Biophysics (Bio322)

Credits: 4

Hrs/week: 3

Evaluation:

50%: Internal assessment, assignments, tests

50%: Mid- and End-semester exams

Instructors

Dr. Chaitanya Athale, Dr. Sai Krishna, Dr. G.V. Pavankumar, Dr. Shiva Patil, Dr. Arnab Mukherjee, Dr. K. N. Ganesh

Chaitanya's lecture slides (not including derivations)- largely based on the PBoC book, with modifications. This is only for teaching purposes, and not meant to be a public distribution of copyright material.

[1] Introduction

[2] Spatial scales

[3] Temporal scales

[4] Energy and Equilibrium

[5] Macromolecules as random walks

Problem Sets

Problem Set 01: Molecular and Cellular scales

Problem Set 02: Clocks and timers

Lac operon model: Paper modelling dynamics of the lac operon

2010-10-28: DNA as a polymer: Paper measuring AFM based flexibility of DNA using image processing to fit.[paper][supplementary]
TASK Use the supplementary material to determine how to fit a polymer model as described and attempt to reproduce it. Ask me by email for help if needed.
NOTE: This is treated as a problem set and will be graded.

Assignment to be finished as group work. You will be graded on the basis of the following:

1) understanding of the topic

2) clarity of the presentation and keeping to time (max. 30 min)

3) ability to answer questions

4) any additional work e.g. recalculating results of the paper

5) team-work

Research article reading groups:

Contents:

1. Introduction (4)

1.1 Motivation and introduction (3)

1.2 Physics and biology – understanding the connection (1)

2. Molecular biophysics (15)

2.1 Chemical forces – translation and rotation

2.2 Biomolecules as machines – work, power and energy

2.3 Thermal, chemical and mechanical switching via biomolecules.

2.4 Organization of biomolecules – self assembly and thermodynamics

2.5 Electromagnetic effect on biomolecules – ion channels and nerves.

2.6 Nucleic acids, peptides and proteins

2.7 ATPsynthases and motor proteins

2.8 Dynamics of molecular motors

2.9 Chemical kinetics

2.10 Biological reactions and interactions –

2.11 Function aspects of various bio-molecules

2.12 Protein folding and challenges in protein folding,

2.13 Engineering and design of biomolecules.

2.14 Mechanical properties of single macromolecules (experiments)

3. Cellular biophysics (22)

3.1 Biology by numbers

3.2 Construction plans for cells and organisms: E. coli

3.3 Time keeping at many scales

3.4 Model systems across the scales

3.5 Random walks

3.6 Statistical view of biological dynamics

3.7 Life in crowded and disordered environments

3.8 Rate equations and dynamics of the cell

3.9 Network organization in space and time

4. Biophysical techniques (7)

4.1 Light in biology

4.2 Microscopy – Fluorescence, Raman, IR, circular dichroism etc.

4.3 Crystallography

4.4 Measurement of diffusion in cells (FCS and FRAP) (experiments)

References:

1.     Philip Nelson, Biological Physics:Energy, Information, Life

2.     R., Kondev, J., Theriot, J. (2008) Physical Biology of the Cell. Garland Sciences.

3.     David Boal, (2008) Mechanics of the Cell, Cambrdige University Press

4.     Van Holde KE, Johnson C, and Ho PS (2005) Principles of Physical Biochemistry, 2^nd Edition, Prentice-Hall

5.     Cantor CR, Schimmel PR (1980) Biophysical Chemistry: Part 1 - The Conformation of Biological Molecules. ^1st Edition, WH Freeman

6.     Cantor CR, Schimmel PR (1980) Biophysical Chemistry: Part 2 - The Study of Biological Structure and Function. 1^st Edition, WH Freeman