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.