple compounds, as complex organisms cannot sustain themselves using solely exergonic reactions • Building these complex molecules are likely not simple exergonic reactions o Therefore, these reactions are likely not going to be spontaneous and require the energy input to proceed o These are endergonic reactions (+ΔG⁰) that create more complex products with higher potential energy than the reactants • Coupled reactions: o Reactions can be coupled together if they share one or more intermediates o In this case, the overall free energy is just the sum of their individual ΔG⁰ values  Thus, a reaction with a positive ΔG⁰ value can be coupled with a reaction with a negative ΔG⁰ value in order to make that energetically unfavourable reaction possible. o Allows cells to carry out the synthesis of complex energy-rich molecules w/o violating the laws of thermodynamics Rates of Spontaneous Reactions: • Even if an exergonic reaction is spontaneous and can occur by itself, it does not necessarily mean that it occurs quickly enough to be of any use. o Ex. Sugar  CO and H O is a spontaneous reaction, but occurs VERY slowly 2 2 • Bonds need to be broken before new ones are formed, which are dependent on the right molecules colliding o By extension, collision depends on temperature and concentration of molecules • Therefore in biological system, a catalyst is required to speed up these re
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