Life in a nut: cell

A hike on the borderline between life and not-life

Dr. Alkan Kabakçıoğlu

Koc Univ, Istanbul

“ The human race is just a chemical scum on a moderate-sized planet, orbiting around a very average star in the outer suburb of

one among hundreds of billion of galaxies. ”

Stephen W. Hawking

David Deutsch’s universe(www.ted.com/tedtalks)

http://antwrp.gsfc.nasa.gov/

http://antwrp.gsfc.nasa.gov/

http://antwrp.gsfc.nasa.gov/

Arecibo Radio Telescope, Puerto Rico

Arecibo Radio Telescope, Puerto Rico

A closer inspection

Iron crystal

Complex organization

EVEN SMALLER SCALES

Simple organization

Liquid water

Life makes its copies

• A cell is the smallest unit of organized matter (on earth) that can copy itself.

• Virtually all living organisms are composed of cells.

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Icomytherefore

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Borderline gets blurred at smaller scales

Chromosome duplication

Transport along microtubules

Laws of physics governing the behavior of many particles are

approximate

N = PV / kT

If you measure the # of particles in a box for given (P,V,T) the value will depart from the law by √N .

For N=100 deviation is 10%

For N=1 million deviation is 0.1%

It’s shaky in a cell

Thermal fluctuations are dramatic…

DIFFUSION… r ~ sqrt(Dt)

Diffusion constant (D) ~ 1/(Radius x viscosity)

D for GFP inside the cell = 25 μm^2/s (one round a sec)

Small parts are constantly on the move!

A collection of atoms with a predictable

behavior has to be large, with its parts

sufficiently strongly connected in order to

remain intact under thermal agitation.

Chemical bonds

Covalent/ionic bonds : few eV Hydrogen bonds : 0.1 eV Thermal energy at 24 C : 0.026 eV (=kT) p ~ exp(-E/kT)

Biological molecules are linear chains

• sequence held by covalent bonds• 3D structure held by hydrogen bonds

Proteins

• They do all the work: – transport material– catalyze reactions– serve as building blocks– etc

A protein is a long word of with a 20-letter alphabet

Protein Folding Problem

Sequence Structure?

• Still unsolved after 50 years..• Computers can simulate only the first μs of folding which may take 1ms – 1s.

How is the protein action coordinated in the cell?

DNA

A long chain of 4 letters: A,T,C,G.A TG C

Two complementary strands.

Carries all the information required to construct proteins.

Complete human DNA sequence isknown since 2003.

Reading: “The Double Helix”, J.D. Watson

Original drawing by Francis Crick

Detailed structure of DNA

Genetic Code

…GTTGTATGCTCC… …-Leu-Leu-Thr-Trp-…

Genes talk to each other!

.“Gene expression profiles” can be monitoredusing microarrays. Correlations in the datagive indirect evidence on gene-gene interactions.

Cell activity is controlled by a complex regulatory network

Resolving the underlying complexity is the next challenge.

How did this complexity come about?

First there was the soup..

Next came the replicator “A” (an RNA?)

A AA AAAA AAAAAAAA …

When soup was full As fought for resources

Let there be natural selection!

Reading: “The Selfish Gene”, R. Dawkins

“There is nothing on which a free man ponders less than death; his wisdom is, to meditate not on death but on life.”

Spinoza(as quoted by Erwin Schrodinger in “What is life?”)