Syllabus Spring 2018 Physics 42200/V3800

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.

Suggested Texts:
Proteins: Structures and Molecular Properties, 2nd Edition. Thomas E. Creighton
Molecular Driving Forces: Statistical Thermodynamics in Chemistry & Biology. Ken
Dill
Biochemistry, Voet and Voet, any edition

Course Objectives:
1) Be able to describe the 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% Homework, class participation, quizzes
25% Midterm
25% Final

Date Topic
1/30 Course intro.
Section I: Macromolecular Structure
2/1 Intro to Molecular structure.
Boltzman distribution. Conformational distributions of small molecules
2/6 Basic Definitions, Nucleic Acids, DNA/RNA structure and
conformational equilibrium
2/8 DNA nanotechnology, Amino Acids
2/13 Amino Acid Properties, Peptide Bonds
2/15 No class, Monday schedule
2/20 protein structure, protein visualization
2/22 sequence homologies, structural homologies, protein families
Section II: Intermolecular Forces and Computational Biophysics
2/27 Review of statistical thermodynamics
3/1 electrostatics, hydrogen bonds, pKa’s
3/6 the hydrophobic effect, Lenard-Jones potentials
3/8 statistical thermodynamics and protein folding, rotamer libraries
3/13 Computational structure calculation
3/15 Binding - Midterm handed out
3/20 Transition state theory, catalysis
Section III: Biophysical Methods
3/22 spectroscopy– Midterm due
3/27 ultracentrifugation, circular dichroism,
3/29 magnetic resonance 1
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Spring Break 3/30-4/8
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4/10 magnetic resonance 2
4/12 magnetic resonance 3
4/17 crystallography
4/19 microscopy
4/24 calorimetry
4/26 single molecule methods
5/1 plasmonics
Section IV: Biological design
5/3 Nucleic acid design
5/8 Protein design – Rosetta/ProCAD
5/10 Synthetic biology, CRISPR
5/15 Metabolic control analysis, metabolic engineering Final Handed out
5/24 Final Due