BioE-3380 Biomolecular Dynamics and Control Lecture 1 PDF

BioE-3380 Biomolecular dynamics and control Lecture 1 Dr. Rouhanifard 220 ISEC [email protected]  Assessment overview Quizzes (4 total) (32%) Problem Sets (8 total) (16%) Midterms (2)...

BioE-3380 Biomolecular dynamics and control Lecture 1 Dr. Rouhanifard 220 ISEC [email protected]  Assessment overview Quizzes (4 total) (32%) Problem Sets (8 total) (16%) Midterms (2) (32%) Final Exam (20%) Kinetics of molecular processes Biology is just a bunch of chemical reactions Why do bioengineers care about kinetics? How fast do concentrations change with time? Reactants need to collide in order to react  In a mixture of molecules A and B, the frequency with which A-B collisions occur is proportional to the concentrations [A] and [B].  Elementary reactions are single-step reactions with one transition state and no intermediates https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Kinetics/Rate_Laws/ Reaction_Mechanisms/Elementary_Reactions Which statement is correct? a. a. An elementary step has 0 intermediates. b. An elementary step has 1 intermediate. c. An elementary step has 2 intermediates. d. An elementary step has 0 transition states. e. An elementary step has 1 transition state. f. An elementary step has 2 transition  Molecularity is the number of molecules taking part in the reaction Unimolecular Bimolecular Termolecular https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Kinetics/Rate_Laws/ Reaction_Mechanisms/Elementary_Reactions Chemical equilibrium: no net change in the concentrations of reactants and products  Practice Which reaction system took the longest to form chemical equilibrium? Which reaction system has reached chemical equilibrium? Chemical equilibrium: no net change in the concentrations of reactants and products K = equilibrium constant Law of mass action  Practice Write the equilibrium constant expression for each reaction  The reaction quotient can be used to determine direction If Q K, the reaction will proceed to the left as written. If Q = K, then the system is at equilibrium.  Practice Hydrogen and nitrogen react to form ammonia according to the following balanced chemical equation: Values of the equilibrium constant at various temperatures were reported as: At which temperature would you expect to find the highest proportion of H2 and N2 in the equilibrium mixture? Assuming that the reaction rates are fast enough so that equilibrium is reached quickly, at what temperature would you design a commercial reactor to operate to maximize the yield of ammonia?  Extent of reaction: progress of a chemical reaction A is any chemical species involved in the reaction vA, its stoichiometric coefficient—(+) for products and (-) for reactants nA0, the moles of species A at the beginning of the reaction nA, moles of species A when has been reached  Practice Consider a reaction 2 A + 6 B −−→ 3 C + D. Suppose the initial concentration of A and B are 4 mM and 6 mM, respectively. After 1 hour, the concentration of A reaches 0.003 M. 1. Determine the extent of reaction. 2. Determine the concentration of B after 1 hour.