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LECTURE 1

BB 101

MODULE: PHYSICAL BIOLOGY

Ambarish Kunwar

Lab No. 204 Department of Biosciences and Bioengineering IIT Bombay

Reference Books

Following books have most of the Physical Biology Module content:

books have most of the Physical Biology Module content: 1. Physical Biology of the cell, R.
books have most of the Physical Biology Module content: 1. Physical Biology of the cell, R.
books have most of the Physical Biology Module content: 1. Physical Biology of the cell, R.

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

     

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), D3-T3 (LT004), D3-T4 (LT005), D3-T5 (LT006)

1

18-03-2019

MON

 

D3

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

5

What you are going to learn …

Physical Biology or Biophysics

A bridge between Biology and Physics

6

Biology

• Biology studies life in its variety and complexity

• Biological studies range from level of molecules and cells to organisms and ecosystems

7

Physics

• On the other hand, physics looks for mathematical laws of nature

• Make detailed predictions about phenomenon that drive the systems

8

Physical Biology or Biophysics

Look

phenomena

at

with math

biological

them

and physics to gain

the

and

analyze

important insights

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.

work on the same principles. They use energy to do work. How do these biological nano-machines
work on the same principles. They use energy to do work. How do these biological nano-machines

How do these biological nano-machines work?

Insights gained may help you to design artificial nano-machines

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

" for the design and synthesis of molecular machines Figure Source:
" for the design and synthesis of molecular machines Figure Source:
" for the design and synthesis of molecular machines Figure Source:
" for the design and synthesis of molecular machines Figure Source:
" for the design and synthesis of molecular machines Figure Source:
" for the design and synthesis of molecular machines Figure Source:

ri

mi

tr

2016

df

11

12
12

How swimming of a bacteria is different from swimming of a fish?

swimming of a bacteria is different from swimming of a fish? What type of forces play
swimming of a bacteria is different from swimming of a fish? What type of forces play

What type of forces play dominant role in bacterial swimming (inertial or something else)?

Insights gained may help you to design artificial micro-swimmers

13

Importance of Thermal Energy in Biology

Importance of Thermal Energy in Biology Figure Source: https://www.youtube.com/watch?v=P0ioCoZJcTQ It can shake &
Biology Figure Source: https://www.youtube.com/watch?v=P0ioCoZJcTQ It can shake & bend objects a microscopic scales

It can shake & bend objects a microscopic scales

Can thermal energy bend DNA into loops for storage?

Can thermal energy bend DNA into loops for storage? Figure Source: http://www.cellimagelibrary.org/images/38912 15

15

Boltzmann Law

Action Potential

Boltzmann Law Action Potential Atmosphere https://mounteverestwondering.weebly.com/vocabulary.html 16
Boltzmann Law Action Potential Atmosphere https://mounteverestwondering.weebly.com/vocabulary.html 16

Atmosphere

Boltzmann Law Action Potential Atmosphere https://mounteverestwondering.weebly.com/vocabulary.html 16

Biofilaments: DNA, Microtubule and Actin

Why some bio-filament can generate pushing forces

and Actin Why some bio-filament can generate pushing forces Video Sources : http://multimedia.mcb.harvard.edu/,
pushing forces Video Sources : http://multimedia.mcb.harvard.edu/, http://www.molbiolcell.org/content/21/24/4418.full 17
pushing forces Video Sources : http://multimedia.mcb.harvard.edu/, http://www.molbiolcell.org/content/21/24/4418.full 17

17

Protein perform their function by folding into different shapes

perform their function by folding into different shapes How structure of various proteins is decided? Video

How structure of various proteins is decided?

18

In this part of the course…

We

will

quantitative

attempt

to

provide

a

description of a few

biological phenomena

Why biological problems are among the most exciting science problems and most challenging engineering problems

Let’s start with proteins!!!

Physical Properties of a globular protein

with proteins!!! Physical Properties of a globular protein Magnitude of different forces acting on a proteins

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

constrained object (deform)

Effect

on

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?

Forces acting on a protein molecule

Forces acting on a protein molecule Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard

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

Since ignored

effect

of

gravity

can

be

Oscillatory

motions

such

as

of

pendulum and occupy so much

textbooks, simply do not occur at level of single molecule

planets,

of

which

mechanics

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

Motion of Mechanical element: Mass

Motion of Mechanical element: Mass Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard 26

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

26

Motion of Mechanical element: Spring

Motion of Mechanical element: Spring Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard 27

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

27

Motion of Mechanical element: Dashpot

Responds to force by elongating at constant velocity

No net force, external force is balanced by drag force

Dashpot

to

describe how an object move in fluid

model

is

used

Strategy: model submerged object connected to dashpot)

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

model submerged object connected to dashpot) Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard

28

Motion of combination of mechanical elements

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

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

Object

damped

by

viscous fluid

Low

mass

object

deformed

fluid

in

viscous

Undamped objects

29

Motion of combination of mechanical elements

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

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

30

Inertia of moving bacterium

Inertia of moving bacterium Consider a bacterium swimming through water at a speed of 10 micron/s.

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/m 3 ).

Time constant   0.28 x 10 -6 s 0.28s Distance travelled 0.028 x 10 -10 m 0.028 Angstrom

Sedimentation of a 100 kDa globular protein

Sedimentation of a 100 kDa globular protein Consider the sedimentation of a globular protein of radius

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 10 9 seconds 38.05 years

Why biologists need ultra-centrifuges

Why biologists need ultra-centrifuges Ultracentrifuges are very expensive. Typical prices $150000

Ultracentrifuges are very expensive. Typical prices $150000

Motion of combination of mechanical elements:

Mass and Spring with Damping

Elastic Solid in a fluid
Elastic Solid in a fluid
Mass and Spring with Damping Elastic Solid in a fluid Source: Mechanics of Motor Proteins and
Mass and Spring with Damping Elastic Solid in a fluid Source: Mechanics of Motor Proteins and
Mass and Spring with Damping Elastic Solid in a fluid Source: Mechanics of Motor Proteins and

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

35

Similarity with series LCR circuit

Similarity with series LCR circuit

Homework

Derive expression for x(t) for overdamped, underdamped and critically damped motion

for overdamped, underdamped and critically damped motion Source: Mechanics of Motor Proteins and the Cytoskeleton,

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

underdamped and critically damped motion Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard
underdamped and critically damped motion Source: Mechanics of Motor Proteins and the Cytoskeleton, Jonathan Howard

1.

2.

Hint

Write

down

2b(=/m) and =

equation

of

motion

in

terms

of

Assume

=

a

/m) and = equation of motion in terms of Assume = a general solution = ℎ

general

solution

=

and = equation of motion in terms of Assume = a general solution = ℎ either

either

variable

of

p

the

(=kx-F),

form

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