Friday, December 4, 2009

Tuesday, December 1, 2009

Lab #4

DNA extraction, click here

Tuesday, November 17, 2009

Try these engines

Computational Knowledge Engine WolframAlpha
Peer-reviewed publications in life sciences
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

Thursday, October 8, 2009

Lab #3

Click here.

Monday, October 5, 2009

Ardi and Lucy's daughter link

Ardi, click here
Lucy's daughter, click here

Sunday, September 13, 2009

Request to support our classroom

Adopt-a-classroom has created this video for my classes to forward to people who may want to consider adopting our classroom as their act of service to commemorate the nation's first 9/11 National Day of Service and Remembrance.

Last year, thanks to Adopt-a-classroom, my class was able to purchase equipment to measure pH, light and humidity of soils, which is a great asset for our new greenhouse, also product of a grant received last year. Please, help us make our class and our school a better place for our students to learn. One small donation at a time can make a big difference.

Message from Jamie Rosenberg, Adopt-A-Classroom Founder & Executive Director

As little as $5 can make a big difference for your children's classroom!

Earlier this year, President Obama signed into law the Edward M. Kennedy Serve America Act, establishing September 11th as a National Day of Service and Remembrance. The call to service challenges Americans to make an ongoing commitment to civic engagement. One of the core elements highlighted in this historic initiative is supporting education and helping to close the achievement gap. You can learn more about the National Day of Service and Remembrance at

How you can commemorate 9/11 Day of Service and Remembrance

  • Already adopted a classroom this year? We thank you and ask that you forward this message to friends, family, or colleagues who may want to help teachers and students.

You can choose to adopt a classroom on September 11 or any other day this month that you want to make your commitment to service. For assistance, feel free to email us at or call us at 877-444-7666.

James Rosenberg
Founder, Executive Director

Signing of the Edward M. Kennedy Serve America Act

Helping Communities Help Schools
Visit our website at
Nationally recognized by Follow Us
Adopt-A-Classroom mission
Adopt-A-Classroom invites the community into the classroom in support of teachers and their students. By adopting a classroom, donors form partnerships with specific classrooms providing financial and moral support. The result is a meaningful contribution to education in which donors experience the impact of their efforts and celebrate in a classroom's success.

Friday, September 4, 2009

Honors Biology Syllabus, Code of Conduct and Lab Safety Agreement

Click here.

Letter to parents for back to school night, click here.

Saturday, August 29, 2009

Math & Science - Practice your algebra

The contemporary view of the sciences - physics, chemistry and biology, is that they are heavily dependent on mathematics. Visit The Mathematical Biology Pages at Brandeis University to understand some examples in biology and its reliance on advanced math. To quote the site: "Four full years of high school math are a requirement for any student who may want to pursue a career involving biology." MDCPS Competency Based Curriculum for Honors Biology indicates in all its components at least one math-based issue in the biological sciences.
Our Honors Biology Course at MAST Academy will rely on your knowledge of many algebraic concepts, so, you need to review them to be able to complete your textbook and laboratory component activities. Some of them include Punnett square analysis, 
Practice your algebra here. Make sure to review the four main topics in this page, since they are an integral part of our course: 1- the language of algebra, 2- equations and inequalities, 3- the basis of algebra, and 4- graphing equations and inequalities. If you haven't seen any of these algebra aspects before, please come see me.

Practice your conversions to scientific notation & algebra

Contemporary biology relies heavily in advanced math. The examples at the Brandeis University Math in Biology website illustrate just a few examples of this. Practice scientific notation and conversion here and your basic algebra here.

Space elevator

Read material or watch videos from reputable sources about the space elevator. Explore how nanotubes can be used to construct it. Share your comment in a ONE paragraph max about either: 1- cost, 2- feasibility of nanotube polymerization for the length required, 3-timeline, 4- alternatives. Comments are to be substantiated by sources.

Lab safety notices

Check out your "safe lab practice" and "lab cleanliness" notices at

Monday, August 24, 2009

Saturday, August 22, 2009

Honors Biology 2009-2010

Welcome to our blog space for Honors Biology!
Refer to this calendar for our weekly activities.
For additional questions, e-mail me at

Saturday, August 1, 2009