BIOC 4224 Physical Chemistry for Biologists SPRING 2010 SYLLABUS INSTRUCTORS: Dr. Andrew Mort, Regents Professor E-mail: amort@okstate.edu Phone : 744-6197 Office : l51 NRC CLASSROOM AND CLASS HOURS Dr. Jose L. Soulages, Associate Professor E-mail: jose.soulages@okstate.edu Phone: 744-6212 Office: 147 NRC Classroom: 348B 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) Solution and discussion of 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. Instructors will be able to arrange by e-mail consultation meetings at times convenient for the student. TEXT: Physical Chemistry for the Biosciences/Raymond Chang/2005/ ISBN: 978-1-891389-33-7 GRADING The following activities will be graded:
1. Weekly quizzes and answers to questions about homework problems. These questions will be asked during recitation classes. 2. Short presentations about biochemical or biophysical topics related to the basic concepts discussed in lectures. 3. Hour-exams (two or three tests will be given) 4. Final Comprehensive Exam Grades: 100-80 = A; 79-65 = B; 65-50 = C; 49-40=D, and < 40 = F. The final grade will be the higher of either: 1) the grade of the comprehensive final exam or 2) the grade calculated through the following addition: 30 % of the average grade obtained in quizzes, homework, presentations and responses to questions in problem solving classes 30 % of the average grade in hour exams 40 % of the grade achieved in the comprehensive final (***) 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. ATTENDANCE: Attendance to lectures is not required but is highly recommended. Take into account that on Thursdays the students will be evaluated according to their participation in class and ability to answer a quiz. (***) 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 exam, the final grade for the course will be that of the final exam. 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.
BIOC 4224 Physical Chemistry for Biologists SPRING 2010 OBJECTIVES OF BIOC 4224: This physical chemistry course will provide the students some of the basic tools required to understand, generalize, and sometimes predict processes of biological interest. These tools include knowledge on thermodynamics, electrochemical principles, kinetic properties of chemical reactions, structure and properties of matter, interaction between electromagnetic radiation and matter, matter-matter interaction, etc. Why should we, biochemistry students, study physical chemistry? We may define biochemistry as the field of science comprising the knowledge of the properties of chemical reactions and physical processes involving molecules of biological interest (*). Under this definition we can easily understand the importance of knowing basic physical principles, which ultimately explain the driving forces defining both the feasibility and rates of chemical and physical processes. Chemical reactions and physical interactions are responsible for the function, malfunction, or death of individual cells or multi-cellular organisms. We can see, then, that as our knowledge of the physical principles governing biological processes improves so does our ability to understand biology, physiology and even medicine. Why do schools require a course in physical chemistry for students pursuing a degree in biochemistry? An elementary class of physical chemistry is a key element of a plan of study designed for a degree in biochemistry and/or molecular biology. Basic elements of physical chemistry are needed to understand protein synthesis and folding, protein stability, protein-protein interaction, protein-ligand interactions, biogenesis of membranes, lipid-lipid and lipid-protein interactions, enzyme kinetics, RNA or DNA synthesis, protein-nucleic acid interactions, control of metabolic pathways, membrane potential and excitability, etc. P. Chem. gives you the opportunity to understand why something happens. Without it you may know a few facts, you may have information. However, you will not have the knowledge to predict a similar occurrence under similar circumstances. How can P. Chem. benefit my career? Medicine: An elementary class of physical chemistry will greatly benefit students planning on attending medical school. The greater the depth of the physical chemical perspective of a medical student the easier will be the understanding and memorization of important medical topics. The information and rationale provided by a Physical Chemistry course contribute to the global education of medical doctors increasing their knowledge and improving the common sense that cannot be achieved in a formation based only on information. For example thermodynamics is a key element in the understanding, research and practice of sports physiology; P. Chem. will enhance the ability to understand the complex processes of ion and water transport in kidney, or the delicate acid-base equilibrium in blood that must be carefully monitored and balanced to allow the survival of numerous intensive care patients; similarly, the students will be better prepared to understand the phenomena of gas and water exchange that takes place in lungs and the role of the composition of the breathing atmosphere in the acid-base equilibrium and oxygenation of blood.
Research in biosciences: Successful experimental research in biosciences, such as that required for students pursuing a Ph.D. in biochemistry, requires the consideration of the possible interactions and effects among the components and conditions of a reaction mixture: solvent, salts, ph, protein, lipids, RNA, DNA, substrates, temperature, etc. Biotechnology: Physics and chemistry are also essential disciplines for the advancement of biotechnology. Students pursuing a career in biotechnology will be highly benefited by a strong physical chemical background. Food processing, or food technology, is based on the physical chemical manipulation of mixtures of proteins and lipids, among other components, to achieve products of different physical properties. A successful career in pharmaceutical sciences will be more likely for graduates with strong backgrounds in physical chemistry. Most experimental and theoretical approaches used in the pharmaceutical industry to design, discover and test potentially useful drugs require physical chemical methods. (*)The definition of biochemistry provided above also includes the discipline so called molecular biology, which refers to the study of reactions involving nucleic acids.
Topics that will be 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 Earth atmosphere; Effect of altitude on pressure; Barometric formula; greenhouse effect; Toxicity of gases: how much of a toxic gas can accumulate in air? Examples HCN; CO 2 ; CO; others 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 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 The role of 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
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
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.