Biophysical chemistry

By Prof. Pramit Kumar Chowdhury | IIT Delhi

Learners enrolled: 446

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.

INTENDED AUDIENCE : Post-Graduate Level and Above

PRE-REQUISITES : Basic Course in Physical Chemistry

Summary

Course Status :	Completed
Course Type :	Elective
Language for course content :
Duration :	12 weeks
Category :	Chemistry
Credit Points :	3
Level :	Postgraduate
Start Date :	25 Jul 2022
End Date :	14 Oct 2022
Enrollment Ends :	08 Aug 2022
Exam Date :	30 Oct 2022 IST

Note: This exam date is subject to change based on seat availability. You can check final exam date on your hall ticket.

Page Visits

Course layout

Week 1: Introduction to Protein Structure (Lectures 1 and 2),

Secondary and Tertiary Structure of Proteins (Lectures 3, 4 and 5)

Week 2: Forces in Protein Folding 1 (Lectures 6, 7 and 8)

Week 3: Forces in Protein Folding 2 (Lectures 9, 10 and 11)

Week 4: Forces in Protein Folding 3 (Lectures 12, 13 and 14-part)

Protein Denaturation 2 (Lectures 17, 18 and 19-part)

Week 5: Protein Denaturation 1 (Lectures 14, 15 and 16)

Week 6: Protein Folding Pathways (Lectures 19 and 20)

Diffusion 1 (Lectures 21, 22 and 23)

Week 7: Diffusion 2 (Lectures 24, 25 and 26-part)

Electrochemical Potential (Lectures 26, and 27-part)

Week 8: Nucleation Mechanism (Lectures 27 and 28)

Mutational Analyses (Lectures 28, 29, 30 and 31-part)

Week 9: Protein Folding Kinetics 1 – Rapid Mixing (Lectures 31, 32, and 33-part)

Protein Folding Kinetics 2 – Relaxation Techniques(Lectures 33, and 34)

Week 10: Experimental Tools 1 (Lectures 35, 36, 37 and 38-part)

Week 11: Experimental Tools 2 (Lectures 38, 39, and 40)

Week 12: Experimental Tools 3 (Lectures 41 and 42)

Books and references

Given below are an assortment of books that I found very useful while designing the present course. Along with the name of each book I have highlighted the focus of the books wherever possible for your convenience. I encourage you to go through as many of these to have a good grasp of the content of the course and biophysical chemistry in general.

Introduction to protein structure, by Carl Branden and John Tooze. New York: Garland Publishing Company (Has a comprehensive treatise on different types of protein structure; the first part of this course on protein structure has primarily been based on this book)
Protein Structure and Function (Primers in Biology) 1st Edition by Gregory A. Petsko, Dagmar Ringe (Introduces general principles of protein structure, folding, and function, then goes beyond these basics to tackle the conceptual basis of inferring structure and function from genomic sequence; part of the discussion on structure of proteins in this course is based on this book)
Biophysical Chemistry: Part I: The Conformation of Biological Macromolecules 1st Edition by Charles R. Cantor, Paul R. Schimmel
Biophysical Chemistry: Part II: Techniques for the Study of Biological Structure and Function (Pt. 2) 1st Edition by Charles R. Cantor, Paul R. Schimmel
Biophysical Chemistry: Part III: The Behavior of Biological Macromolecules, 1st Edition by Charles R. Cantor, Paul R. Schimmel
Modern Biophysical Chemistry: Detection and Analysis of Biomolecules, 2nd Edition, Author: Peter Jomo Walla (Recommended for an advanced overview on biophysical methods including state-of-the-art techniques)
Biophysical Chemistry, Author: Dagmar Klostermeier, Markus G. Rudolph (Explores the concepts of physical chemistry and molecular structure that underlie biochemical processes)
Biophysical Chemistry Author: Alan Cooper (It is a tutorial text and covers the physical chemistry of biological macromolecules and the experimental techniques used to study them. Provides a very simple yet pragmatic approach without delving into the rigors of physical chemistry)
Introduction to proteins—structure, function, and motion, Authors: Amit Kessel and Nir Ben‐Tal, CRC Press (Provides a comprehensive and state-of-the-art introduction to the structure, function, and motion of proteins)
Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Alan Fersht (Concentrates on the basic principles of kinetics and mechanism of processes concerning proteins. Provides a broad overview on the fundamental principles and understanding underlying the physics and chemistry. A significant part of the discussion in this course on protein folding and kinetic methods applied for protein folding is based on this book)
Protein Folding Kinetics: Biophysical Methods, Author: Nölting, Bengt
Proteins: Structures and Molecular Properties, Author: Thomas E. Creighton (Offers an expert introduction to all aspects of proteins--biosynthesis, evolution, structures, dynamics, ligand binding, and catalysis. This book works equally well as a reference or as a classroom text)
Proteins: Structure and Function, Author: David Whitford (Comprehensive introduction to the study of proteins and their importance to modern biochemistry. Amongst many other topics, this book discusses the ‘building blocks’ of proteins and their respective chemical and physical properties)
Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience, Book by Ken A. Dill and Sarina Bromberg (Describes the principles and forces that drive chemical and biological processes. A large part of the discussion in this course on thermodynamics in protein folding, electrostatic interactions using point charge and dipoles and diffusion are based on this book)
Principles of Physical Biochemistry: 2nd (second) Edition, Authors: Pui Shing Ho Kensal E. Van Holde, Curtis Johnson (Provides insights into the theory and techniques used in the study of the physical chemistry of biological and biochemical molecules)
Physical Chemistry: Principles and Applications in Biological Sciences (5th Edition), Authors: Ignacio Tinoco Jr., Kenneth Sauer, James C. Wang, Joseph D. Puglisi, Gerard Harbison, David Rovnyak

Instructor bio

Prof. Pramit Kumar Chowdhury

IIT Delhi

Prof. Pramit K Chowdhury works on protein folding and dynamics using a range of spectroscopic techniques.

Course certificate

The course is free to enroll and learn from. But if you want a certificate, you have to register and write the proctored exam conducted by us in person at any of the designated exam centres.
The exam is optional for a fee of Rs 1000/- (Rupees one thousand only).
Date and Time of Exams: 30 October 2022 Morning session 9am to 12 noon; Afternoon Session 2pm to 5pm.
Registration url: Announcements will be made when the registration form is open for registrations.
The online registration form has to be filled and the certification exam fee needs to be paid. More details will be made available when the exam registration form is published. If there are any changes, it will be mentioned then.
Please check the form for more details on the cities where the exams will be held, the conditions you agree to when you fill the form etc.

CRITERIA TO GET A CERTIFICATE

Average assignment score = 25% of average of best 8 assignments out of the total 12 assignments given in the course.
Exam score = 75% of the proctored certification exam score out of 100

Final score = Average assignment score + Exam score

YOU WILL BE ELIGIBLE FOR A CERTIFICATE ONLY IF AVERAGE ASSIGNMENT SCORE >=10/25 AND EXAM SCORE >= 30/75. If one of the 2 criteria is not met, you will not get the certificate even if the Final score >= 40/100.

Certificate will have your name, photograph and the score in the final exam with the breakup.It will have the logos of NPTEL and IIT Madras .It will be e-verifiable at nptel.ac.in/noc.

Only the e-certificate will be made available. Hard copies will not be dispatched.

Once again, thanks for your interest in our online courses and certification. Happy learning.

- NPTEL team

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