better living through biochemistry figuring it all out from the bottom up
Post on 19-Dec-2015
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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 @#$*?!!• Possibly result of weird ‘channeling’ molecules in
membranes.• Molecules are made of atoms sharing electrons.• Electrons move according to Schrodinger’s
equation!
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!
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.
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
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.