Introduction to course Centre for Structural Biology Currency Pair by MikeJenny


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                      Richard Neutze
                       Ph. 773 3974


    Present a detailed analysis of the mechanisms of energy
 transduction within the cell. Emphasis placed on the interplay
between structure & function for membrane proteins governing
                      energy transduction.

Aim to provide skills & resources for the literature project.
• Using structural & citation data bases.
• Packages for structural analysis.
• Making figures.
• Writing scientific reports.
• Presentation of literature study.

Literature study will:
• Work in pairs.
• Choose one structure-related research article.
• Ask what new information concerning the functional mechanism of this
protein has emerged from its structure?
• Write a report of not more than eight pages.
• Give a 15 minute presentation of the project.
                          Course Assessment:

50 % written exam.
• Wednesday December 12th - time we discuss now.

A literature project.
• 40 % written project.
     - Due Monday December 6th.
• 10 % presentation.
     • Thursday December 2nd.

Grades 5, 4, 3 or fail.
                      Science: the way it is!

•1900 Physicists thought they were close to a theory of everything.
    • Newton gravitation worked well.
    • Electricity & magnetism unified by Maxwell.
    • Milky Way seemed to encompass everything.
• Within the first two decades of 20th century:
    • Quantum Mechanics.
    • Theory of Relativity.
    • Other galaxies discovered.

• 21st century: the century for biology!
    • Piecing together the jig-saw of life will uncover numerous
    remarkable phenomenon.
                             The Big Bang
•14 billion years ago the universe began from a point.
     - Quantum fluctuations ``borrowed'' just enough from the vacuum
     to kick it all off.
     - Positive mass energy + negative gravitational = 0!
• After ~300 thousand years hydrogen condensed from a plasma.
     - Stars condensed from hydrogen.
     -Inhomogeneities led to galaxy formation.

• 200 billion stars in a galaxy.
• 100 billion galaxies in the universe.
                              Star cycle:
• Stars ``burn'' hydrogen:
    • Hydrogen fusion product is helium.
    • Fusion products of helium & hydrogen etc. = heavier atoms (eg.
    carbon, oxygen, nitrogen etc).
• When stars ``burn out'' they collapse.
    • Massive gravitationally driven heating.
    • Heating drives supernova (huge explosions).
    • More complex atoms created.
                         Solar system creation:
• Began after one (or more) local supernova 4.6 billion years ago.
     - Our sun a second or third generation star.
• Inner planets formed from collisions of moon-sized planetismals.
• Venus, Earth & Mars received similar inventories of C, O & H2O.
     • Mars still has frozen water below the surface.
     • Thin (not massive enough) CO2 atmosphere & cold!

• Venus lost water due to a runaway greenhouse effect.
    - Water vapor in the high atmosphere is photolysed into H2 & O,
    & H2 lost to space.
• Thick CO2 atmosphere & hot (500oC)!
• Most CO2 in carbonate materials (eg. limestone).
    - CO2 blanket much less & no runaway greenhouse effect.
    - Water on the surface.
• Volcanic activity.
    - Recycles the biosphere.
• Magnetic field.
    - Protects against solar (ions) radiation.
• Pro-Earth struck by an inner planet ~Mars 4.5 billion years ago.
    - Ejected molten mantel into the orbit.
    - Some coalesced into the moon.
• Gave the earth its spin & tilt.
    - Heating & cooling pattern (day/night & seasons) critical.
• Exaggerated tides.
    - Powers plate tectonics & volcanism.
    - Volcanism provides reducing cations & recycles biosphere.
• Role in evolution?
                             Early bioenergetics:
• First life about 3.8 billion years ago.
• Earliest replicating system possibly an RNA molecule.
     - RNA world located in rock pores around volcanic springs.
     - Lived on redox contrast of more oxidised atmosphere/ocean &
     more reduced fluids in contact with volcanic magma.
     - Dissolved suplhate provide oxidation power for organisms to
     react against hydrothermal fluids, eg. hydrogen & methane.
• ATP addiction probably emerged from the RNA world.
     - Ribozymes (catalytic RNA) can polymerise RNA-NTP molecules
     (NTP = nucleotide tri-phosphates).
     - 14 nucleotide addition with 97 % fidelity was demonstrated.
     - Early metabolism of RNA world based on an NTP.
     - Triphosphate bond releases 10 kcal/mol & is stable (10 -10/min).
                           Cell membranes:
• RNA based life contained some cellular compartmentalization.
    - Compartments keep replicase & genomic RNA together.
    - Evolutionary advantages remain with the organism which
    produced it.
• Cells in contemporary biology surrounded by amphiphatic lipids.

• In early life compartmentalization could be achieved by:
     - Organising centres (like a rybozome).
     - Organisation along a surface.
     - Passive compartmentalization within pores of rocks, or surface of
     fine particles.
               DNA & proteins:
• RNA world invented of protein synthesis.
    - Crowning achievement.
    - Protein synthesis instructed & catalysed
    by RNA.
    - Rybosome has RNA @ amino-acid
    polymerisation active site.
    - Proteins more versatile & efficient in
• DNA more chemically stable than RNA.
    - Allows larger genomes.
• DNA not catalytically active.
    - Forms a partnership with proteins.
                    Evolution of photosynthesis:
• Accidental use of pigments where disequillibria easily exploited.
     - Anoxygenic photosynthesis may have evolved from bacterium
     using infrared thermotaxis.
     - Organism drifted into shallow water & used sunlight.
     - Later evolution of an oxygen generating complex exploiting
     Mn4O4 to Mn4O6 chemistry to generate O2 from H2O.
• 3.5 billion years ago cyanobacteria evolved.
     - Probably a genetic exchange between interdependent green
     & purple bacteria.
     - Created an organism which could live freely on the planet
     wherever H2O, CO2 & light available.
• Tremendous increase in the biosphere.
             Rubisco & carbon dating:
• Rubisco is an ancient enzyme which fixes
atmospheric CO2.
     - When there is excess it prefers 12C to 13C.
     - Measuring 12C to 13C ratio in rocks the
     standard method of carbon dating.
• Rubisco predates oxygenic photosynthesis.
• A qwerty enzyme.
     - The qwerty keyboard - designed to avoid
     mechanical jamming & far from optimal.
     - Rubisco fixes CO2, but may also fix O2 (ie.
     undo the benefits of photosynthesis).
     - This ineffeciency maintains reasonable CO2
     levels in the atmosphere.
       Change of atmosphere:
• Debate as to when the
atmosphere became O2 rich.
     - Entire biosphere now ``rich'' in
     redox potential.
• Oxygenic photosynthesis
appeared 3.5 billion years ago.
     - Global oxygen production
     similar order of magnitude ever
     - But levels depend on
     consumption also!
• Evidence that O2 levels increased
2.2 billion years ago.
     - Possibly due to complex
• Biodiversity took off.
             Four aeons:
• Hadean:
    - From formation of the planet to
    early life.
• Archaean:
    - Prokaryotic life.
• Proterozoic:
    - First eukaryotes.
• Phanerozoic.
    • Life visible without need of a
                      Amphipathic molecules
• Solubility depends on favorable interactions with water.
    - Hydrogen bonds.
    - Ionic interactions.
    - Polar compounds.
•Hydrocarbons are non-polar, non ionic & cannot form H-bonds.
    - Hydrophobic not hydrophilic substances.
• Amphipathic molecules have a hydrophilic head group & a
  hydrophobic tail.
    - Form mono-layers, micelles and bilayer vesicles.
                Lipid bilayers
• Lipids have polar hydrophilic ``head'' &
hydrophobic ``tail''.
• Form lipid-bilayer membranes.
     - Most biological membrane lipids
     have two hydrocarbon tails.
     - Divide different compartments of the
     - Allow non-polar molecules to move
     within the membrane.
     - Prevent the diffusion of polar
     molecules across the membrane.
     - Can with-stand 200 mV over ~ 40Å
     (50 MV/m).
• Glycerophospholipids.
     - Major class of naturally occurring
     phospholipids (phosphate containing
    Transport across membranes
• A cell is neither entirely open or
closed to its surroundings.
     - Interior of cell protected from
     toxic substances.
     - Metabolites imported into the
     - Waste products extracted from
     the cell.
     - Changes in cell environment
     - Inter-cellular signals transmitted.
• Passive transport.
    - Accomplished by the random diffusion of molecules through
    the membrane (non-polar molecules only).
• Facilitated transport:
    - Ion pores, which define ``holes'' in the membrane.
    - Carrier molecules, which form a hydrophobic casing.
    - Both allow only specific ions to move through the membrane.
• Active transport.
    - Integral membrane proteins use chemical or light energy to
    pump ions against a concentration gradient (eg. H+ or K+).
                         Modern bioenergetics
• Biology harvests the energy content of light.
     - Photosynthesis → chemical energy.
• ATP is the basic ``energy currency'' of the cell.
     - Produced by energy-transducing membrane proteins.
     - Protons are first pumped across a cell membrane.
     - ATP-synthase harvests the proton concentration gradient to
     generate ATP from ADP + Pi.

      Chemical energy to light    Light to chemical energy
• Found within eukaryotic cells.
• Primary producer of ATP.
     - Basic ``workhorse'' of the cell.
• Typically 0.7 to 1.0 mm long.
• Outermembrane has porins allowing free access of small particles.
• Approximately 500 mg/ml of the inner membrane is protein.
              Respiratory chain of mitochondria
• Membrane proteins transfer e- from NADH or Succinate to O2.
    - Electrons enter at complex I or II.
    - Complex I, III and IV pump protons.
    - Complex IV reduces O2 to H2O.
• Complex V (ATP-synthase) uses the proton-gradient to
generate ATP from ADP & Pi.
• ATPsynthase harvests the H+
gradient to regenerate ATP from
ADP & Pi.
    - Back diffusion of H+ causes
    membrane portion to rotate.
    - Mechanically coupled to the
    soluble portion.
    - Maintains the ATP/ADP ratio 10
    orders of magnitude from
    - Excess ATP used as the energy
    currency of the cell.
• Mechanism conserved throughout
                      Summary of lecture 1:
• Universe 14 billion years old.
• Earth/solar system 4.5 billion years old.
• First life appeared 3.5 billion years ago.
• ATP addiction inherited from RNA world.
• Overwhelming source of ATP is highly a conserved process in
energy-transducing membranes.
• To understand the bioenergetics must understand proton
translocation processes.

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