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Building Blocks of Living Systems

Life is Diverse BUT Unified
In simplest term, any living system is constituted of a bunch of chemical reactions involving molecules and molecular machines Interactions: •Covalent, •Non-covalent: Electro-static Hydrogen Bond Van der Walls

Building Blocks: •Water, •Metals, •Ions and radicals •Macro-molecules: Protein Nucleic acids: DNA, RNA Lipid Carbohydrate

Proteins
• Proteins are polymer made up of Amino Acids. • There are 20 amino acids • Functions of Proteins: Enzyme, Ion channels, Signaling, Mechanical structure Common structure of amino acids:

R is different in different amino acids Examples of some amino acids with different functional groups:

Proteins
Proteins are formed by polymerization of amino acids by formation of Peptide Bonds

Peptide bond

Proteins
The long Polymer of Amino Acids, fold in 3D to give rise to a Protein

Nucleic Acids:
DNA stores the information on how to create a protein

Multiple Copies of RNA

Multiple copies of Protein

DNA

Lipids
1. Diverse group of molecules. 2. Have long chains of carbon, 3. Hydrophobic in nature

Fatty Acids

Lipids
Phospholipid

Why Life is made up of Carbon?
• Biological Macro-molecules are organic compounds. • Organic compounds: Made up of C and H, where H can get replaced by O, N, P, S, halogen Valence Electron = 4

Reactivity

Diversity of Carbon Compounds

sp3

Tetrahedral Arrangement

Flexible single bond

Can form long complex structure including branched and ring type

sp2
Rigid, planar structure; have pi-electron

sp1

Very rigid, rare in living system

Diversity of Carbon Compounds
Configurational Isomers: They cannot be inter-converted without temporarily breaking one or more covalent bonds. Geometric Isomers: Different orientation of functional groups around non-rotative bond (i.e double bond, ring structure)

Diversity of Carbon Compounds

Enantiomers: non-superposable on its mirror image Achiral Chiral

Life is L-handed
In laboratory, by synthetic chemistry we usually get racemic mixture. But in living system one form of chiral molecule is predominant over the other. For example: Amino Acids in protein are L-isomers. Molecular Recognition is Enantiomer specific

Can We Have Silicon Based Life?
Large molecules with multiple Si-Si are less stable than molecules with multiple C-C bonds Element E-E bond energy (kJ/mol) E-O bond energy (kJ/mol) C 356 335 Si 230 370 C-C is more suitable for energy storage Large Atomic radius of Si prohibit structural diversity Element Atomic radius (Å) C 0.91 Si 1.46 Electronegativity of C is suitable for reaction in Aqueous environment

Encapsulating Reaction System
•A living system requires encapsulation to preserve the reaction networks and energy. •Encapsulation must be Mechanically Flexible, Selectively Permeable

Molecules like Phospho Lipids forms Micelle Hydrophilic

Hydrophobic

A Cell Is A Liposome
Self-assembly of molecules to hide hydrophobic part from water

Hydrophilic Core

A Cell Is A Liposome
• Cell Membrane is a lipid bilayer, made up of Phospho Lipids. • This bilayer has channels for selective exchange of materials. • This bilayer has molecules in it for communication with surrounding.

What Determines The Shape of A Cell?
Liposomes are spherical. Then why not all cells are spherical? Shape is determined by: Requirement of cellular function; Mechanical Aspects; Surface to Volume Ratio For regular shapes like sphere, surface does not increase adequately with increase in volume. If a cell is spherical, this will limit exchange of nutrients and gases.

What Determines The Shape of A Cell?
Irregular shapes, like projected finger structures in cells of Gut, increases surface area.

However extended surfaces can also have disadvantages. Upper limit of cell size is defined by the diffusion limits of nutrients and gases.

Effect of Cellular Size

Reynolds number, Re = ρ.V.L/ = V.L/ν V = velocity, L = Characteristic length, ρ = density of fluid, ν = Kinematic viscosity = viscosity of fluid

In Fluid flow, Low Re means laminar flow; High Re means turbulent flow Re Inertial Force / Viscous Force

Effect of Cellular Size
L Human Swimmer: L = 180 cm V = 100 cm/sec ν = 10-2 cm2/sec Re = V.L/ν = 1.8 x 106 So, Inertial force helps the swimmer Bacteria: L = 10-4 cm V = 30x10-4 cm/sec ν = 10-2 cm2/sec Re = V.L/ν = 3 x 10-5 So, Viscous drag is very high (even if it swim with a speed of human)

Effect of Cellular Size
Troubles at Low Reynolds number: Can not coast on momentum Calculated based on the Stokes Drag on a sphere as,

Fs = 6πµ LV
Here L is the radius and initial velocity = L /sec

Swimming like a human will not work
Google: Life at Low Reynolds Number. E.M. Purcell.

The Cage Inside the Cell
The Cell Membrane is flexible and can collapse if not supported The Cell structure is supported by internal Cytoskeleton

Eukaryotic Cytoskeleton is made up of Microfilaments, intermediate filament and microtubules. These are all created by polymeric proteins. Cytoskeletons are dynamic and help the cell change the shape.

The Cage Inside the Cell Is Dynamic

Compartments Within The Cells Prokaryotes (i.e Bacteria and Archaea) has comparatively homogenous Cytoplasm with out any compartment.

Cell Wall and capsule provides rigidity and protection. DNA is condensed to form Nucleoid. Flagella helps in motion. Pilli helps in intercellular interactions

Compartments Within The Cells Eukaryotic cells are bigger and have comparatively more complex operations.

Compartmentalization helps in distribution of labor, reduces effect of molecular diffusion. Compartments, called Organelles, are membrane bound. Examples: Nucleus, Golgi, Endoplasmic Reticulum (ER), Mitochondria, Plastid

Compartments Within The Cells

Compartments Within The Cells

Nucleus: Stores the Genome Golgi: Involved in modifying, sorting, and packaging these macromolecules for secretion Endoplasmic Reticulum (ER): Folding, modification and sorting of specific proteins. Mitochondria: production of ATP through respiration Plastid: Photosynthesis

Origin of Organelles: Theory of Endosymbiosis

Mitochondria and Plastid carry Genomes (i.e DNA)

Self-replication of a Cell
In Biology division means multiplication Prokaryotes multiply by Binary Fission

In case of Eukaryotic cells the process of division is bit complicated and are of two types, Mitosis and Meiosis. Do you believe these types of self-replication would be faithful like Photocopying?

The Algebra of Binary Fission
With binary fission number of cells changes in the following series 1 2 4 8 …. 2n n = number of division, varies form 0 to x So, Nt = No. 2n
Nt = number of cells after time t; No = number of cells at t = 0; n = number of division in time t. Generation Time, G = t/n For E. coli, G is ~ 20 min

Why does the death phase has logarithmic behavior?

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