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Biol 130 Units 3&4 Review.docx

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BIOL 130
Heidi Engelhardt

Biol 130 – Midterm 2 Study Notes Unit 3 – Thermodynamics and Catalysis  Cells need to carry out a multitude of chemical reactions  They need to form complex molecules to function o Energetically intensive process o Must obey same thermodynamic principles as non-living matter  Many of these reactions do not occur at rates capable of sustaining life under physiological conditions o They need a mechanism to help – ENZYMES (protein and RNA based catalysts)  Thermodynamics = the relationship between forms of energy and heat o The interconversion between forms of energy  1 Law of Thermodynamics o Energy can be transferred and transformed BUT it cannot be created nor destroyed  Energy = the capacity to do work/ to move matter against opposing forces / to rearrange matter  Kinetic energy (Ek) = the energy of motion, heat  Potential energy (Ep) = stored energy o As a result of location or structure o Chemical bonds contain stored energy and therefore can provide a source of useful cellular energy  Electrons participating in chemical bonds are a source of potential energy o Bond formation is favourable o But forming some types of new bonds can free more energy than required to break the old bonds and energy is therefore released  2nd Law of Thermodynamics o Energy tends to spontaneously disperse, from being localized, ordered to becoming spread out, disordered o Entropy = disorder  Chemical Reactions o Making or breaking of chemical bonds o Shifting of atoms from one molecule to another o Spontaneous = if they occur on their own, without external input = energy is released o Exergonic Reactions = heat released/products are less ‘ordered’/have lower Ep than the reactants o Endergonic Reactions = heat inputted/products are more ‘ordered’/have higher Ep than the reactants  Gibbs Free Energy (G) = quantitative measures the ‘useful’ work obtainable from a system at a constant temp/pressure o Predicts the spontaneity of reactions o Does not predict reaction rates o Does predict chemical equilibria o A chemical reaction that is spontaneous must have a negative  Gproducts – Greactants =  Free energy and standard free energy o Need a standard energy to compare different reactions,  Independent of concentration  Ideal conditions (1M concentration of all reactants) o Allows us to compare the spontaneity of different reactions  Chemical reactions and biological systems o At some point, organisms have to build more complex molecules out of simple compounds  Not likely to be spontaneous o Chemical evolution – the idea that simple chemical compounds in the ancient atmosphere and oceans combined to form larger, more complex substances o Requires endergonic reactions  Non-spontaneous (+ve – need energy input to proceed  Products are more complex (higher Ep) than reactants  Coupling of Reactions – Energetics o In biology, we synthesize more complex molecules by coupling their synthesis to energetically favourable reactions o Happens if they share one or more intermediates  Energy Recaps o Potential energy is stored in bonds = chemical energy o Exergonic reaction results in a net RELEASE of energy  Thermodynamically favourable – spontaneous  Energy can be used or lost as heat  Less complex/loss of order/-ve o Endergonic reactions needs ENERGY INPUT to drive it  Thermodynamically unfavourable  More complex products/storage of Ep/+ve o The magnitude of informs us on the equilibrium position in a reaction o Due to the additive nature of we have the thermodynamic basis for how cells are able to carry out the synthesis of complex energy- rich molecules  RATES of spontaneous reactions o Even if the reaction is spontaneous, doesn’t mean it is a fast reaction o Often one bond has to break before a new one forms; requires the right molecules to collide o Odds of collision are influenced by: temperature (speed of molecules) or the concentrations (crowdedness) o We need mechanisms to help reactions occur quickly enough  Many proteins are enzymes o Catalysis of chemical reactions may be the most important role of proteins in the cell o Protein name will end in –ase o The mechanisms by which enzymes catalyze reactions are multifaceted and complex  Enzymes o Catalyze thermodynamically favourable reactions  Allow them to proceed at rapid rates o Enzyme DO NOT:  Change equilibrium position of reaction  Catalyze non-spontaneous reactions  Activation Energy (Ea) o Reaction needs energy to get over the ‘hill’ o Hill analogy: even to roll a boulder downhill sometimes requires a small push o In chemical terms: making new bonds may first require breaking/weakening of existing bonds  Activation Energy and Catalysts o Catalysts lower the Ea for a reaction o Changes the rate of a reactions but it is not consumed by the reaction o Enzyme catalyst are amazingly effective  How do enzymes catalyze a reaction o Brings reactants together  Rather than colliding randomly, substrates are oriented very specifically by binding to the enzyme’s active site typically through non-covalent interactions  Correct 3D structure of active site is essential for binding o Interactions between substrates and R groups in the active site the conversion of substrates to products  Activation energy lowered  Often involves enzyme changing shape o Energy level of produc
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