Download Life in a nut: cell

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
EVEN SMALLER SCALES
Simple organization
Iron crystal
Liquid water
Complex organization
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.
I
copy
there
fore
I
am
I
copy
there
fore
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am
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copy
there
fore
I
am
I
copy
there
fore
I
am
I
copy
there
fore
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copy
there
fore
I
am
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copy
there
fore
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copy
there
fore
I
am
I
comy
there
fore
I
am
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copy
there
fore
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am
I
copy
there
fore
I
am
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
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
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T
GC
Two complementary strands.
Carries all the information required
to construct proteins.
Complete human DNA sequence is
known 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 monitored
using microarrays. Correlations in the data
give 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?”)