Tuesday, November 17, 2009

Try these engines

Computational Knowledge Engine WolframAlpha
Peer-reviewed publications in life sciences pubmed.gov
Searchable database of genes at NCBI: Entrez Gene
Finding similarities between biological sequences: BLAST
Searchable database of genome projects at NCBI: Genome Project
USDA Ethnobotanical database:  Dr. Duke's Phytochemical Database
U Michigan Native American Ethnobotanical database: Dearborn AED

Monday, November 2, 2009

Balancing equations

First, let's try to balance the combustion equations for these simple hydrocarbons:
Example: CH4 + O2 --> CO2 + H2O
              CH4 + 2 O2 --> CO2 + 2 H2O

C5H12 + O2 --> CO2 + H2O


C2H6 + O2 --> CO2 + H2O


Now, try with sugars:
Example: C3H6O3 + O2 --> CO2 + H2O
              C3H6O3 + 3 O2 --> 3 CO2 + 3 H2O


C5H10O5 + O2 --> CO2 + H2O

C8H16O8 + O2 --> CO2 + H2O


How about equilibrating the combustion reactions of lipids?
The molecular formula in the first reaction is stearic acid. Stearic acid is used in candles. When you burn a candle, stearic acid undergoes combustion and turns into CO2 and H2O.


The molecular formula in the second reaction is oleic acid. Oleic acid is the main component of olive oil. When you add olive oil to your salad, and eat it, your cells catabolize the oleic acid into CO2 and H2O


You probably noticed that the only difference between stearic acid and oleic acid is that the first one has more hydrogens. This indicates that stearic acid is a saturated fatty acid (solid at room temperature), whereas oleic acid is an unsaturated fatty acid (liquid at room temperature). 


Arachidonic acid is the fatty acid in peanut oil, the source of all phospholipids in our membranes, as well as the basic unit that our body uses to synthesize the intermediaries of inflamation (prostaglandins and thromboxanes). The equilibrated equation for the combustion of arachidonic acid looks like this:
Example: C20H32O+ O2 --> CO2 + H2O
              C20H32O+ 27 O2 --> 20 CO2 + 16 H2O


Try to equilibrate the following combustion reactions for stearic acid and oleic acid.


C18H36O2 + O2 --> CO2 + H2O


C18H34O2 + O2 --> CO2 + H2O




A note about equilibrating equations for long unsaturated fatty acid chains ... 


When you keep trying small coefficients and nothing seems to work, try using the rule of the least common multiple (back to 3rd grade algebra), and if that takes too long, just multiply the highest numbers of your main reactant to get the coefficient needed for your CO2. Then finding the other coefficients will be just a matter of adding and subtracting. 


For example, if you try to equilibrate the combustion of palmitoleic acid, an unsaturated fatty acid common in macadamia nuts (yeah, Haagen Datz's macadamia brittle!), it will end up looking like this:




C18H34O2 + O2 --> CO2 + H2O (before equilibrating)
34 C18H34O2 + 867 O2 --> 612 CO2 + 578 H2O

This was my reasoning:

  • I need a minimum of 18 carbons, 34 hydrogens and 2 oxygens.
  • But when I try using 18 as the coefficient for the COthat gives me 36 hydrogens, which is 2 more than what I have in one molecule of palmitoleic acid (34 hydrogens). 
  • I quickly realize that it will take some number juggling to get the right coefficient.
  • So, instead of losing my time trying one coefficient after the next, I find the l.c.m. or basically on the case of 18 and 34, its multiplication (search in wikipedia if you don't remember how to calculate l.c.m.).
  • How to find the l.c.m:
    • 18 can be decomposed as 2 * 3 * 3 = 2 * 3^2
    • 34 can be decomposed as 2 * 17
    • Choose the decomposition of the factor with the highest exponent
    • Multiply all the chosen factors: 2 * 3^2 * 17 = 612
    • In our case the number obtained is the maximum possible of 18 x 34 = 612. 
    • 612 is the coefficient you will need for your CO2.

  • 34 C18H34O2 + X O2 --> 612 CO2 + X H2O
    • Now, we have the same number of carbons on each side of the equation

  • Next, is equating the number of hydrogens on both sides of the equation. To do that, I multiply 34 (the coefficient of palmitoleic acids) x 34 (the number of hydrogens in one molecule of palmitoleic acid).
    • 34 x 34 = 1,156
    • This is the number of hydrogens I need on the side of the products, basically coming only from the molecules of water.
    • 1,156 / 2 = 578
    • 578 is the coefficient you will need for your H2O

  • 34 C18H34O2 + X O2 --> 612 CO2 + 578 H2O

  • Finally, we need to equate the number of oxygens on each side of the equation. To do that, I need to know how many oxygens I have on each side by now:
    • On the reactants side, we have 34 * 2 + X * 2 = 68 + X * 2
    • On the products side, we have 612 *2 + 578 * 1 = 1,224 + 578 = 1,802 
    • Ergo:
      • 68 + X * 2 = 1,802
      • X = (1,802 - 68) / 2
      • X = 1,734 / 2 = 867
    • 867 is the coefficient you will need for your O2.
  • Voila!

  • 34 C18H34O2 + 867 O2 --> 612 CO2 + 578 H2O
    Simplify by dividing by 17

    2 C18H34O2 + 51 O2 --> 36 CO2 + 34 H2O