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Thermodynamics notes

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Department
Biological Sciences
Course
55-204
Professor
kaplan
Semester
Summer

Description
[2.1] THERMODYNAMICS – study of energetics of chemical rxns; there are 2 relevant forms: o Heat Energy – movement of molecules o Potential Energy – energy stored in chemical bonds st – 1 Law of Thermodynamics (Law of Conservation of Energy) o energy of the universe is constant o implies that when energy of system ↓, energy of the universe (surroundings) must ↑ – 2 Law of Thermodynamics o disorder (entropy [S]) of the universe tends to ↑ o spontaneous rxns ↑ the disorder of the universe – this is discussed mathematically by (Gibbs) free energy ∆G = ∆H - T∆S (T – temp, H – enthalpy) ∆H = ∆E - P∆V (E – bond energy, P – pressure, V – vol) – change in GFE determines if rxn is favourable (spontaneous, –∆G) or unfavourable (nonspontaneous, +∆G) – Spontaneous Rxns (favourable) o occur w/o a net addition of energy or w/ energy to spare, ∆G < 0 o rxns with –∆G are exergonic (energy exits the system) – Nonspontaneous Rxns (unfavourable) o requires energy input o rxns with +∆G are endergonic (energy enters the system) – rxns w/ –∆H are exothermic (liberate heat) – rxns w/ +∆H are endothermic (require input of heat) ∆G⁰’ = –RTlnK’ eq (R – gas constant, eq – ratio of products to reactants at equilibrium) ∆G = ∆G⁰’ + RTlnK NOTE - K and K eqe not the same; K – ratio of products to reactants; Keq ratio at equilibrium – Equilibrium o is the point where the rate of rxn in one direction equals the rate of rxn in the other o there is constant product and reactant turnover, but overall concentrations stay the same o when K = K ,eqe are at equilibrium o when ∆G = 0, you are at equilibrium (forward rxn=back rxn, net concentrations do not change) o equilibrium tends toward the lowest energy state SUMMARY There are 2 factors that determine whether a rxn will occur spontaneously (–∆G) in the cell: (1) intrinsic properties of the reactant and products (∆G⁰’) (2) concentrations of reactants and products (RTlnK) Thermodynamics vs Rxn Rates – Thermodynamics will tell you where a system starts and finishes but nothing about the path travelled – therefore, ∆G doesn’t depend on the pathway a rxn takes or the rate of rxn; it is only a measurement of the difference in free energy b/w reactants and products [2.2] KINETICS & ACTIVATION ENERGY (E ) A – Chemical Kinetics is the study of rxn rates – all rxns go through an unstable intermediate or transition state (TS) – symbol: [TS]‡ – the energy required to produce this intermediate is called the activation energyA(E ) o this is the barrier that prevents rxns from proceeding (even though ∆G for the rxn may be –) – Catalyst o lowers the E Af the rxn w/o changing ∆G by stabilizing the transition state, making its existence less thermodynamically unfavourable o is not consumed in the rxn; it is regenerated with each rxn cycle – enzymes are catalysts – they ↑ rate of a rxn by lowering the A but don’t affect ∆G b/w reactants and products ATP as an Energy Source: Reaction Coupling – enzymes increase the rate of rxn’s that have –∆G – BUT, there are many rxn’s in the body that occur which have a +∆G o thermodynamically unfavourable rxn’s in the cell can be driven forward by reaction coupling – where one very favourable rxn is used to drive an unfavourable one  this is possible b/c free energy changes are additive SUMMARY – one rxn in a test tube o enzyme is a catalyst w/ a kinetic role o enzyme influences the rate of the rxn, but not the outcome – many real life rxns in the cell o enzyme controls outcomes by selectively promoting unfavourable rxns via reaction coupling [2.3] ENZYME STRUCTURE AND FUNCTION – most enzymes are proteins that must fold into specific 3D structures to act as catalysts – folding is imp in enzyme function b/c this leads to proper formation of the active site o region in an enzyme’s 3D structure that is directly involved in catalysis o contains amino acid residues that stabilize the transition state of the reaction  this lowers the activation energy barrier b/w reactants and products – reactants in an enzyme-catalyzed rxn are called substrates – active site for enzymes is highly specific in its substrate recognition – many proteases (protein-cleaving enzymes) have an active site w/ a serine residue whose OH group can act as a nucleophile, attacking the carbonyl carbon of an amino acid residue in a polypeptide chain – these enzymes also have a recognition pocket near the active site o this is a pocket in the enzyme’s structure which attracts certain residues on substrate polypeptides o the enzyme always cuts polypeptides at the same site  ie: enzymes that act on hydrophobic substrates have hydrophobic amino acids in their active sites, while hydrophilic/polar amino acids have hydrophilic substrates in
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