biochemistry

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					   Better Living Through
       Biochemistry


figuring it all out from the bottom up
  Finding a Date in Paris
• First must deal with language barrier!
• Review hospital records, decide brain
  necessary for language.
• Dissect brain, note it has many neurons.
• Neurons conduct electricity? What the @#$*?!!
• Possibly result of weird ‘channeling’ molecules in
  membranes.
• Molecules are made of atoms sharing electrons.
• Electrons move according to Schrodinger’s
  equation!
To get a date in Paris just need
to solve Schrodinger’s Equations!!!
   3 Years and 3,000,000 CPU
         Hours Later…
• Realize Schrodinger’s equation is hard to
  solve past the hydrogen atom.
• It’s not an entire waste though, simple
  Schrodinger solutions help explain
  tetrahedral arrangement of covalent bonds
  around a carbon atom.
• Hmm, perhaps *chemistry*, not physics is
  the key to finding a date in Paris!
Schrodinger’s Tetrahedrons
             Basic Chemistry
• For cool quantum reasons, atoms like having 8
  electrons in their ‘valence’ shells.
• Elements in columns of the periodic table have the
  same # of valence electrons.
• Elements with 5 or more valance electrons will
  tend to grab electrons from elements with 3 or
  less. (Having 0 electrons in outer shell is also
  quantumly stable.)
• Carbon has 4 valance electrons, can go either way.
           Chemical Bonds
• Electrons can transferred completely from
  one atom to another. This creates a pair of
  ions – one negatively and one positively
  charged. Opposite charges attract leading
  to an ‘ionic’ bond.
• Electrons can also be shared by both atoms,
  leading to a ‘covalent’ bond. Covalent
  bonds can involve 1, 2, or 3 electrons.
   Electronegativity & Covalent
              Bonds
• Electrons are shared in a covalent bond, but not
  necessarily shared equally.
• Water is made up of oxygen bonded covalently to
  two hydrogens.
• Oxygen (6 valance electrons wanting 8) tends to
  get most of electrons rather than hydrogen (1
  valance electron wanting 0)
• The H-O bond is ‘polar.’ There is a fractional
  negative charge on the oxygen, a fractional
  positive charge on the hydrogen.
    Polarity of Common Bonds
• H-O is the most polar bond that is common in
  biology.
• H-N bond is also quite polar.
• C=O bond is fairly polar.
• H-S bond is somewhat polar.
• S-C bond not very polar
• C-H bond is almost entirely non-polar.
• C-C bond is entirely non-polar.
 Weak Interactions: Polar Bonds
• Polar Bond/Ion attraction. Based on charge.
  Leads to salt dissolving readily in water.
     H+-O- … Na+
• Polar Bond/Polar Bond – also charge based
     C+= O- … C+= O-
• Hydrogen Bonds – polar bond/polar bond where
  hydrogen is practically shared. Has a semi-
  covalent aspect. Like covalent bonds has
  geometrical constraints
     H+ - O-…H+-O-
  ~ 5% the strength of a covalent bond.
A Very Important Set of Hydrogen Bonds
   The Secret of Salad Dressing
• Water with H-O-H mixes well with itself,
  lots of opportunity for hydrogen bonding.
• Water will prefer sticking to itself to mixing
  with C-H (hydrocarbon) materials leading
  to so called ‘hydrophobic forces’ that
  separate oils and waters.
• Hydrophobic forces involve entropy as well
  as energy.
       Weak Interactions:
      Van Der Waals Forces
Orbits of electrons synchronize so that
electrons in neighboring molecules stay as
far away from each other as possible:

          +    -         +    -


This leads to a very weak very short range
attraction perhaps 1% as strong as a
covalent bond.
           Velcro Chemistry
• Large molecules shaped to fit well against
  each other can stick quite tightly from large
  numbers of weak interactions. This can
  even help catalyze reactions.
  Basic Classes of Biochemicals
• Lipids: mostly hydrocarbons. Form cell
  membranes and used for energy storage.
• Carbohydrates: sugar monomers can be joined to
  form starch and cellulose.
• Nucleic acids: formed from nucleotide monomers.
  DNA & RNA store and circulate information
  primarily.
• Proteins: formed from amino acid monomers.
  Diverse in shape and function. Basis of most
  enzymes.
                   Lipids
• Triacylglycerides: used for energy storage.
  The $100.00 bills of the cell. Three long
  hydrocarbon chains joined to glycerol.
• Phospholipids: Two long hydrocarbon
  chains joined to a phosphate (charged) head
  group. The main component of membranes.
• Sterols: Many-ringed non-polar structures.
  Cholesterol strengthens cell membranes.
  Testosterone & estrogen are also sterols.
          Carbohydrates
• Most composed of 6-carbon sugars, which are
  produced during photosynthesis. Glucose is the
  $20 bill of the cell. Mostly is a semi-rigid ring.
• Table sugar is glucose and fructose joined.
  (Fructose converts to glucose easily.)
• Starch is glucose joined together in a branched
  form that is easily converted back to glucose.
• Cellulose is glucose joined together in a straight
  form that is relatively hard to convert back to
  glucose.
• Fancy sugars decorate outside of animal cells.
        Nucleic Acids
• Nucleic acids are synthesized from
  nucleotide-tri-phosphates (NTPs).
• ATP is an aromatic base (A) linked to a five
  carbon sugar (ribose) and three phosphates (PO4-)
• ATP is the dollar bill of the cell. The reaction
  ATP -> ADP directly powers most of cell.
• dATP is like ATP but with one oxygen removed
  from the ribose, which makes it more stable.
• RNA is made from NTPs, DNA from dNTPs
       Proteins
• Proteins are made up of 20
  different amino acids.
• All amino acids share common
  central structure which forms
  backbone of proteins.
• Side chains of amino acids can be non-polar,
  polar, charged, and aromatic.
• Proteins may fold into a specific shape or remain
  fairly wiggly.
• Cell often adds phosphates to OH groups on side
  chains to modulate shape and activity
The Cell Membrane
       How A Nerve Cell Fires
• Nerve cell memberne is a lipid bilayer with
  embedded proteins.
• ATP-powered ion pumps keep outside of
  membrane + charged, inside – charged.
• Channels in membrane can let + ions pass
  through. Channels normally closed.
• Neurotransmitter gated channels collapse
  (‘depolarize’) voltage gradient.
• Voltage gated channels propagate depolarization
  in a wave down axon.
                Conclusion
• Careful study of biochemistry and
  macromolecules enables bottom up
  understanding of how a nerve works.
• Bottom up understanding of how French
  works should not be much harder.
• It’s very likely the astute biochemist will
  get laid *next* time they go to Paris.

				
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posted:8/19/2012
language:English
pages:25