Tutorial 1: Chemistry of Biology - Using Avogadro to Investigate Organic Chemicals

Tutorial 1:  Chemistry of Biology - Using Avogadro to Investigate Organic Chemicals

If you have not already taken the Pre-Instruction test, go back to my previous post and follow the directions there.

Download and install Avogadro on your computer.

Here's a screencast of how to use avogadro.

Biology happens in 3 dimensions.  Molecules have shapes which are the result of the atoms involved and how they are bonded.  It is not important that you memorize the names of any of these compounds.  Focus on how the shape of the molecule is affected by changes in the structure.


Use Avogadro to explore the structure of the following molecules in 3 dimensions:

a. methane, 

--> CH4

b. ethane, 

--> C2H6   

what kinds of motion can ethane molecules do that methane

molecules can't?

c. ethene (ethylene), 

--> C2H4

d. ethyne (acetylene), 

--> C2H2

   Compare the range of motion among ethane, ethene and ethyne.

   What is the effect of double and triple bonds?

   What do the suffixes -ane, -ene, and -yne mean?

2. How many different ways can you make butane, C4H10?

3. How many different ways can you make hexane with the formula C6H12?

4. How many different ways can you make hexane with the formula C6H14?

5. What are these molecules with the same number of each element called?  Why is this important?

6. Functional Groups are the ‘decorations’ that organic molecules have that give them

certain chemical properties. For each of the following, add the functional group to an ethane and see what happens to the molecule.

It is not necessary to memorize these functional groups (though you will need to if you take Organic Chemistry in college).  Note that the word carboxyl is a contraction of carbonyl hydroxyl.

With this background information, take a look at this site The Biology Project.