BO1020: Concepts in Life Sciences

Course Content:
Relevance of Biological Principles to Engineering undergraduates how the knowledge and
application of Biological principles can elevate the relevant contributions by engineers?
Water and its special properties of relevance to life
Building blocks of life: Bio-molecules and their structure-function aspects
Cell structure and organelles, cell membrane, cellular transport and signaling
How does a cell sustain life? Cell metabolism and its regulation; Cell energetics: harvesting
chemical & solar energy
Classical and Molecular genetics principles; Applications of advances in molecular genetics
Introduction to the molecular basis of human diseases: genetic diseases (Huntingtons, Downs
etc.,), non-infectious diseases (Cancer) and infectious diseases (HIV, Prion diseases etc.,)
Life adapts into new life forms: Origin of life and Evolution current beliefs
Human physiology, Developmental biology, Behavioral biology some interesting aspects
Text Book:
Biology by N.A. Campbell and J.B. Reece, 2005. VII edition (International edition),
Pearson- Benjamin-Cummings Publications, San Francisco.
Reference Book:
Molecular Biology of The Cell -by B. Alberts, 5th edition, Garland Science, New
York.
Evaluation:
40% Mid-Sem Exam + 60 % End-Sem Exam

Power of Biotechnology

Fish with green

fluorescent protein
(GFP) gene

Tobacco plant with

firefly glow gene

Pig with green

fluorescent protein
(GFP) gene

Myoelectric prosthesis

From wikipedia

A myoelectric prosthesis uses potentials from voluntarily

contracted muscles within a person's residual limb on the surface of the skin
to control the movements of the prosthesis

Interfaces: Engineering & Life Sciences

Bioinformatics & Systems biology
Fermentation technology
Bio-electronics
Nano-biotechnology
Genomics & Proteomics
Biomedical Engineering
Biomaterials
Bio-mechanics etc..

Biomedical Imaging:
CT scan
MRI
X-ray

Machines engineered for

Biotech application:
EM
AFM
NMR
X-ray diffraction

Everyday biology:
Example: Why does curd form?

How is curd made?

-Take a vessel and pour milk into it
(milk is the medium)
- Warm it, say upto 37oC
- Add some old curd to it
(old curd is the inoculum)
- Close it, set it aside in a warm place
(the mixture is the culture/broth)
- Curd is formed in a few hours

Nutrient

Cow

Water, g
Energy, kcal
Protein, g
Fat, g
Lactose, g
Minerals, g

Buffalo

88.0
61.0
3.2
3.4
4.7
0.72

84.0
97.0
3.7
6.9
5.2
0.79

Human
87.5
70.0
1.0
4.4
6.9
0.20

http://babcock.cals.wisc.edu/downloads/de/19.en.pdf

Acid formation, and consequent protein aggregation

Where does the acid come from?

From some among the thousands of reactions that occur
inside the lactic acid bacteria (Lactococcus lactis)

Lactic acid

www.jccc.net/~pdecell/cellresp/glycolysis.html

What kind of a molecule is lactic acid?

C3H6O3
2-hydroxy propanoic acid

Lactic acid belongs to a class of biomolecules called

Carbohydrates
General formula: (CH2O)n

Usually n > 3

Now, let us look at the next part: curd forms due to protein aggregation

What is aggregation?

Reverse question:

What happens at a molecular level when a substance

dissolves in water?

Water

Hydrogen
bonds

From Pearson Education, Inc. publishing as Benjamin Cummings

Ice: crystalline structure and floating barrier

Hydrogen
bond
Ice
Hydrogen bonds are stable

Insulation of water bodies by ice

Liquid water
Hydrogen bonds
constantly break and re-form

From Pearson Education, Inc. publishing as Benjamin Cummings

A crystal of table salt dissolving in water

Negative
Oxygen regions
of polar water
molecules are
attracted to sodium
cations (Na+).
Positive
hydrogen regions
of water molecules
cling to chloride
anions (Cl).

Na+
+

+
+

Na+

+
Cl

Cl

+
+

From Pearson Education, Inc. publishing as Benjamin Cummings

Water transport in plants

Water conducting cells

100 m
Cohesion

From Pearson Education, Inc. publishing as Benjamin Cummings

A water-soluble protein

This oxygen is
attracted to a slight
positive charge on
the lysozyme
molecule.

This hydrogen is attracted to a slight

negative charge on the lysozyme molecule.
(a) Lysozyme molecule
in a nonaqueous
environment

(b) Lysozyme molecule (purple)

in an aqueous environment
such as tears or saliva

(c) Ionic and polar regions on the proteins

surface attract water molecules.

From Pearson Education, Inc. publishing as Benjamin Cummings

Walking on water

High surface tension

From Pearson Education, Inc. publishing as Benjamin Cummings

Now, let us look at aggregation aggregation happens when molecules

fall out of solution, and are attracted to each other.

Which protein aggregates?

Casein of milk, mainly

From a molecular view-point, why does a protein aggregate?

From a molecular view-point, what is a protein?

Proteins are polymers of amino acids

What is an amino acid?

carbon
R
O

H
N

C
OH

H
H
Amino
group

Carboxyl
group

From Pearson Education, Inc. publishing as Benjamin Cummings

Making a polypeptide chain

Peptide
bond
OH
CH2

SH
CH2

H
N

OH

C C

CH2

N C C OH H

N C

H O

H O

(a)

C OH
O

DESMOSOMES

H2O
OH

DESMOSOMES
DESMOSOMES

OH
CH2
H

H N C C

N C C

N C C

H O

H O

H O

Amino end
(N-terminus)

Side chains

SH
Peptide
CH2 bond CH2
OH

Backbone

Carboxy end
C-terminus
From Pearson Education, Inc. publishing as Benjamin Cummings

The 20 amino acids that build the proteins

CH3
CH3
H
H3N+

CH3

O
H3N+

H
Glycine (Gly)

H3N+

H
Alanine (Ala)

CH

CH3
CH3

CH2

CH2

O
H3N+

H
Valine (Val)

CH3

CH3

H3N+

H
Leucine (Leu)

H3C

CH
C

O
C

H
Isoleucine (Ile)

Nonpolar

CH3

CH2

S
NH

CH2
CH2
H3N+

C
H

CH2

O
H3N+

C
O

Methionine (Met)

C
H

CH2

O
C
O

Phenylalanine (Phe)

H3N+

C
H

H2C

CH2

H2N

O
C

C
O

Tryptophan (Trp)

Proline (Pro)

From Pearson Education, Inc. publishing as Benjamin Cummings

Contd.

OH

OH

Polar

CH2
H3N+

CH

O
C
O

Serine (Ser)

H3N+

CH2

O
C
O

H3N+

CH2

O
C

H3N+

O
C

H3N+

Electrically
charged

CH2
H3N+

H3N+

NH3+

O
C
O

Glutamine
(Gln)

CH2

CH2

CH2

CH2

CH2

CH2

C
O

H3N+

C
H

Glutamic acid
(Glu)

NH+

NH2

CH2

Aspartic acid
(Asp)

H3N+

CH2

C
O

CH2

Basic
O

Asparagine
(Asn)

Acidic
O

CH2

CH2

Tyrosine
(Tyr)

Cysteine
(Cys)

Threonine (Thr)

NH2 O
C

SH

CH3

OH

NH2 O

Lysine (Lys)

H3N+

CH2

O
O

NH2+

CH2
H3N+

C
H

NH
CH2
O
C C
O
H

O
C
O

Arginine (Arg)

Histidine (His)

From Pearson Education, Inc. publishing as Benjamin Cummings

Example of a polymer of amino acids

in water environment
lysozyme
Protein found in saliva,
tears, etc., breaks down
cell wall of bacteria

Ribbon model

Space-filling model
From Pearson Education, Inc. publishing as Benjamin Cummings

H3 N
Amino end

Gly Pro ThrGly

5
Thr
Gly

Glu
CyaLyaSeu
Leu Pro
Met
10
Val
15 Lya
Val
Leu
Asp

pleated sheet
Amino acid
subunits

R H
C
O C N H
N H
N H
O C
O C
H C RH C
H C RHC R
R
N HO C
H
N
O C
O C N H
O C N H
C
C
R
R
H
N
N H

20
Ala Val Arg
Gly
Ser
Pro
25
Ala

Primary
level

O H
O H
O H H
O H
H R
H R
H
R
C
C H
C CN
C CH
C C N C N CC N
CC N C
C C
R
R
R
R
OH H
OHH
O
O HH
R
R
R
R
O
C H O
C H O
C
H O
C H
H
H
H
C NH C N
C N CN
C NH CN
C NHC
C
H
H O C
H O C
C
H ON
H O C
R
R
R
R H
C
O C
C N
H

helix

Secondary

Tertiary

level

level

Quarternary
level

From Pearson Education, Inc. publishing as Benjamin Cummings

Secondary Structure of Proteins

pleated sheet
H

Amino acid
subunits

C
N

N
C

N
H

C
H

C
R

N
O

O
C

H C
O

N
H

C
H

C
H

H
C

N
H

N
C

N
C

H
C
O

O
H

N
C
R

C
N
H

H
C
O

O
H

N
C

C
N
H

H
C

helix

C
R

N
O

R
R

C
C

R
O

More:
Loops & Turns
(for changing direction of the polypeptide)
From Pearson Education, Inc. publishing as Benjamin Cummings

Tertiary structure of Proteins

CH2

Hydrogen
bond

H3C

CH

CH3
H3C
CH3
CH

O
H
O

Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone

OH C
CH2

CH2 S S CH2
Disulfide bridge

O
CH2 NH3+ -O C CH2
Ionic bond

From Pearson Education, Inc. publishing as Benjamin Cummings

Structure-function relationship

Primary
structure

Normal hemoglobin
Val

His

Leu

Glu

Glu

Sickle-cell hemoglobin
Val

His

Leu

Molecules do
not associate
with one
another; each
carries oxygen
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen

Quaternary
structure

Thr

Pro

Val

Glu

structure 1 2 3 4 5 6 7

Secondary
subunit and tertiary
structures

Quaternary Hemoglobin A
structure

Red blood
cell shape

Pro

1 2 3 4 5 6 7

Secondary
and tertiary
structures

Function

Thr

. . . Primary

...

subunit

Function

10 m

10 m
Red blood
cell shape

Exposed
hydrophobic
region

Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced
Fibers of abnormal
hemoglobin deform
cell into sickle
shape

From Pearson Education, Inc. publishing as Benjamin Cummings

Now, let us return to our protein aggregation issue

+
H

H
H

H
H

H
Hydronium
ion (H3O+)

H
Hydroxide
ion (OH)

When acid is introduced into the medium by the cells, the medium pH goes down
i.e. H+ concentration increases
Hydration layer of the protein changes
Protein conformation may change, and it can no longer be in solution