212L (Spring 2009)

Week 2

The second week of lab focused on models of common biological molecules. Using Jmol molecular modeling software, available on the Darwin Server, we looked at properties of twenty different organic molecules. Images of these molecules, along with their respective groupings (lipid, amino acid, etc.) can be found here. Important properties of interest in these twenty molecules, in addition to their classifications, included molecules:

• Covalent bonds, and other bonds
• Polarity (and the effect of polarity on solubility)
• Carbon backbones
• Functional groups
• Molecular size and weight
• Polymers

We compared and contrasted structures for all of these molecules, and learned how general molecular structures relate to the functions of the molecules. Powerpoint slides for review are available on the Darwin Server. 

Week 1

The first week of lab covered a variety of topics. After reviewing safety in the lab, we focused our attention on practical tools that will be necessary for future weeks. Tools that were introduced included laboratory equipment such as micropipettes and the spectrophotometer, as well as statistical tools to be used in Microsoft Excel such as percent error and standard deviation.

Important information on the first week's lab can be accessed in Lab Topic 5 of the Dolphin Lab Manual, and in the blue notebook titled "BIOL 212L Laboratory Supplemental Material." Further information can be found on the biology website; here you can review how to create graphs in Excel and create an absorbance curve. The Darwin server is found by accessing the "Current Students" page, and here you can find a lot of the materials that I use in lecture, such as the Powerpoint presentations.

The lab for week one revolved around a quantitative analysis assignment that first compared the precision and accuracy of a micropipette and a graduate cylinder. Precision and accuracy are important terms to know and be able to use correctly, and they are often confused. A great comparison of the two terms can be found here. The two quantitative measurements that we used to measure precision and accuracy were standard deviation and percent error respectively.

Students also created an absorption curve for Bromophenol Blue. The curve was constructed by measuring the absorption of light by a sample of Bromophenol Blue in a spectrophotometer. The purpose for constructing this curve was to find the wavelength at which Bromophenol Blue absorbed the most light, as this wavelength would be the optimal one for constructing another curve, the standard curve.

The standard curve was constructed to measure the relationship between the concentration of Bromophenol Blue and its absorption of light (here we kept the wavelength constant at the maximum value found from the standard curve). This procedure takes advantage of Beer's Law, which states that the amount of light absorbed by a material is proportional to its concentration (i.e., the higher the concentration of a material such as Bromophenol Blue, the more light we can expect it to absorb). By making a set of known concentrations in test tubes, we were able to get the log-linear relationship between the concentration of Bromophenol Blue and the light absorbed. From this, we could then find the concentration of an unknown solution by measuring its absorption in the spectrophotometer, and mapping the absorption algebraically to a concentration.