BB 101

MODULE: PHYSICAL BIOLOGY

LECTURE 1

Ambarish Kunwar

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
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PHYSICAL BIOLOGY LECTURES
Lecture
Batch No. Date Time Day
D1 1 09-3-2019 2:00 PM - 3:25 PM SAT

D3 1 09-3-2019 3:30 PM - 4:55 PM SAT

D1 2 12-3-2019 11:35 AM - 01:00 PM TUE

D3 2 12-3-2019 3:30 PM - 4:55 PM TUE

D1 3 14-3-2019 08:00 AM - 09:25 AM THU

D3 3 15-3-2019 3:30 PM - 4:55 PM FRI

D1 4 16-3-2019 6:00 PM - 7:25 AM SAT

D3 4 16-3-2019 7:30 PM - 8:55 PM SAT

D1 5 19-3-2019 11:35 AM - 01:00 PM TUE

D3 5 19-3-2019 3:30 PM - 4:55 PM TUE

QUIZ 27-3-2019 8:15 AM - 9:15 AM WED

D3 6 20-3-2019 8:00 AM - 9:25 AM WED

D1 6 26-3-2019 11:35 AM - 01:00 PM TUE

D3 7 26-3-2019 3:30 PM - 4:55 PM TUE

D1 7 28-3-2019 11:35 AM - 01:00 PM TUE

 TUTORIALS
4
Tutorial No. Date Day Batch Venue

1 13-03-2019 WED D1 D1-T1 (LT002), D1-T2 (LT003),

D1-T3 (LT004), D1-T4 (LT102),
D1-T5 (LT103)
2 20-03-2019 WED D1

3 27-03-2019 WED D1

4 03-04-2019 WED D1

1 11-03-2019 MON D3

D3-T1 (LT002), D3-T2 (LT003),

1 18-03-2019 MON D3 D3-T3 (LT004), D3-T4 (LT005),
D3-T5 (LT006)

2 25-03-2019 MON D3

3 01-04-2019 MON D3

D1 (T1, T2, T3, T4, T5) Batch: WED 02:00-2:55 PM

D3 (T1, T2, T3, T4, T5) Batch: MON 08:30-9:25 AM
 You learned about many
interesting biological phenomena
in previous module

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 What you are going to learn …

Physical Biology or Biophysics

A bridge between
Biology and Physics
Source: http://www.biophysics.org/Education/WhatisBiophysics/tabid/2287/Default.aspx 6
 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 7
 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
8
Physical Biology or Biophysics

Look at the biological

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

9
 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.

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 10
 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- 11

chemistryprize2016.pdf
12
 How swimming of a bacteria is different from swimming of a
fish?

What type of forces play dominant role in bacterial swimming

(inertial or something else)?

Insights gained may help you to design artificial micro-swimmers

Video Source:http://multimedia.mcb.harvard.edu/
Figure Source: http://cliparts.co/clipart/7800 13
 Importance of Thermal Energy in Biology

Figure Source: https://www.youtube.com/watch?v=P0ioCoZJcTQ

It can shake & bend objects a microscopic scales

 Can thermal energy bend DNA into loops for storage?

Figure Source: http://www.cellimagelibrary.org/images/38912 15

Boltzmann Law

Action Potential

Atmosphere

https://mounteverestwondering.weebly.com/vocabulary.html

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 Biofilaments: DNA, Microtubule and Actin

Why some bio-filament can generate pushing forces

Video Sources :http://multimedia.mcb.harvard.edu/,

http://www.molbiolcell.org/content/21/24/4418.full
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 Protein perform their function by folding into different shapes

How structure of various proteins is decided?

Video Source:http://multimedia.mcb.harvard.edu/ 18
 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
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 Let’s start with proteins!!!
Physical Properties of a globular protein

Magnitude of different forces acting on a proteins

Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard 20
 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?

21
 Forces acting on a protein molecule

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

22
 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
23
• 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

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• 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

26
 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
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Motion of combination of mechanical elements

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

30
 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
 Sedimentation of a 100 kDa globular protein

Consider the sedimentation of a globular protein of radius

3nm and mass 100 KDa, initially right below the surface, in
an Eppendorf tube filled with water upto 1cm height. How
much time it would take for this protein to sediment under
the effect of gravity assuming that protein attains a
constant velocity as soon as it starts to descend in the
tube?
Answer: ~1.2 x 109 seconds  38.05 years
Figure Source: http://www.nature.com/scitable/content/eppendorf-tube-6488888
 Why biologists need ultra-centrifuges

Ultracentrifuges are very expensive. Typical prices $150000

https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/centrifugation/index.htm
 Paperfuge

https://www.youtube.com/watch?v=pPePaKnYh2I
Motion of combination of mechanical elements:
Mass and Spring with Damping

Elastic Solid in a fluid

35
Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard
Similarity with series LCR circuit
 Homework
Derive expression for x(t) for
overdamped, underdamped
and critically damped motion

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

 Hint
1. Write down equation of motion in terms of variable p (=kx-F),
2b(=/m) and =

2. Assume a general solution either of the form

= = ℎ
 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. Similarity with
LCR circuit
39