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    Module: Physical Biology: Ambarish Kunwar

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    This document outlines the course details for a Physical Biology module taught by Ambarish Kunwar. It includes the lecture and tutorial schedule, list of reference books, and sample lecture topics that will be covered. The module aims to apply principles of physics to understand biological phenomena at the molecular and cellular levels. Some example topics that will be discussed are molecular motors, bacterial swimming, protein folding and forces acting on proteins. The document emphasizes that mechanics concepts need to be applied differently at small scales relevant to biology.

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    Module: Physical Biology: Ambarish Kunwar

    Uploaded by

    King of Kings
    50 views28 pages
    This document outlines the course details for a Physical Biology module taught by Ambarish Kunwar. It includes the lecture and tutorial schedule, list of reference books, and sample lecture topics that will be covered. The module aims to apply principles of physics to understand biological phenomena at the molecular and cellular levels. Some example topics that will be discussed are molecular motors, bacterial swimming, protein folding and forces acting on proteins. The document emphasizes that mechanics concepts need to be applied differently at small scales relevant to biology.

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    A_Kunwar_BB101_2019_2020_I_L1

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    This document outlines the course details for a Physical Biology module taught by Ambarish Kunwar. It includes the lecture and tutorial schedule, list of reference books, and sample lecture topics that will be covered. The module aims to apply principles of physics to understand biological phenomena at the molecular and cellular levels. Some example topics that will be discussed are molecular motors, bacterial swimming, protein folding and forces acting on proteins. The document emphasizes that mechanics concepts need to be applied differently at small scales relevant to biology.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    50 views28 pages

    Module: Physical Biology: Ambarish Kunwar

    Uploaded by

    King of Kings
    This document outlines the course details for a Physical Biology module taught by Ambarish Kunwar. It includes the lecture and tutorial schedule, list of reference books, and sample lecture topics that will be covered. The module aims to apply principles of physics to understand biological phenomena at the molecular and cellular levels. Some example topics that will be discussed are molecular motors, bacterial swimming, protein folding and forces acting on proteins. The document emphasizes that mechanics concepts need to be applied differently at small scales relevant to biology.

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    © All Rights Reserved
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    of 28

    BB 101

    MODULE: PHYSICAL BIOLOGY


    Ambarish Kunwar
    LECTURE 1

    Lab No. 204


    Department of Biosciences and Bioengineering
    IIT Bombay

    [email protected]
    http://www.bio.iitb.ac.in/~akunwar/
    Reference Books
    Following books have most of the Physical Biology Module content:

    1. Physical Biology of the cell, R. Phillips, J. Kondev, J. Theriot, H. Garcia (Publisher:


    Garland Science)

    2. Biological Physics, Philip Nelson (Publisher: W. H. Freeman)

    3. Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard (Publisher:


    Sinauer Associates Inc.)
    A topic guide for each lecture will be provided
    2
    PHYSICAL BIOLOGY LECTURES
    Lecture No.
    Date Day Batch Venue

    1 24-09-19 TUE D2 LA 002 03:30 PM-05:00 PM

    1 25-09-19 WED D4 LA 002 09:30 AM-11:00 AM

    2 27-09-19 FRI D2 LA 002 03:30 PM-05:00 PM

    2 27-09-19 FRI D4 LA 002 09:30 AM-11:00 AM

    3 01-10-19 TUE D2 LA 002 03:30 PM-05:00 PM

    3 04-10-19 FRI D4 LA 002 09:30 AM-11:00 AM

    4 04-10-19 FRI D2 LA 002 03:30 PM-05:00 PM

    4 09-10-19 WED D4 LA 002 09:30 AM-11:00 AM

    09-10-19 WED QUIZ 08:15 AM-09:25 AM

    5 11-10-19 FRI D2 LA 002 03:30 PM-05:00 PM

    5 11-10-19 FRI D4 LA 002 09:30 AM-11:00 AM

    6 15-10-19 TUE D2 LA 002 03:30 PM-05:00 PM

    6 15-10-19 TUE D4 LA 002 10:30 AM-12:00 AM

    7 16-10-19 WED D2 LA 002 08:00 AM-09:30 AM

    7 16-10-19 WED D4 LA 002 09:30 AM-11:00 AM


    TUTORIALS
    Tutorial No. Date Day Batch Venue Time

    1 26-09-2019 THU D2 LT – 201(T1), 202(T2), 203(T3) 08:30 AM-09:30 AM


    LT – 301(T4), 302(T5), 303(T6)

    1 26-09-2019 THU D4 LT – 204(T1), 205(T2), 206(T3) 08:30 AM-09:30 AM


    LT – 304(T4), 305(T5), 306(T6)

    2 03-10-2019 THU D2 LT – 201(T1), 202(T2), 203(T3) 08:30 AM-09:30 AM


    LT – 301(T4), 302(T5), 303(T6)

    2 03-10-2019 THU D4 LT – 204(T1), 205(T2), 206(T3) 08:30 AM-09:30 AM


    LT – 304(T4), 305(T5), 306(T6)

    3 10-10-2019 THU D2 LT – 201(T1), 202(T2), 203(T3) 08:30 AM-09:30 AM


    LT – 301(T4), 302(T5), 303(T6)

    3 10-10-2019 THU D4 LT – 204(T1), 205(T2), 206(T3) 08:30 AM-09:30 AM


    LT – 304(T4), 305(T5), 306(T6)

    4 17-10-2019 THU D2 LT – 201(T1), 202(T2), 203(T3) 08:30 AM-09:30 AM


    LT – 301(T4), 302(T5), 303(T6)

    4 17-10-2019 THU D4 LT – 204(T1), 205(T2), 206(T3) 08:30 AM-09:30 AM


    LT – 304(T4), 305(T5), 306(T6)
    In this module you are going to learn

    Physical Biology or Biophysics

    a bridge between
    Biology and Physics

    5
    Biology

    • Biology studies life in its variety


    and complexity

    • Biological studies range from


    level of molecules and cells to
    organisms and ecosystems

    Source: http://www.biophysics.org/Education/WhatisBiophysics/tabid/2287/Default.aspx 6
    Physics

    • On the other hand, physics


    looks for mathematical laws
    of nature

    • Make detailed predictions


    about phenomenon that drive
    the systems
    Source: http://www.biophysics.org/Education/WhatisBiophysics/tabid/2287/Default.aspx
    7
    Physical Biology or Biophysics

    Look at some of the biological


    phenomena and analyze them
    with math and physics to gain
    important insights

    8
    Why our bodies need protein machines (molecular motors)
    for transportation?
    Millions of times smaller than everyday machines, molecular
    machines work on the same principles. They use energy to do work.
    Can we design them by a simple scaling?

    How do these biological nano-machines work?


    Insights gained may help you to design artificial nano-machines
    Video Source:http://multimedia.mcb.harvard.edu/
    Figure Source: http://www.wpclipart.com/working/vehicles/dump_truck/dump_truck_green.png.html 9
    Figure Source: http://edition.cnn.com/2016/10/05/world/nobel-prize-2016-chemistry-molecular-
    machines/index.html

    " for the design and synthesis of molecular


    machines

    Figure Source: https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2016/popular-chemistryprize2016.pdf 10


    11
    How swimming of a bacteria is different from swimming of a frog?

    What type of forces play dominant role in bacterial swimming?

    Insights gained may help you to design artificial micro-swimmers

    Video Source:http://multimedia.mcb.harvard.edu/
    Figure
    Source:https://commons.wikimedia.org/wiki/File:Frog_%C5%BE%C3%A1ba.gif 12
    Importance of Thermal Energy
    Protein perform their function by folding into different shapes

    How structure of various proteins is decided?


    Video Source:http://multimedia.mcb.harvard.edu/ 14
    In this part of the course…
    • We will attempt to provide a
    quantitative description of a few
    biological phenomena
    • Why biological problems are among
    the most exciting science problems
    and most challenging engineering
    problems
    15
    Let’s start with proteins!!!
    Physical Properties of a globular protein

    Sedimentation of a globular
    protein of radius 3nm and mass
    100 KDa in an Eppendorf tube
    filled with water upto 1cm height

    Answer: ~1.2 x 109 seconds  38.05 years

    Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard 16


    What is force?
    • Force is a push or pull

    • Effect on free object (accelerate) and Effect on


    constrained object (deform)

    • Net force is sum of all forces irrespective of their origin

    • SI Unit of Force Newton

    • What is 1N (weight of ___ gram object)

    • Forces at single molecule level are measured in pN

    • How small is 1 pN?

    17
    Forces acting on a protein molecule

    Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard


    18
    Protein and other biomolecules
    • Protein and other biomolecules are
    so tiny that inertial forces are very
    small in comparison to viscous forces
    due to surrounding medium
    • Most of the mechanics discussed in
    standard school Physics text books is
    irrelevant at molecular and cellular
    levels as inertial forces are small
    19
    • Since effect of gravity can be
    ignored

    • Oscillatory motions such as of


    pendulum and planets, which
    occupy so much of mechanics
    textbooks, simply do not occur at
    level of single molecule

    20
    • However, we can still use
    mechanics to understand biological
    systems
    • Some biological systems can be
    modelled as combinations of three
    fundamental mechanical elements
    mass, springs and dashpots
    • Let’s review their properties
    21
    Motion of Mechanical element: Mass

    Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard


    22
    Motion of Mechanical element: Spring

    Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard


    23
    Motion of Mechanical element: Dashpot

    • Responds to force by elongating


    at constant velocity

    • No net force, external force is


    balanced by drag force

    • Dashpot model is used to


    describe how an object move in
    fluid

    • Strategy: model submerged


    object connected to dashpot)

    Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard


    24
    Motion of combination of mechanical elements

    Object damped by
    viscous fluid

    Low mass object


    deformed in viscous
    fluid

    Undamped objects
    Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard
    25
    Motion of combination of mechanical elements

    Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard


    26
    Inertia of moving bacterium

    Consider a bacterium swimming through water at a speed


    of 10 micron/s. How far bacterium will continue to move
    after its flagellar motors stop working? Assume bacteria
    to be a sphere of radius 0.5 micron with density 5 times
    that of water (5 1000 kg/m3).

    Time constant   0.28 x 10-6s  0.28s


    Distance travelled  0.028 x 10-10 m  0.028 Angstrom
    Video Source: https://www.youtube.com/watch?v=6bEacq-ow50
    Summary
    • What is Physical Biology/Biophysics?

    • Proteins molecules and forces acting on protein


    molecules

    • Inertial forces are negligible and effect of gravity


    can be ignored

    • Many biological systems can be modeled as


    combination of three fundamental mechanical
    elements-mass, spring and dashpot.
    28

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