Fall 2014: PHYS570G, 57000 (CRN 27151) Webpage: http://www.physics.purdue.edu/academic- programs/courses/course_detail.php?SEM=fall2014&c=phys570G

Introduction to Biophysics

Biophysics is the area where problems related to structure and dynamics/functioning of biological entities are addressed using physical methods and underlying theories and models. The goal of this introductory course is to provide (or refresh) the necessary biology background and to educate physics students about the problems and methods of biophysics.

Students will be introduced to physical descriptions of a wide range of phenomena, from molecular and cell mechanisms to the function of the human brain. An additional introductory overview of frontiers in photobiophysics, neurophysics, bioinformatics and synchrotron-based biological spectroscopy will help students to broaden their views. This course prepares physics students for research and development work in interdisciplinary/biomedical environments.

Topics include molecular forces in biological structures, cell organization, structure and function of proteins, nucleic acids, and biological membranes, flow of genetic information, biological thermodynamics and kinetics (enzymatic reactions), electrostatic interactions in biology, physico-chemical basis of neuron signaling (membrane potentials, action potential generation and propagation, synaptic transmission, sensory receptor function), interaction of biological molecules with light (primary processes in photosynthesis, vision), and functional studies of brain.

This course is designed for students at the senior undergraduate or entering graduate level. The course will be self- contained (i.e. no prior biology courses are required). One of the aims of the course is to increase the comfort level physics students have concerning biology/biochemistry-related issues. Interested students from non-physics majors, presumably biology and chemistry are very welcome.

Time and place: M, W 10:30 -11:45, PHYS room 234. Professor: Dr. Yulia Pushkar; PHYS 70 , DNA translocating through a solid-state (765) 4963279 [email protected] nanopore

Text(s): Philip Nelson, Biological Physics, 2008 Research papers (reviews) of professor’s choice. Lecture notes will be provided.

Suggested additional readings: Glaser “Biophysics” Schrödinger “What is life” Meyer B. Jackson, Molecular and Cellular Biophysics, 2006. Introductory biochemistry text, for example Jeremy M. Berg, John L. Tymoczko, and Lubert Stryer “Biochemistry”. Selected chapters from Eric R. Kandel and James H. Schwartz, Principals of Neural Science, 2000.

Grading: Midterm (take-home problem-solving exam) 20% Oral presentation of paper from research journal. 20% (Selection of papers on modern aspects of Biophysics will be provided by instructor.) In class short quizzes 20% Final exam (problemsolving) 40%

Course outline

Week Topic 1 Introduction: Historical overview. What do biophysicists do? Carries in biophysics. Molecular forces in biological structures: Electrostatic, dipole, H-bond, π-interaction, steric repulsion, hydrophobic forces. Chemical terminology 2 Cell organization: Vocabulary of cell anatomy. Biological space, time and energy scales. Cell membrane. Electron microscopy: Study of the of cell and membrane organization 3 Proteins structural principles : Primary, secondary, tertiary and quaternary organization. Ramachandran plots. Organization of membrane proteins. Hydrophobic plots 4 Nucleic acids : flow of information in the cell 5 Free energy, entropy . Helmholtz and Gibb’s free energy, entropy, Jarzynski equality, osmotic forces, medical application of dialysis 6 Electrostatic interactions in biology: Poisson-Boltzmann equation and the Debye length, activity coefficient of an ion, ionization of proteins, Gouy–Chapman theory and membrane surface charge. Structure of water 7 Chemical potential : dissociation, molecular associations, self- assembly in cells 8-9 Enzyme catalysis: fundamental rate processes, activation energy, reaction coordinate, Kramer’s theory, Michaelis-Menten kinetics, electron transfer reactions, Marcus theory 10 Biological applications of Synchrotron techniques. X-ray Absorption spectroscopy, X-ray imaging 11 Interaction of bi ological molecules with light: primary processes in Photosynthesis, vision 12 – 13 Molecular machines (pumps) – Nernst potentials, Donnan equilibrium, active pumps, the chemiosmotic mechanism 14 – 15 Nerve impulses – History and phenomenology, the action potential, Hodgkin-Huxley mechanism, synapses 16 Function of the brain: memory, sleep and dreaming, positron emission tomography, magnetic resonance imaging, electroencephalogram