Better Living Through Biochemistry

1. Better Living Through Biochemistry figuring it all out from the bottom up

2. 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!

3. To get a date in Paris just need to solve Schrodinger’s Equations!!!

4. 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!

5. Schrodinger’s Tetrahedrons

6. 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.

7. 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.

8. 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.

9. 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.

10. 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.

11. A Very Important Set of Hydrogen Bonds

12. 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.

14. 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.

15. 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.

16. 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.

17. 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.

18. 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.

19. 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

20. 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

21. The Cell Membrane

22. 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.

25. 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.