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Life in a nut: cell

Life in a nut: cell. A hike on the borderline between life and not-life Dr. Alkan Kabak çıoğlu 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. ”.

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Life in a nut: cell

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  1. Life in a nut: cell A hike on the borderline between life and not-life Dr. Alkan Kabakçıoğlu Koc Univ, Istanbul

  2. “ 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

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

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

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

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

  7. Arecibo Radio Telescope, Puerto Rico

  8. Arecibo Radio Telescope, Puerto Rico

  9. A closer inspection

  10. EVEN SMALLER SCALES Simple organization Complex organization Iron crystal Liquid water

  11. 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.

  12. Borderline gets blurred at smaller scales Chromosome duplication Transport along microtubules

  13. 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%

  14. 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! It’s shaky in a cell

  15. 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.

  16. 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

  17. Proteins A protein is a long word of with a 20-letter alphabet • They do all the work: • transport material • catalyze reactions • serve as building blocks • etc

  18. Protein Folding Problem Sequence  Structure ? • Still unsolved after 50 years.. • Computers can simulate only the first μs of folding which may take 1ms – 1s.

  19. How is the protein action coordinated in the cell?

  20. DNA A long chain of 4 letters: A,T,C,G. A  T G  C Two complementary strands. Carries all the information required to construct proteins. Complete human DNA sequence is known since 2003. Original drawing by Francis Crick Reading: “The Double Helix”, J.D. Watson

  21. Detailed structure of DNA

  22. Genetic Code …GTTGTATGCTCC…  …-Leu-Leu-Thr-Trp-…

  23. Genes talk to each other!

  24. . “Gene expression profiles” can be monitored using microarrays. Correlations in the data give indirect evidence on gene-gene interactions.

  25. Cell activity is controlled by a complex regulatory network Resolving the underlying complexity is the next challenge.

  26. 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

  27. “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?”)

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