The Essential Biopolymers

January 10, 2017

My notes on the four macromolecules that are essential to life as we know it: proteins, fats (lipids), carbohydrates (saccharides), and nucleic acids.

Carbohydrates/saccharides.

Carbohydrates/saccharides.

Fats/lipids.

Fats/lipids.

Nucleic Acids (DNA and RNA).

Nucleic Acids (DNA and RNA).

Proteins.

Proteins.

Citing this post: Urbano, L., 2017. The Essential Biopolymers, Retrieved January 17th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

Carbon in the Ground and Free Oxygen in the Air

September 6, 2016

A couple new article relevant to our study of Earth History.

Carbon

Image by Rajdeep Dasgupta, via pyhs.org.

Image by Rajdeep Dasgupta, via pyhs.org.

Research on the high pressure and temperature conditions at the Earth’s core suggest that most of the carbon in the early Earth should have either boiled off into space or been trapped by the iron in the core. So where did all the carbon necessary for life come from? They suggest from the collision of an embryonic planet (with lots of carbon in its upper layers) early in the formation of the solar system.

Free Oxygen

Typical surface view of purple mat surface at Middle Island showing purple filaments.  Some white filaments can also be observed. Image from Thunder Bay Sinkholes 2008 via oceanexplorer.noaa.gov.

Typical surface view of purple mat surface at Middle Island showing purple filaments. Some white filaments can also be observed. Image from Thunder Bay Sinkholes 2008 via oceanexplorer.noaa.gov.

It took a few billion years from the evolution of the first photosynthetic cyanobacteria to the time when there was enough oxygen in the atmosphere to support animal life like us. Why did it take so long? NPR interviews scientists investigating purple microbial mats in Lake Huron.

Citing this post: Urbano, L., 2016. Carbon in the Ground and Free Oxygen in the Air, Retrieved January 17th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

MolView: Website for Drawing Molecules

September 5, 2016

MolView is a great site for drawing molecules and rendering them in 3D.

Screen capture from MolView showing the 2d window on the left where the molecule is drawn, and the rotatable 3d view on the right.

Screen capture from MolView.

Citing this post: Urbano, L., 2016. MolView: Website for Drawing Molecules, Retrieved January 17th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

The Flint Water Crisis

January 25, 2016

What happened:

  • Flint switches from Detroit’s water system to the Flint River to save money,
  • E. coli bacteria show up in water (E.coli can make you sick) so the water system adds chlorine to kill the bacteria,
  • Trichloromethane shows up in the water (trichloromethane is a carcinogen)
  • Water from the Flint River is more corrosive compared to Detroit’s because it has higher levels of chlorine ions (Cl),
  • Chlorine dissolves lead from old water pipes — the lead goes into solution in the water (lead causes issues with mental development in kids, among other things),

References

Detailed article from Mashable: The poisoning of a city

A timeline from Michigan Radio: TIMELINE: Here’s how the Flint water crisis unfolded

An excellent, detailed program from Reveal: Do not drink: The water crisis in Flint, Michigan. The second part in particular is a good summary of the science issues.

A NPR summary from September 29th, 2015: High Lead Levels In Michigan Kids After City Switches Water Source

Citing this post: Urbano, L., 2016. The Flint Water Crisis, Retrieved January 17th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

Limiting Chemical Reactions

January 1, 2015

Figuring out the limiting reactant in a chemical reaction integrates many of the basic chemistry concepts including: unit conversions from moles to mass and vice versa; the meaning of chemical formulas; and understanding the stoichiometry of chemical reactions. So, since we’ll need a number of these, I wrote a python program to help me design the questions (and figure out the answers).

Program examples come zipped because they require the program file and the elements_database.py library:

Baking Powder and Vinegar (Common Molecules)

Limiting_component-Common.py: This has the baking powder and vinegar reaction limited by 5 g of baking soda. It’s nice because it uses a few pre-defined “common molecules” (which are defined in the elements_database.py library.

You enter the reactants and products and the program checks if the reaction is balanced, then calculates the moles and masses based on the limiting component, and finally double checks to make sure the reaction is mass balanced.

Limiting_component-Common.py

from elements_database import *
import sys

print "LIMITING REACTANT PROGRAM"
print 
print "  Determines the needed mass and moles of reactants and products if reaction is limited by one of the components"

c = common_molecules()

'''Create Reaction'''
rxn = reaction()
# Add reactants (and products)
#   Use rxn.add_reactant(molecule[, stoichiometry])
#       molecule: from molecule class in elements_database
#       stoichiometry: integer number
rxn.add_reactant(c.baking_soda,1)
rxn.add_reactant(c.hydrochloric_acid,1)
rxn.add_product(c.carbon_dioxide)
rxn.add_product(c.water, 1)
rxn.add_product(c.salt)

'''Print out the reaction'''
print 
print "Chemical Formula"
print "  " + rxn.print_reaction()
print 

'''Check if reaction is balanced'''
balanced = rxn.check_for_balance(printout=True)

'''Calculate limits of reaction'''
if balanced:
    rxn.limited_by_mass(c.baking_soda, 5, printout=True)

Outputs results in the Results table (using scientific notation):

LIMITING REACTANT PROGRAM

  Determines the needed mass and moles of reactants and products if reaction is limited by one of the components

Chemical Formula
  NaHCO3 + HCl  --> CO2 + H2O + NaCl 

Check for balance
 --------------------------------------------- 
| Element | Reactants | Products | Difference |
 --------------------------------------------- 
|   Na    |    1      |    -1    |     0      |
|   H     |    2      |    -2    |     0      |
|   C     |    1      |    -1    |     0      |
|   O     |    3      |    -3    |     0      |
|   Cl    |    1      |    -1    |     0      |
 --------------------------------------------- 
Balance is:  True

Given: Limiting component is 5 g of NaHCO3.
  Molar mass = 84.00676928
  Moles of NaHCO3 = 0.0595190130849

 Results
   ------------------------------------------------------------------ 
  | Molecule | Stoich.*| Molar Mass (g) | Moles req. |    Mass (g)   |
   ------------------------------------------------------------------ 
  |NaHCO3    |    1    |    84.0068     |  5.952e-02 |   5.000e+00   |
  |HCl       |    1    |    36.4602     |  5.952e-02 |   2.170e+00   |
  |CO2       |    -1   |    44.0096     |  5.952e-02 |   2.619e+00   |
  |H2O       |    -1   |    18.0156     |  5.952e-02 |   1.072e+00   |
  |NaCl      |    -1   |    58.4418     |  5.952e-02 |   3.478e+00   |
   ------------------------------------------------------------------ 
 * negative stoichiometry means the component is a product

  Final Check: Confirm Mass balance: 
     Reactants:    7.1701 g 
     Products:    -7.1701 g 
     --------------------------
          =      0.0000 g 
     --------------------------

General Example

If not using the common molecules database, you need to define the components in the reaction as molecules yourself. This example reacts magnesium sulfate and sodium hydroxide, and limits the reaction with 20 g of magnesium sulfate.

Limiting_component-General.zip

The main file is:

Chem_Exam-limiting.py

from elements_database import *
import sys

print "LIMITING REACTANT PROGRAM"
print 
print "  Determines the needed mass and moles of reactants and products if reaction is limited by one of the components"

# create reaction

rxn2 = reaction()
# Add reactants (and products)
#   Use rxn.add_reactant(molecule[, stoichiometry])
#       molecule: from molecule class in elements_database
#       stoichiometry: integer number
rxn2.add_reactant(molecule("Mg:1,S:1,O:4"))
rxn2.add_reactant(molecule("Na:1,O:1,H:1"), 2)
rxn2.add_product(molecule("Mg:1,O:2,H:2"))
rxn2.add_product(molecule("Na:2,S:1,O:4"))

'''Print out the reaction'''
print 
print "Chemical Formula"
print "  " + rxn2.print_reaction()
print 

'''Check if reaction is balanced'''
balanced = rxn2.check_for_balance(printout=True)

'''Calculate limits of reaction'''
if balanced:
    rxn2.limited_by_mass(molecule("Mg:1,S:1,O:4"), 20, True)

# print out masses
print "Masses Involved in Reaction"
print "  Reactants:"
for i in rxn2.reactants:
    #print "rxn", i
    print "    {m}: {g} g".format(m=i.molecule.print_formula().ljust(10), g=i.mass)
print "  Products:"
for i in rxn2.products:
    #print "rxn", i
    print "    {m}: {g} g".format(m=i.molecule.print_formula().ljust(10), g=-i.mass)

This program is slightly different from the common molecules example in that, at the end, it prints out masses calculated in a more easily readable format in addition to the other data.

Masses Involved in Reaction
  Reactants:
    MgSO4     : 20.0 g
    NaOH      : 13.2919931774 g
  Products:
    MgO2H2    : 9.69066512026 g
    Na2SO4    : 23.6013280571 g

When I have some time I’ll convert this to JavaScript like the molecular mass example.

Citing this post: Urbano, L., 2015. Limiting Chemical Reactions, Retrieved January 17th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

Molar Mass of Molecules

December 5, 2014

Calculate the molar mass of a molecule:

The notation for the chemical formula is a little funky: you put the element symbol and then the number of atoms separated by a colon; each element/number of atoms pair are separated by commas, so sodium chloride (NaCl) would be “Na:1,Cl:1“.

This will have to do until I can write something to parse the regular chemical formula notation.

On the plus side, you can link to a specific molecular mass calculation by adding the formula to the url. So magnesium chloride (MgCl2) can be found with this url:

http://soriki.com/js/chem/chem_db/molecular_mass.html?formula=Mg:1,Cl:2

Citing this post: Urbano, L., 2014. Molar Mass of Molecules, Retrieved January 17th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

Peer Teaching

November 20, 2014

Ms. R. helps a peer with her experiment.

Ms. R. helps a peer with her experiment.

Half the Chemistry class was gone yesterday, so they had to make up their experiment today. Well, one student of the students who did her work yesterday entreated me to lead her peers through the experiment. It was pretty awesome, because she had been struggling with the topic for the last week and had finally gotten it yesterday.

And she did an excellent job. She not only walked the rest of the class through the theoretical calculations, but guided them through the experiment itself.

Peer teaching works best when students are excited about what they’ve learned and want to share. I’m still trying to figure out the best way of inciting this excitement when I break the groups up for their projects. Giving them choice is important, but also, I think, giving them challenging work that they’re proud to accomplish.

Citing this post: Urbano, L., 2014. Peer Teaching, Retrieved January 17th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

Calibration Curves for Salt (NaCl) Solutions

August 29, 2014

Calibration curves produced by different student groups to determine the relationship between density and concentration of salt (NaCl) solutions.

Calibration curves produced by different student groups to determine the relationship between density and concentration of salt (NaCl) solutions.

To start with chemistry class, we’re studying the properties of substances (like density) and how to measure and report concentrations. So, I mixed up four solutions of table salt (NaCl) dissolved in water of different concentrations, and put a drop of food coloring into each one to clearly distinguish them. The class as a whole had to determine the densities of the solutions, thus learning how to use the scales and graduated cylinders.

However, for the students interested in doing a little bit more, I asked them to figure out the actual concentrations of the solutions.

One group chose to evaporate the liquid and measure the resulting mass in the beakers. Others considered separating the salt electrochemically (I vetoed that one based on practicality.

Most groups ended up choosing to mix up their own sets of standard solutions, measure the densities of those, and then use that data to determine the densities of the unknown solutions. Their data is shown at the top of this post.

Finding the mass of solution in order to calculate its density.

Finding the mass of solution in order to calculate its density.

The variability in their results is interesting. Most look like the result of systematic differences in making their measurements (different scales, different amounts of care etc.), but they all end up with curves where the concentration increases positively with density.

I showed the graph above to the class so we could talk about different sources of error, and how scientists will often compile the data from several different studies to get a better averaged result.

Then, I combined all the data and added a linear trend line so they could see how to do it using Excel (many of these students are in pre-calculus right now so it ties in nicely):

Trend line from combined data.

Trend line from combined data.

What we have not talked about yet–I hope to tomorrow–is how the R-squared value, which gives the goodness of the fit of the trend line to the data, is more a measure of precision rather than accuracy. It does say something about how internally consistent the data are, but not necessarily if the result is accurate.

It’s also useful to point out that the group with the best R-squared value is the one with only two data points because two data points will necessarily give a perfectly straight line. However, the groups that made more solutions might not have as good of an R-squared value, but, because of the multiple measurements, probably have more reliable results.

As for which group got the most accurate result: I added in some data I found by googling–it came off a UCSD website with no citation so I’m going to need to find a better reference. Comparing our data to the reference we find that team AC (the red squares) best match:

The straight line shows my (currently) accepted values for the concentration/density relationship.

The straight line shows my (currently) accepted values for the concentration/density relationship.

Citing this post: Urbano, L., 2014. Calibration Curves for Salt (NaCl) Solutions, Retrieved January 17th, 2017, from Montessori Muddle: http://MontessoriMuddle.org/ .
Attribution (Curator's Code ): Via: Montessori Muddle; Hat tip: Montessori Muddle.

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