Chapter 2 - CHEM 204

Chapter 2 - CHEM 204 - CHEM 204 Fall 2009 Physical...

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Unformatted text preview: CHEM 204 Fall 2009 Physical Chemistry for Biological Sciences Dr. Amy S. Blum Pulp and Paper 105 Textbook Physical Chemistry for the Biological Sciences, by Raymond Chang, available at McGill University Bookstore. Problems and solutions to accompany Physical Chemistry for the Biological Sciences, by Helen O. Leung and Mark D. Marshall Midterm 1, Wed. Oct. 7th, 6:00PM-9:00PM, Otto Maass #112/10 Midterm 2, Wed. Nov. 11th, 6:00PM-9:00PM, Otto Maass #112/10 Course Grading 25% 30% Midterm 1, Wed. Oct 7th, 6:00PM-9:00PM, Otto Maass #112/10 Midterm 2, Wed. Nov 11th, 6:00PM-9:00PM, Otto Maass #112/10 5% Assessments/Quiz, To be done with every module. 40% Final Exam (yet to be scheduled between Dec 4 and Dec 19) Midterm Conflicts ? MUST be identified as soon as possible Exam Policy No make up exams—if you have an excused absence, the missed points will be redistributed between the other midterm and final exam. Missed exams due to illness require a doctor’s note. Exams are closed book. You can bring your own formula/note sheet consisting of handwritten notes on one side of one letter size sheet of paper. Calculators are required. Problem Sets, Office Hours & Tutorials Problem Sets assigned every section (on the first day covered), usually ~10 questions from the textbook, at the end of the chapters. Numerical answers will be found in the back of the Book and given with the assignment. Answers are also available in the solutions manual Use the solutions manual only after doing the problems alone. accompanying the textbook. Problem sets will not count towards final grade, however they help identifying those aspects you might have not grasped all that well. Office Hours: Every Monday and Wednesday, from 10:00 AM to 11:00 AM, Pulp and Paper 105. Tutorials Wednesdays, 6:05 to 7:55 PM Otto Maass #328 Jon Saari Office Hours: Tues 10-12 Resources Lectures: Lecture notes will be posted on WEB CT Vista prior to class. You can print them to add in-class notes (http://www.mcgill.ca/webct/ ). Email: Use WEB CT Vista email to communicate all questions, the replies will be posted on the site. Emails will be responded to within 24 hours, unless I give prior notice of my absence. Course Material Questions: Use the Web CT Vista site to post your questions. The discussions area is a good resource. You can often get help faster from your classmates. Course Recording: Recordings will be available after the lecture with the link within the WEB CT Vista site. Hints for Doing Well in CHEM 204 1) Briefly review the notes and textbook soon after class 2) Read ahead of the lectures, even by just a day or two 3) Work through the homework problems 4) Attend the lectures, and try and keep track of where we are in the progression of ideas and goals of the course Course Prereqs • Chem 110 or 111 AND Chem 120 or 121 • One full course of calculus When lecturing, knowledge of the prereqs will be assumed. Please see the links available on WebCT for review of math concepts. Goals Learn physical chemistry concepts and apply them to relevant problems in biological systems. Place in quantitative terms phenomenological observations. Quantitative problems solving skills. Course Outline 1) 2) 3) 4) 5) Molecules and Their Energies, a Brief Overview. The 1st Law of Thermodynamics — Conservation of Energy. The 2nd Law of Thermodynamics — Ever-Increasing Entropy. Equilibrium in Aqueous Solution — Putting it All Together The Rates of Biological Processes — Quantifying the Changes We will learn about 1) MOLECULES to understand 2) HEAT ENERGY stored, to then understand 3) TOTAL ENERGY, from which we can predict 4) EQUILIBRIA and then finally 5) REAL PROCESSES. Why Physical Chemistry? • Microscopic understanding • Predicting macroscopic phenomena The Goals of This Course The BIG picture (from an idealist’s viewpoint) : understand BIOLOGY thermo to explain CHEMISTRY ? using MATHEMATICS quantum chem phys to explain PHYSICS Molecules and their energies molecular rotations 0.01 kJ/mol molecular vibrations 10 kJ/mol molecular excitations 1000 kJ/mol (Chang fig. 14.5) Conservation of Energy The combustion of glucose yields ca. 2800 kJ/mol of energy. C6H12O6(s) + 6 O2(g) 6 CO2(g) + H2O(l) rH = 6 x (-393.5 kJ/mol)+ 6 x (-285.8 kJ/mol) – (-1274.5 kJ/mol) = -2801.3 kJ/mol DNA stretching, transition from ds to ss DNA Entropy and spontaneity: S >0 spontaneous Free Energy ( G) and spontaneous change G 0 1 2 3 4 5 6 Base pairs G = Gibbs Free Energy 4) Equilibrium in Aqueous Solution Predicting an equilibrium from a G. Direction of any chemical reaction. Solubility and insolubility. Coupled reactions and ATP. 5) Kinetics Ion gradient is critical; how does cell regulate it? Nobel Prize in Chemistry 2003 Dolye et al, Science 280, 69 (1998) Use physical chemistry techniques to understand bio-structure. ATP an energy reservoir Glucose oxidation proceeds with the transfer of 24 e- to O2 C6H12O6(s) + 6O2(g) rG = -2878kJ/mol 6CO2(g) + 6H2O (l) Glucose combustion energy is stored in 38 ATP molecules according to ADP3- + H+ + HPO4ATP4- + H2O rG = 31.4 x 38 = 1193.2 kJ/mol Energy storage The terminal phosphate hydrolysis in ATP yields ca. 30 kJ/mol of usable energy. ATP + H2O ADP + Pi D. Gust et al. Acc. Chem. Res., 34, 40 (2001) ATPase activity Kinosita K, Nature 410, 898 (2001) Nature 427, 465 (2004) Coupling ATP hydrolysis to molecular machines C. Bustamante et al. Nature 413, 748, (2001) Direct observation of base-pair stepping by RNA polymerase S. Block et al. Nature 438, 460, (2005) ATPase activity M Yoshida http://www.res.titech.ac.jp/~seibutu/ Rates of Biological Processes P. F. Barbara et al. Biophys. J. 87, 3470 (2005) Catalysis Anslyn, Dougherty, Modern Physical Organic Chemistry (2005) University Science ooks Course Outline 1) 2) 3) 4) 5) Molecules and Their Energies, a Brief Overview. The 1st Law of Thermodynamics — Conservation of Energy. The 2nd Law of Thermodynamics — Ever-Increasing Entropy. Equilibrium in Aqueous Solution — Putting it All Together The Rates of Biological Processes — Quantifying the Changes We will learn about 1) MOLECULES to understand 2) HEAT ENERGY stored, to then understand 3) TOTAL ENERGY, from which we can predict 4) EQUILIBRIA and then finally 5) REAL PROCESSES. Read: R. Chang, chapter 2 and 3 ...
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