09-12 - BIO 5099 Molecular Biology for Computer...

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BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 7: More chemistry http://compbio.uchsc.edu/hunter/bio5099 [email protected] Balancing equations Conservation of matter and definite proportions mean that chemical equations have to balance . The matter on each side of the reaction has to be the same. We set integer coefficients in the reaction (stoichiometry) to achieve this. Burning methane in oxygen. CH 4 + O 2 CO 2 + H 2 O 1C, 4H, 2O versus 1C, 2H, 3O, so. .. Stoichiometry is: CH 4 + 2O 2 CO 2 + 2H 2 O Coefficients describe amounts in Moles. Equilibrium When the rates of the forward and backward directions of a reversible reaction are equal, the reaction is in dynamic equilibrium . The equilibrium constant K is defined as where [X] is the activity of X at equilibrium. Activity in aqueous solution is concentration divided by 1M (therefore a unitless number) Concentration of water is 1000 g/l / 18 g/M = 55.5M/l
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Non-equilibrium concentrations If we start out with concentrations not at equilibrium, the reaction will drive the concentrations toward it. We can calculate the initial, change and equilibrium E.g. 1M of Cl 2 and .5M of CO -> COCl 2 If at equilibrium K is 0.68 = [CO][Cl 2 ]/[COCl 2 ] we have 0.680 = ((0.5 - x) (1 - x)) / x Change in concentration, con't 0.680 = ((0.5 - x) (1 - x)) / x can be rewritten as x 2 - 2.18x + 0.5 = 0, so x = 1.09 ± 0.83 But which root? Concentrations are always positive, and the concentration of CO at equilibrium is 0.5-x. To ensure that is positive, x must be 0.26. COCl 2 concentration goes up by .26, and CO and Cl 2 concentrations go down by .26, so equilibrium concentrations are [COCl 2 ] = .26, [CO] = .24 and [Cl 2 ] = .74 Dissociation of water A proton (i.e. hydrogen ion, H + ) can be transferred from one water to another, resulting in the formation of one hyroxide ion (OH - ) and one hydronium ion (H 3 O + ). 2H
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09-12 - BIO 5099 Molecular Biology for Computer...

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