Introduction to life sciences

BO1020: Concepts in Life SciencesCourse Content:

Relevance of Biological Principles to Engineering undergraduates how the knowledge andapplication of Biological principles can elevate the relevant contributions by engineers?Water and its special properties of relevance to lifeBuilding blocks of life: Bio-molecules and their structure-function aspectsCell structure and organelles, cell membrane, cellular transport and signalingHow does a cell sustain life? Cell metabolism and its regulation; Cell energetics: harvestingchemical & solar energyClassical and Molecular genetics principles; Applications of advances in molecular geneticsIntroduction to the molecular basis of human diseases: genetic diseases (Huntingtons, Downsetc.,), non-infectious diseases (Cancer) and infectious diseases (HIV, Prion diseases etc.,)Life adapts into new life forms: Origin of life and Evolution current beliefsHuman 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, NewYork.

Evaluation:40% Mid-Sem Exam + 60 % End-Sem Exam

Power of Biotechnology

Tobacco plant withfirefly glow gene

Pig with greenfluorescent protein

(GFP) gene

Fish with greenfluorescent 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 scanMRI

X-ray

Machines engineered forBiotech 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

Acid formation, and consequent protein aggregation

Where does the acid come from?

Nutrient Cow Buffalo Human

Water, g 88.0 84.0 87.5Energy, kcal 61.0 97.0 70.0Protein, g 3.2 3.7 1.0Fat, g 3.4 6.9 4.4Lactose, g 4.7 5.2 6.9

Minerals, g 0.72 0.79 0.20

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

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

General formula: (CH2O)n Usually n > 3

Carbohydrates

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?

Hydrogenbonds

+

+

H

H+

+

From Pearson Education, Inc. publishing as Benjamin Cummings

Water

Ice: crystalline structure and floating barrier

Liquid waterHydrogen bonds

constantly break and re-form

IceHydrogen bonds are stable

Hydrogen bond

From Pearson Education, Inc. publishing as Benjamin Cummings Insulation of water bodies by ice

A crystal of table salt dissolving in waterNegative

Oxygen regionsof polar watermolecules are

attracted to sodiumcations (Na+).

+

+

+

+Cl

Na+Positivehydrogen regionsof water molecules

cling to chlorideanions (Cl).

+

+

+

+

Na+

Cl


Water transport in plants

Water conducting cells

100 mFrom Pearson Education, Inc. publishing as Benjamin Cummings Cohesion

This oxygen isattracted to a slightpositive charge onthe lysozymemolecule.

This hydrogen is attracted to a slightnegative 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.

+

A water-soluble protein


Walking on water

From Pearson Education, Inc. publishing as Benjamin Cummings High surface tension

Now, let us look at aggregation aggregation happens when moleculesfall 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?

H

H

N C

R

H

C

O

OH

Aminogroup

Carboxylgroup

carbon


DESMOSOMES

OH

DESMOSOMESDESMOSOMES

OH

CH2

CN

H

C

H O

H OH OH

Peptidebond

OH

OH

OH

H H

HH

H

H

H

H

H

H H

H

N

N N

N N

SH Side chains

SH

OO

O O O

H2O

CH2 CH2

CH2 CH2 CH2

C C C C C C

C CC C

Peptidebond

Amino end(N-terminus)

Backbone

(a)


Making a polypeptide chain

Carboxy endC-terminus

SO

O

O

O

H

H3N+ C C

O

OH

CH3

H3N+ C

H

C

O

O

CH3 CH3CH3

C C

O

OH

H3N+

CH

CH3

CH2

C

H

H3N+

CH3CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

C

O

O

CH2

CH3N+

H

CO

O

CH2

NH

H

CO

OH3N+ C

CH2H2C

H2N C

CH2

H

C

Nonpolar

Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

C

O

O

Tryptophan (Trp) Proline (Pro)

H3C

The 20 amino acids that build the proteins


O

OH

CH2

C C

H

H3N+O

OH3N+

OH CH3CH

C C

H O

O

SH

CH2C

H

H3N+ CO

OH3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

OC

C CO

O

NH2 OC

CH2CH2C CH3N+

O

O

O

Polar

Electricallycharged

O OC

CH2C CH3N+

H

O

O

O OC

CH2

C CH3N+

H

O

O

CH2

CH2CH2

CH2

NH3+

CH2C CH3N+

H

O

O

NH2

C NH2+

CH2CH2CH2

C CH3N+

H

O

O

CH2

NH+

NHCH2C CH3N+

H

O

O

Serine (Ser) Threonine (Thr) Cysteine (Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

(Gln)

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)

Contd.


Example of a polymer of amino acids in water environment

lysozyme

Ribbon model

Space-filling model


Protein found in saliva, tears, etc., breaks downcell wall of bacteria

NCH

C

O

CH

O

H

NR

CR

CH

NH

O

C

H

CR

H

N CO

R

CH

NH

O

C

HCRHH

CO

RCH

NH

O

C

H

CR

HH C

O

O

CC

N

H

RC

HCO

H

NH

CR

O

C NH

RCH C

O

H

NH

CR

O

C NH

RC

H C

O

H

NHCR

O

C NH

RC

H CO

H

N C

N H O C N H O C

RC

H RC

H

O CN H

CON H

H C RH C RCN H O

O C N HCR N

H C R H C RN H O C

O C N HCR H

Gly GlyThr

Gly

GluSeuLyaCyaProLeu

MetVal

Lya

ValLeuAsp

Ala Val ArgGlySer

ProAla

Pro Thr

Amino acidsubunits

pleated sheet

helix

+H3NAmino end

1

5

10

15

20

25

C


Primarylevel

Quarternarylevel

Secondary

level

Tertiary

level

O C helix

pleated sheet

Amino acidsubunits NC

H

C

O

C N

H

C

OH

R

C N

H

C

O H

C

R

N

HH

RC

O

R

C

H

N

H

C

OH

NC

O

R

C

H

N

H

H

C

R

C

O H

C

R

N

H

C

O

C

C

O

C

N

HH

R

C

C

O

N

HH

C

R

C

O

N

H

R

C

H C

O

N

HH

C

R

C

O

N

H

R

C

H C

O

N

HH

C

R

C

O

N

H

R

C

H C

O

N

H

C

N H

H C R

N H O

O C N

C

RC

H

H O

CHR

N H

O C

R

CH

N H

O C

H C R

N H

C

CN

R H

H

O C

H C R

N H

O C

RC

H


Secondary Structure of Proteins

More:

Loops & Turns(for changing direction of the polypeptide)

CH2OHOCOH

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH

CH3CH3

H3C

H3C

Hydrophobicinteractions andvan der Waalsinteractions

Polypeptidebackbone

Hydrogenbond

Ionic bond

Disulfide bridge


Tertiary structure of Proteins

Exposedhydrophobicregion

Structure-function relationship

Primarystructure

Secondaryand tertiarystructures

Quaternarystructure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother; eachcarries oxygen

Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen

10 m 10 m

Primarystructure

Secondaryand tertiarystructures

Quaternarystructure

Function

Red bloodcell shape

Hemoglobin S

Moleculesinteract withone another tocrystallize into afiber, capacity tocarry oxygen isgreatly reduced

Fibers of abnormalhemoglobin deformcell into sickleshape

subunit subunit

1 2 3 4 5 6 7 3 4 5 6 721

Normal hemoglobin Sickle-cell hemoglobin. . .. . .Val His Leu Thr Pro Glu Glu Val His Leu Thr Pro Val Glu


Now, let us return to our protein aggregation issue

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

H

Hydroniumion (H3O+)

H

Hydroxideion (OH)

H

H

H

H

H

H

+

+

Documents

Introduction to life sciences