BB 101

MODULE: PHYSICAL BIOLOGY

Ambarish Kunwar
LECTURE 1

Lab No. 204

Department of Biosciences and Bioengineering
IIT Bombay

akunwar@iitb.ac.in
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

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 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?

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 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
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• 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
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 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

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 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

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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

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 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.
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