Better Living Through Biochemistry

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Better Living Through Biochemistry

• figuring it all out from the bottom up

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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 _at_?!!
• Possibly result of weird channeling molecules
  in membranes.
• Molecules are made of atoms sharing electrons.
• Electrons move according to Schrodingers
  equation!

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To get a date in Paris just need to solve
Schrodingers Equations!!!
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3 Years and 3,000,000 CPU Hours Later

• Realize Schrodingers equation is hard to solve
  past the hydrogen atom.
• Its 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!

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Schrodingers Tetrahedrons
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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.

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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.

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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.

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Polarity of Common Bonds

• H-O is the most polar bond that is common in
  biology.
• H-N bond is also quite polar.
• CO 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.

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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.

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A Very Important Set of Hydrogen Bonds
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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.

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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

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This leads to a very weak very short range
attraction perhaps 1 as strong as a covalent
bond.
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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.

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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.

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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.

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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.

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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 -gt 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

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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

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The Cell Membrane
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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.

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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.
• Its very likely the astute biochemist will get
  laid next time they go to Paris.