life in a nut: cell a hike on the borderline between life and not-life dr. alkan kabakçıoğlu koc...
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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)
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.
Icopytherefore
Iam
Icopytherefore
Iam
Icopytherefore
Iam
Icopytherefore
Iam
Icopytherefore
Iam
Icopytherefore
Iam
Icopytherefore
Iam
Icopytherefore
Iam
Icomytherefore
Iam
Icopytherefore
Iam
Icopytherefore
Iam
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?”)