Post on 18-Dec-2015
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
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Icopytherefore
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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?”)