Biophysical Chemistry CHEM348 and CHEM348L Credits: 3 (CHEM 348), 1 (CHEM 348L) South Dakota State University, 015 Lecture: 9:00-9:50 am, MWF, SAV 07. Lab: -4:50 pm, Wed. SAV 378 or as stated in class. Instructor: Dr. Adam Hoppe, phone: 605-688-5315, email: adam.hoppe@sdstate.edu; office: SAV 373 Office hours: MWF 1-pm, after class or by appointment Instructor: Dr. Suvobrata Chakravarty, phone: 605-688-5694 email: suvobrata.chakravarty@sdstate.edu; office: SAV 367 Office hours: MWF 10-11 am, after class or by appointment Lab Instructor: Dr. Suvobrata Chakravarty Course Description: A study of the fundamental principles governing the physical chemistry of biological systems. Topics covered include the forces governing protein and nucleic acid stability, the thermodynamics of protein folding and protein-ligand interactions, bioenergetics, kinetics of biochemical reactions, biological membranes and membrane transport. The physical basis of protein purification, probing protein-ligand interactions, and the determination of macromolecular structure are also discussed. CHEM 348L, The Laboratory Course accompanying CHEM 348: Fundamental physical chemistry principles and techniques of physical chemistry used in studying biomacromolecules and biological systems. Pre-requisites: MATH 13, CHEM 464; co-requisite CHEM 348L Instructional Methods: Dr. Hoppe s course content will largely come from his lecture notes. Papers from the primary literature will also be used for both reading material and problem solving. Dr. Hoppe s instructional methods will include in class discussions of both foundational concepts and their applications to problems. Students are expected to contribute to these discussions. Dr. Chakravarty s portion will also come from lecture notes based primarily on the Tinoco s Physical Chemistry book. The primary literature will also be used. Classroom sessions will involve a mixture of instructor lecture, group problem solving, discussion and brief presentations by students over homework problems. Lecture Text: Required: Physical Chemistry, Principles and Applications in Biological Sciences, 5 th Edition. Tinoco, Sauer, Wang, Puglisi, Harbison, Rovnyak. PEARSON 014 (ISBN-13: 978-0-13-605606-5) Reference: Physical Biology of the Cell nd Edition. Phillips, Kondev, Theriot. Garland Science 01. (ISBN 978-0-8153-4450-6). Reference: Principles of Physical Biochemistry (1 st or nd edition), van Holde, Johnson and Ho; Pearson Prentice Hall, 006 (ISBN0-13-04647-9). You may also find basic biochemistry and cell biology texts useful. Examples include: Biochemistry by Lehninger or Voet and Voet, and The Cell by Alberts. Course Goals: including. Introduce foundational principles and research methods of biophysical chemistry Student Learning Outcomes:
1. Broad understanding of the molecules and cells of life as explained by the principles of physics and chemistry.. The ability to apply concepts and make quantitative predictions about living systems using tools from physics and chemistry. This course will specifically focus on the laws of thermodynamics, elementary statistical mechanics, intramolecular forces, reaction kinetics and diffusion. 3. Gain confidence in quantitative problem solving in biochemistry and molecular biology, including the application of new computational tools. Evaluation: Two exams, a midterm and final, will be given. Each is worth 100 pts. There will be 5 homework assignments each worth 40 pts/ea for a total of 00 pts. Final grades will be determined from the averaged exam and homework scores as a percentile. Curving will be applied if necessary. A 85; 84.5>B 70; 69> C 55; 54> D 40; 39>F. Homework grading: Problem solving is a major component of this course. There are four recitation sessions scheduled. Homework must be submitted prior to the recitation session for full credit. Any homework turned in after a recitation session will be worth 50% of its original value, if submitted prior to the next class period. Homework submitted later than one class period after recitation will be given a score of zero, zip, nada, no points or 0%.
General Attendance: Attendance in lecture is strongly encouraged. This course will move at a brisk pace and the instructor s notes will not be available and lectures will not be repeated. Strong attendance and class participation may positively influence grades that are on the cusp. Honesty Policy: Work submitted is to be the effort of the individual, unless otherwise advised. Anyone participating in an act of dishonesty (including plagiarism) will receive a failing grade for the course and may be referred through appropriate university procedures for further disciplinary action. For more information about what plagiarism and when to appropriately cite references please see http://www.plagiarism.org/. Make-up Policy: All exams must be taken as scheduled. If you have a legitimate reason for missing the exam you must notify me within 4 hrs and the makeup will be scheduled at the earliest convenience. Late Homework: Homework must be turned in at the beginning of the class period it is due (e.g. prior to the recitation session). Students may turn in revised solutions to problems following the recitation for 50% credit. Freedom in Learning Statement: Students are responsible for learning the content of any course of study in which they are enrolled. Under Board of Regents and University policy, student academic performance shall be evaluated solely on an academic basis and students should be free to take reasoned exception to the data or views offered in any courses of study. Students who believe that an academic evaluation is unrelated to academic standards but is related instead to judgment of their personal opinion or conduct should first contact the instructor of the course. If the student remains unsatisfied, the student may contact the Department Head, Dean, or both, of the college which offers the class to initiate a review of the evaluation. Student Academic Integrity and Appeals: The University has a clear expectation for academic integrity and does not tolerate academic dishonesty. University Policy :4 sets forth the definitions of academic dishonesty, which includes but is not limited to, cheating, plagiarism, fabrication, facilitating academic dishonesty, misrepresentation, and other forms of dishonesty relating to academics. The policy and its procedures also set forth how charges of academic dishonesty are handled at the University. Academic Dishonesty is strictly proscribed and if found may result in student discipline up to and including dismissal from the University. ADA Statement: Any student who feels s/he may need an accommodation based on the impact of a disability should contact Nancy Hartenhoff-Crooks (or successor) Coordinator of Disability Services (605-688-4504 or Fax, 605-688- 4987) to privately discuss your specific needs. The Office of Disability Services is located in room 065, the University Student Union. Tentative 015 Fall Schedule Date Lecturer Reading Lecture Topic Lab August 4 AH PBOC Ch. 1 (ref) What is Biophysical Chemistry? Biology by the Numbers Scaling laws, higher order processes 6 AH Construction of Cells 8 AH Physical Chemistry of Macromolecules
31 AH Intramolecular Forces I September AH Intramolecular Forces II Lab 1: Cells and Molecules 4 AH Intramolecular Forces III equilibrium 7 Labor Day - No Class 9 AH Molecular Dynamics I Lab : Macromolecular Structure Determination and Informatics 11 SC Energy, Heat & Thermodynamics 14 SC Mathematical Operations 16 SC First Law 18 SC First Law 1 SC Entropy 3 SC Second Law Lab 3: Protein Unfolding and Free Energy 5 SC Second Law 8 SC Chemical Potential 30 SC Free Energy Unfolding part October SC Free Energy 5 SC Chemical Equilibrium 7 SC Physical Equilibrium in Biochemical Processes Exam I 9 1 Native American Day No Class 14 AH Statistical Mechanics for Proteins Lab 4: Determining the Free Energy of macromolecular interaction 16 AH 19 AH 1 AH Entropy and Boltzmann Distribution Lab 5: Molecular Dynamics 3 AH 6 AH 8 SC Macromolecular Folding Free Energy 30 SC Macromolecular Folding Free Energy November SC Macromolecular Interactions
4 SC Free Energy of Macromolecular Interactions 6 SC Techniques to study Physical Equilibrium in Biochemical Processes 9 SC Techniques to study Physical Equilibrium in Biochemical Processes 11 Veterans Day No Class 13 SC Macromolecular Structures and Energetics Lab 6: Diffusion, Brownian Motion and the Einstein- Stokes Relation 16 SC Computing with Macromolecular Structures 18 AH Diffusion Lab 7. Reaction Rate Systems, Modeling with the Virtual Cell 0 AH 3 AH 5 Thanksgiving No Class 7 Thanksgiving No Class 30 AH Reaction Rates December AH 4 AH 7 AH 9-16 Final Exam