BIOPHYSICAL CHEMISTRY · PRE - REQUISITES: Basic Course in Physical Chemistry 82. Created Date:...
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BIOPHYSICAL CHEMISTRY COURSE OUTLINE This introductory course in biophysical chemistry touches on some of the fundamentals of this field. Starting from basic elements in protein structure, the course covers other aspects like forces involved in protein folding, protein folding energy landscape, mechanisms of protein folding, mixing and relaxation techniques commonly used to study fast protein folding, and finally winds up with discussion on some spectroscopic tools (Absorption, Fluorescence and IR) that are very popular in the field of proteins. ABOUT INSTRUCTOR Prof. Pramit K Chowdhury works on protein folding and dynamics using a range of spectroscopic techniques. COURSE PLAN Week 1: Introduction to Protein Structure Ribosome, Trigger Factor, Amino Acids, Ramachandran Plot Week 2: Forces in Protein Folding 1Local and Nonlocal interactions, Bjerrum Length, Poisson Boltzmann Equation, Debye length, Case studies Week 3 :Forces in Protein Folding 2 Electrostatics, Ion-Dipole Interactions, Dipole-Dipole Interactions, Orientational Averaging, Dipole-Induced-Dipole Interactions, Dispersion Forces, Empirical Potentials (Hard sphere potential, Lennard- Jones Potential), Brief Insight into Force Fields Week 4: Forces in Protein Folding 3 Hydrophobic Effect (Accessible Surface Area, Molecular Nature, Temperature Dependence, Importance of Heat Capacity, Important Thermodynamic Equations), Hydrogen Bonding in Proteins Week 5: Protein Denaturation 1 Protein Stability Curve, Unfolding of Proteins (Two-State Protein Unfolding), Thermal Denaturation (Protein Unfolding Thermodynamics), Differentiate Between Two-State and Mulit-State Protein Unfolding, Chemical Denaturation and Thermodynamics, Relationship Between Thermal and Chemical Denaturation Protein Denaturation 2 Chemical Denaturation and Thermodynamics, Relationship Between Thermal and Chemical Denaturation, Pressure Induced Protein Denaturation and Thermodynamics, Key Points of Protein Stability Week 6: Protein Folding Pathways Folding Code, Levinthal Paradox, Old and New Views of Protein Folding, Folding Funnel, Mechanisms of Protein Folding Diffusion 1 Fick’s Laws of Diffusion (First and Second Laws), Frictional Forces, Einstein-Smoluchowski Equation, Stokes-Einstein Equations, Diffusion Controlled Reaction, Langevin Equation, Velocity Correlation Function, Mean Square Displacement, Brownian Motion, Week 7: Diffusion 2 Random WalkElectrochemical Potential Nernst Equation, Ion Flow through Membranes, Diffusion Potential, Week 8: Nucleation Mechanism Chymotrypsin Inhibitor 2 (CI2), Transition State, Energy Diagrams in Protein Folding Mutational Analyses Phi-value Analysis, Chevron Plots, Chevron Rollover Week 9: Protein Folding Kinetics 1 – Rapid Mixing Stopped Flow Technique, Continuous Flow Technique, Case study with the heme protein Cytochrome c, Hydrodynamic Focusing-MicrofluidicsProtein Folding Kinetics 2 – Relaxation Techniques Temperature-jump Technique, Temperature-jump Instrument Setup, Optical Triggering-Flash Photolysis Week10: Experimental Tools 1 Einstein’s coefficients, Franck Condon Principle, Franck Condon Factor, Vibronic Coupling, Franck Condon Envelope, Absorption Spectroscopy, Components of an Absorption Spectrophotometer, Oscillator Strength Week 11: Experimental Tools 2 Fluorescence, Jablönski Diagram, Internal Conversion (IC), Intersystem Crossing (ISC), Heavy-Atom Effect, Fluorescence Quantum Yield, Phosphorescence, Stokes Shift, Solvent Effects, Intrinsic Protein Fluorescence, Fluorescence Quenching Week 12: Experimental Tools 3 Infrared (IR) Spectroscopy of Proteins, Transition Dipole, How to collect Protein IR Spectra, Amide (I – III) bands, FTIR Spectrometer Details, Interferometer, ATR-FTIR, Detectors PROF. PRAMIT KUMAR CHOWDHURY Department of Chemistry IIT Delhi TYPE OF COURSE COURSE DURATION EXAM DATE Rerun| Elective | UG 12 weeks (29 Jul’19 - 18 Oct’19) 17 Nov 2019 : : : INDUSTRIES APPLICABLE TO : Pharmaceutical Industry PRE - REQUISITES : Basic Course in Physical Chemistry 82
Transcript of BIOPHYSICAL CHEMISTRY · PRE - REQUISITES: Basic Course in Physical Chemistry 82. Created Date:...
BIOPHYSICAL CHEMISTRY
COURSE OUTLINEThis introductory course in biophysical chemistry touches on some of the fundamentals of this field. Starting from basic elements in protein structure, the course covers other aspects like forces involved in protein folding, protein folding energy landscape, mechanisms of protein folding, mixing and relaxation techniques commonly used to study fast protein folding, and finally winds up with discussion on some spectroscopic tools (Absorption, Fluorescence and IR) that are very popular in the field of proteins.
ABOUT INSTRUCTORProf. Pramit K Chowdhury works on protein folding and dynamics using a range of spectroscopic techniques.
COURSE PLANWeek 1: Introduction to Protein Structure Ribosome, Trigger Factor, Amino Acids, Ramachandran Plot
Week 2: Forces in Protein Folding 1Local and Nonlocal interactions, Bjerrum Length, Poisson Boltzmann Equation, Debye length, Case studies Week 3 :Forces in Protein Folding 2 Electrostatics, Ion-Dipole Interactions, Dipole-Dipole Interactions, Orientational Averaging, Dipole-Induced-Dipole Interactions, Dispersion Forces, Empirical Potentials (Hard sphere potential, Lennard-Jones Potential), Brief Insight into Force Fields Week 4: Forces in Protein Folding 3 Hydrophobic Effect (Accessible Surface Area, Molecular Nature, Temperature Dependence, Importance of Heat Capacity, Important Thermodynamic Equations), Hydrogen Bonding in Proteins
Week 5: Protein Denaturation 1 Protein Stability Curve, Unfolding of Proteins (Two-State Protein Unfolding), Thermal Denaturation (Protein Unfolding Thermodynamics), Differentiate Between Two-State and Mulit-State Protein Unfolding, Chemical Denaturation and Thermodynamics, Relationship Between Thermal and Chemical Denaturation Protein Denaturation 2 Chemical Denaturation and Thermodynamics, Relationship Between Thermal and Chemical Denaturation, Pressure Induced Protein Denaturation and Thermodynamics, Key Points of Protein Stability
Week 6: Protein Folding Pathways Folding Code, Levinthal Paradox, Old and New Views of Protein Folding, Folding Funnel, Mechanisms of Protein Folding Diffusion 1 Fick’s Laws of Diffusion (First and Second Laws), Frictional Forces, Einstein-Smoluchowski Equation, Stokes-Einstein Equations, Diffusion Controlled Reaction, Langevin Equation, Velocity Correlation Function, Mean Square Displacement, Brownian Motion, Week 7: Diffusion 2 Random WalkElectrochemical Potential Nernst Equation, Ion Flow through Membranes, Diffusion Potential, Week 8: Nucleation Mechanism Chymotrypsin Inhibitor 2 (CI2), Transition State, Energy Diagrams in Protein Folding Mutational Analyses Phi-value Analysis, Chevron Plots, Chevron RolloverWeek 9: Protein Folding Kinetics 1 – Rapid Mixing Stopped Flow Technique, Continuous Flow Technique, Case study with the heme protein Cytochrome c, Hydrodynamic Focusing-MicrofluidicsProtein Folding Kinetics 2 – Relaxation Techniques Temperature-jump Technique, Temperature-jump Instrument Setup, Optical Triggering-Flash PhotolysisWeek10: Experimental Tools 1 Einstein’s coefficients, Franck Condon Principle, Franck Condon Factor, Vibronic Coupling, Franck Condon Envelope, Absorption Spectroscopy, Components of an Absorption Spectrophotometer, Oscillator Strength
Week 11: Experimental Tools 2 Fluorescence, Jablönski Diagram, Internal Conversion (IC), Intersystem Crossing (ISC), Heavy-Atom Effect, Fluorescence Quantum Yield, Phosphorescence, Stokes Shift, Solvent Effects, Intrinsic Protein Fluorescence, Fluorescence Quenching
Week 12: Experimental Tools 3 Infrared (IR) Spectroscopy of Proteins, Transition Dipole, How to collect Protein IR Spectra, Amide (I – III) bands, FTIR Spectrometer Details, Interferometer, ATR-FTIR, Detectors
PROF. PRAMIT KUMAR CHOWDHURYDepartment of ChemistryIIT Delhi
TYPE OF COURSECOURSE DURATIONEXAM DATE
Rerun| Elective | UG12 weeks (29 Jul’19 - 18 Oct’19) 17 Nov 2019
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INDUSTRIES APPLICABLE TO : Pharmaceutical Industry
PRE - REQUISITES : Basic Course in Physical Chemistry
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