SPRING 2014 BIOC 4224 Physical Chemistry for Biologists SYLLABUS INSTRUCTORS:

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1 SPRING 2014 BIOC 4224 Physical Chemistry for Biologists SYLLABUS INSTRUCTORS: From Jan 13, March 3, 2014 Dr. Jose L. Soulages, Professor jose.soulages@okstate.edu Phone: ; Office: 147 NRC From March 4, 2014 May 2, 2014 Dr. Andrew Mort, Regents Professor andrew.mort@okstate.edu Phone : ; Office : l51 NRC CLASSROOM AND CLASS HOURS Classroom: 246H Noble Research Center Monday & Tuesday from 10:30 AM 11:20AM Thursday from 10:30AM to 12:20AM Mondays and Tuesdays will be, in general, used for lectures DISCUSSION AND PROBLEM SOLVING CLASSES. In general, Thursday s class will involve: 1) Lecturing; 2) Solving and discussing homework problems; 3) Evaluation of the progress of the students (Quizzes, tests, presentations, homework). OFFICE HOURS. The students are highly encouraged to visit with the instructors to discuss matters related to topics of the lectures and/or homework problems. Most of the time the instructors will be able to arrange consultation meetings at times convenient for the student. TEXT: Physical Chemistry for the Biosciences/Raymond Chang/2005/ISBN: PREREQUISITES: MATH 2123 (6 hrs calculus strongly preferred) and CHEM 1515 or equivalent. STUDENTS WITH DISABILITIES: If any student feels that he/she has a disability and needs special accommodations of any nature whatsoever, the instructors will work with you and the Office of Disabled Student Services, 326 Student Union, to provide reasonable accommodations to ensure that you have a fair opportunity to perform in this class. Please advise the instructor of such disability and the desired accommodations at some point before, during or immediately after the first scheduled class period.

2 GRADING The following activities will be graded: Weekly quizzes and homework problems Hour-exams (three or four tests will be given) Final Comprehensive Exam Grades: = A; = B; = C; 49-40=D, and < 40 = F. The final grade for the course will be the higher of either: 1) The grade of the comprehensive final exam or 2) The grade calculated through the following addition: 5% Attendance 20% of the average grade obtained in quizzes and specifically assigned homework problems 40 % of the average grade in hour exams 35 % of the grade achieved in the comprehensive final (***) (***) Quizzes and/or hour exams that are not taken will be given a grade equal to that of the final comprehensive exam. If a student misses all quizzes and exams, the final grade for the course will be that of the final exam. Note that responses to questions asked during lectures will not be evaluated. Students should feel free and are encouraged to ask or answer questions during lectures. Important Dates: Last day to add a class (without instructor permission) 1/21/2014 Last day to drop a course with no grade and no fees charged for courses 1/21/2014 Last day to withdraw completely from the University and receive a 100% refund 1/21/2014 Last day to add a class (requires instructor & advisor permission) 1/24/2014 Last day to drop a course with an automatic W and receive a 50% refund (requires advisor signature) 1/24/2014 Last day to withdraw completely from the University and receive a 50% refund 1/24/2014 Last day to post 6 week grades for 1000 & 2000 level courses 2/25/2014 Last day to file diploma application (for name to appear in Spring Commencement program) 4/1/2014 Last day to drop a class with an automatic W 4/11/2014 Last day to withdraw completely from the University with an automatic grade of "W" 4/11/2014 Last day to withdraw completely from all OSU classes with an assigned grade of W or F 4/25/2014 Pre-Finals week 4/28 5/2/2014 Final examinations 5/5 5/9/2014 Note: For outreach, internet, and short course drop/add dates, see the Short Courses link on the Registrar s Class Schedule webpage. Syllabus Attachment for Spring 2014 in Word and pdf formats for use as final preparations are made for spring classes. The updated document will be posted to our website (

3 Topics covered in BIOC 4224 lectures and/or problem solving classes The list includes only the topics that will be covered in the first part of the course. The complete list will be posted at a later time. 1. Ideal and Real Gases Perfect Gas Equation Equation of State Isotherms, Isobars The Ideal Gas Temperature Scale Dalton s Law From experiment to theory and vice versa: the kinetic theory of gases Intermolecular interactions Critical Temperature and pressure Some Applications of the Properties of Gases. Toxicity of gases: how much of a toxic gas can accumulate in air? Examples HCN; CO 2 ; CO; others Earth atmosphere; Effect of altitude on pressure; Barometric formula; greenhouse effect; 2. Thermodynamics: First Law (Part-I) Energy Energy Transactions: Work and heat Systems: definition and types System Properties: Intensive and Extensive State of a System Types of Thermodynamic Processes Internal Energy Properties of the Internal Energy Function Heat Capacity Changes of Internal Energy in different types of processes: Constant volume, constant pressure, isothermal and adiabatic processes. Intermolecular Interactions and the change of internal energy at constant temperature 3. Thermodynamics: First Law (Part-II) Enthalpy: Definition and properties of the function Change of enthalpy with temperature for physical processes Thermochemistry Enthalpy changes for chemical reactions: Calculation from known internal energy changes Effect of gases Standard enthalpy changes of reaction, formation, combustion, etc Change of enthalpies of reaction with temperature

4 Applications of the First Law to Biological Systems Enthalpy and heat capacities of reactions of biochemical interest: measurement and examples Enthalpy and heat capacities of proteins: Protein stability Differential Scanning Calorimetry Enthalpy of Ligand-protein and Ligand-membrane interaction Isothermal Titration Calorimetry 4. The Second Law of Thermodynamics (Part-I) What the first law does not tell us Entropy: definition Statement/s of the second law Microscopic and macroscopic view of the second law Changes in energy levels and/or level populations The efficiency of internal combustion engines Spontaneous processes in isolated systems Examples of entropy change calculations Change of entropy with temperature Change in entropy in phase transitions Entropy of mixing 5. The Second Law of Thermodynamics (Part-II) Gibbs Free Energy: Definition Changes in Gibbs energy for spontaneous processes and systems at equilibrium The meaning of free energy changes The chemical Potential: definition Chemical potential in the equilibrium of phases: Liquid-vapor equilibrium: the vapor pressure, humidity Liquid-solid equilibrium Solid-vapor equilibrium Effect of pressure in the equilibrium The chemical potential of liquids: Ideal liquid solutions: Raoult s law Real Solutions: Henry s Law The activity of solute and solvent Solubility: Partition of a solute between two phases The hydrophobic effect Colligative Properties: Osmotic Pressure, Depression of the melting point. Chemical equilibrium The Thermodynamic Equilibrium Constant Reference States and the standard change in free energy of a reaction The reaction quotient Effect of pressure and temperature on the equilibrium constant

5 6. Application of thermodynamics to biological processes Metabolism Biochemical Reactions Metabolic Cycles Direct Synthesis of ATP Receptor/ligand Interaction Binding of Small Molecules to Multiple Identical Binding Sites Macroscopic and Microscopic Equilibrium Constants Experimental Determination of Ligand Binding Isotherms: ITC, dialysis, spectroscopic methods Cooperativity in Ligand Binding, models and kinetic Studies Allosterism Discussion of several Examples: Hemoglobin/O 2 Interaction: effect of ph and CO 2 /CO 3 H - Protein Stability The hydrophobic effect Experimental Determination; Effect of temperature and ph; Osmolites, natural denaturants and stabilizers (urea, glycerol, TMAO, trehalose ) Effect of mutations Lipid Thermotropic Transitions: Cooperativity of the lipid-lipid interactions Effect of lipid-protein interactions on the cooperativity of phase transitions in membranes 7. Electrochemistry Coulomb s Law Electric Field Electric Potential Electrochemical Systems The electrode Potential Thermodynamics of Galvanic Cells Electromotive Force The Nerst Equation Determining the EMF and the equilibrium constant for electrochemical reactions Application of Electrochemistry to Biological Processes The electric potential of cellular membranes Chemiosmotic theory and the synthesis of ATP Donnan effect and the erythrocyte function Active and passive transport

6 Expected learning outcomes: The students will become proficient using the ideal gas equation in a number of ways to estimate concentration of gases, or the effect of changes in variables on the properties of the gas. A number of examples in which the concentration of gases in air is of biological significance will be offered. The students will be able to perform calculations on the toxicity of gases. The students will be able to evaluate a very good example of how experimental laws can be described by theoretical models (kinetic theory of gases) and how even in this case there are significant limitations. The students will acquire a clear notion of the concepts of energy, kinetic and potential energy, and will be able to carry out simple calculations involving energy transactions for a number of chemical and physical processes. The students will be able to describe and understand basic methodologies and principles involved in the determination of energy, enthalpy and entropy changes. Numerous examples involving calculations will illustrate the application of thermodynamics to the prediction of the feasibility of physical and chemical transformations. The students will be able to formulate pathways that allow the calculation of changes in thermodynamic properties. The students will be able to define the thermodynamic concepts of chemical potential and chemical activity. The students will be able to describe and predict the nature of a number of physical and chemical phenomena making use of the concept of chemical activity. These phenomena will include, among other, chemical equilibrium, evaporation of liquids, osmotic pressure, active and passive transport, solubility of gases in liquids, stability of proteins, the origin of electrochemical potentials in biological and in physical systems. Ideally, the students will graduate from the P. Chem. class feeling that physical chemistry is needed to understand biochemistry and natural phenomena, including human physiology and pathology.