Introduction to Biophysics
There is no formal text-book for this course. Useful reference texts will be recommended during the lectures and some lecture notes will be provided. Therefore, it is important to attend the class regularly. The course will be determined by a combination of homework assignments and exams. There will be two in-class exams and a final exam. Homework problems will be assigned each week and are due the following week. This class is cross-listed with PHZ6255 but the assignments may differ.
Grading: The homework, the two in-class exams, and the final exam each will account for a third of the final grade.
Recommended Text: Molecular Driving Forces by Ken A. Dill (MDF); Introduction to Protein Structure by Branden and Tooze; MIT OpenCourseware
Topics covered:
Introduction
Biology: background; The Cell; Complexity of Life; Central Dogma of Molecular Biology
Thermodynamics
Review: State function; First law; Second law; entropy, enthalpy and free energy, general criterion of spontaneous change
Book: any introductory thermodynamics/stat mechanics book, MIT OpenCourseware
Protein Structure
Amino acids, peptide bond, protein secondary structures, Ramachandran Plot, tertiary and higher level structure
References: Introduction to Protein Structure by Branden and Tooze, online material
Biophysical/Biochemical Interactions
Electrostatic interaction, isoelectric point, hydrogen bond and dipole interaction, van der Waals and LJ potentials, Hydropathy
Biomolecular Dynamics
Boltzmann Probability and conformational transitions in biomolecules, Partition function, Protein stability and dynamics, Helix-Coil transition, Polymer properties, polymer chain models (Text: MDF)
Protein Folding
Protein folding mechanisms, Energy landscape, Computer Simulations of Protein folding and dynamics, Lattice Models and MC simulations, MD simulations
Functions of myoglobin and Hemoglobin
Oxygen (Ligand) binding to Myoglobin and Hemoglobin, Hill Model and cooperative binding, Allostery, Importance of cooperativity, BPG binding (Text: MDF)
Ligand Binding: Binding Polynomials
Binding polynomials; multi-site binding; Pre-binding, competitive inhibition; Conformational substates. Revisit: Hill Model, Cooperativity, Allostery; MWC/KNF/General Allosteric models; conformational substates in Proteins (Text: MDF)
Nucleic Acids
Nucleotides, structures, base stacking and pairing, duplex formation, free-energy and melting temperature, RNA folding, secondary structure, DNA, tanscription and translation
Photosysnthesis
ATP, NADP, Photosystem I and II, Light dependent and independent reactions, Z-scheme diagram