Koder, Ronald

City University of New York

City University of New York (CUNY) CUNY Academic Works Open Educational Resources City College of New York 2022 Physics 422 (Biophysics) Ronald Koder CUNY City College How does access to this work benefit you? Let us know! More information about this work at: https://academicworks.cuny.edu/cc_oers/400 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: AcademicWorks@cuny.edu Physics 422/V3800 – Biological Physics  Prof. Ronald Koder       koder@sci.ccny.cuny.edu     (212) 650-5583      1.308 CDI       85 St. Nicholas Terrace      Tue, Thu 5:00 pm – 6:15 pm  Office hours Tue., Thurs.  4:00 pm – 5:00 pm or by appt.  Course email list: physics422@gmail.com  Introduction to the structure, properties, and function of proteins, nucleic acids, lipids and membranes. In depth study of the physical basis for biopolymer structure and function. Introduction to spectroscopic methods for monitoring reactions and determining structure including light absorption or scattering, fluorescence, NMR and X-ray diffraction. The course emphasizes reading and interpretation of the original literature. Prereq.: 1 yr. of Math, 1 yr. of Physics 3 hr./wk.; 3 cr.  Text The bulk of the course material will be from lectures and primary literature.  Suggested reference texts:   • Linus Pauling. The Nature of the Chemical Bond https://archive.org/details/natureofthechemicalbondpauling • Any first year physics textbook with thermodynamics and E&M sections. A good free one is at:  https://cnx.org/contents/dP0ocxV9@14.71:bG-_rWXy@11/Introduction  The following are on reserve for this course in the Marshak Science Library: • Ken Dill. Molecular Driving Forces: Statistical Thermodynamics in Chemistry & Biology.   • Voet and Voet. Biochemistry   Course Objectives: 1) Be able to describe the chemical makeup and three dimensional structures and properties of biopolymers such as proteins and nucleic acids 2) Understand the thermodynamic basis for these structures and be able to formally describe the coupling mechanisms which drive function 3) Become familiar with the techniques with which these biomolecules are interrogated 4) Be able to read and interpret primary literature in this field.    Grading:     • 50% Weekly homework, class participation, quizzes • 25% Midterm • 25% Final  Date  Topic 2/1  Course intro.      Section I:  Macromolecular Structure 2/3 Intro to Molecular structure.    Boltzman distribution. Conformational distributions of small molecules   2/8 No class, Friday schedule  2/10  Basic Definitions, Nucleic Acids, DNA/RNA structure and  conformational equilibrium 2/15  DNA nanotechnology, Amino Acids 2/17  Amino Acid Properties, Peptide Bonds 2/22  protein structure, protein visualization 2/24  sequence homologies, structural homologies, protein families    Section II:  Intermolecular Forces and Computational Biophysics 3/1  Review of statistical thermodynamics  3/3  electrostatics, hydrogen bonds, pKa’s 3/8  the hydrophobic effect, Lenard-Jones potentials 3/10  statistical thermodynamics and protein folding, rotamer libraries 3/15  Computational structure calculation  3/17  Binding - Midterm handed out 3/22  Transition state theory, catalysis    Section III:  Biophysical Methods 3/24  spectroscopy– Midterm due 3/29  ultracentrifugation, circular dichroism 3/31  magnetic resonance 1  4/5  magnetic resonance 2 4/7  magnetic resonance 3 4/12  crystallography 4/14  microscopy  Spring Recess 4/15-4/22  4/26  calorimetry  4/28                 single molecule methods 5/3  plasmonics  Section IV: Biological design    5/5  Nucleic acid design 5/6  Molecular Dynamics 5/10  Protein design – Rosetta/ProCAD 5/12  Synthetic biology, CRISPR Final Handed out 5/22  Final Due  --------------------------------------------------------------------------------------- The AccessAbility Center/Student Disability Services ensures equal access and full participation to all of City College's programs, services, and activities by coordinating and implementing appropriate accommodations. If you are a student with a disability who requires accommodations and services, please visit the office in NAC 1/218, or contact AAC/SDS via email (disabilityservices@ccny.cuny.edu), or phone (212-650-5913 or TTY/TTD 212-650-8441).     Students who find themselves experiencing difficulties obtaining food every day or who lack a stable and safe place to live are urged to come to Benny’s pantry for assistance (https://www.ccny.cuny.edu/bennysfoodpantry). Benny’s pantry is located on the ground floor of the North Academic Center (NAC) and is open to anyone within the CUNY community (students, staff, faculty) in need of support. The pantry is open from 10am to 6pm and is self-serve. Additional emergency support for financial, health and housing needs are also available through Benny’s. Please contact Dee Dee Mozeleski at dmozeleski@ccny.CUNY.edu or Charles Ramirez @cramirez@ccny.CUNY.edu for additional details. 

Physics 422 (Biophysics)

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Physics 422 (Biophysics)

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