Advanced Laboratory in Biochemistry CHEM 477

Below is a list of resources helpful in completing the lab assignments for CHEM 477. If you need help in using these resources, please contact the chemistry librarian.

Extinction coefficient is a term that should be replaced by the more appropriate expression "Molar absorption coefficient (ε)". A University of Texas library webpage gives excellent definitions of Molar Absorptivity and references (print and online) where you can find values. Wikipedia also gives a good definition.

According to the University of Texas webpage, Molar Absorption Coefficients (UV-VIS) are "spectral properties [that] can be found in various reference sources. Values of ε and log ε can be found scattered through spectral and general reference sources, although they are not always clearly indicated. They generally appear in context with wavelength numbers (λ max)."

Here are a couple of references for the molar absorption coefficient (source: University of Texas):

• NIST Chemistry WebBook: Look for the UV/VIS spectra. In the y axis you have the log ε value (scroll over the top of the peak with your mouse to get the value). From that, you could calculate the molar absorptivity (ε = molar absorption (A) / pathlength (l) X concentration (c))
• Sadtler Handbook of Ultraviolet Spectra: "Molar absorptivities are provided in the spectrum's data table for many organic compounds, denoted as a_m. Use the main index set to locate the compound".
• Absorption spectra in the ultraviolet and visible region: This 24 volume series contains tables with UV max (i.e. absorption) and other values which can be plugged into Beer's equation (A=εlc) to get the extinction coefficient. Volume 1-5 and 16-20 have a cumulative index in volumes 5 and 20 respectively. The other volumes must be searched individually.
• Atlas of spectral data and physical constants for organic compounds: "Molar absorption coefficients appear in parentheses next to the wavelengths in the Ultraviolet column."
• CRC handbook of biochemistry and molecular biology: "Vol. A2, pp.383-545, table titled "Molar absorptivity and A(1%1cm) values for proteins at selected wavelengths of the ultraviolet and visible region." "
• Merck Index: "ε is given in parentheses next to the UV max in the properties paragraph of some entries."
• Organic electronic spectral data: "log ε is given in parentheses next to the λ max. There is no cumulative index to this series."

Find out more about Beer's law from Wikipedia, Sheffield Hallam University, or Davidson College.

If you are looking for the Turnover number, the Km value or the Specific Activity (V_max/mg protein used) of chymotrypsin, you can use one of these sources:

• Enzyme Handbook: Located in Vanier Reference, QP 601 E5158 1990, Volume 5, this handbook contains information on chymotrypsin. To use this handbook, you will need to know the EC number for chymotrypsin (3.4.21.1). You can usually find EC numbers by searching for your enzyme in BRENDA (an enzyme database). The Enzyme Handbook will give information on the Turnover number, Km value, and Specific Activity. In some cases, the value will be in the handbook. In other cases, the handbook will refer you to an article where you can find the value (the reference will be a number in [square brackets] which refers to an article in the reference list). All values listed in the handbook are specific to certain substrates.
  
  
  • How to cite: To cite the Enzyme Handbook, use the same format for citing the Merck Index, as indicated in the ACS Guidelines. For example, the 1990 edition of the Enzyme handbook would be cited in the following way:
    • Enzyme Handbook, 2nd ed.; Schomburg, D.;Salzmann, M., Eds.; Springer-Verlag: New York, NY, 1990; entry 3.4.21.1.
      
      
• Brenda - Enzyme database: You can also find kinetic data in this free online database. Search for chymotrypsin. Click on any link with entry number EC 3.4.21.1. In the left hand menu, look for and click on KM Value, Turnover Number or Specific Activity. Note: there are many values for each, each being specific to a particular substrate and organism. These values were retrieved from experiments reported in articles. To get the citation for a specific article where a value was found, click on the corresponding number in the "Literature" column.

The following information is cited from the Chemistry 477 Laboratory Manual.

These are general resources, and collections of biochemistry-related links maintained by others, that contain material likely to be useful throughout the course.

• Expasy: A site that many biochemists visit often. This site provides access to many useful tools for the biochemist, as well as links to other sites.
• PubMed: An indispensable site for searching the recent biochemistry literature is PubMed. In addition to allowing you to search the biochemistry literature, PubMed also provides abstracts of papers and links to the journals themselves.
• Concordia Library: Has electronic subscriptions to many of the major biochemical and chemical journals. In addition, many journals now provide free electronic access to articles 6 months to a year old, or older.

Departmental home pages are a useful source of information about biochemistry and molecular biology research going on at Concordia.

• Chem/Biochem: concordia.ca/artsci/chemistry.html
• Biology: concordia.ca/artsci/biology.html

The following sites are useful resources especially for proteins and enzymes:

• Protein DataBase: Database of protein structures. Here you can download coordinates of protein structures for visualization.
• UnitProt: A comprehensive database of protein information.
• Protein Society: The Protein Society publishes the journal Protein Science, and maintains a number of links that are of interest to protein chemists.
• Genbank: one of the main repositories of nucleotide and protein sequence information.
• ProtParam: A suite of useful tools for analyzing protein properties based on primary amino acid sequence input.

Useful addresses for searching for chemical information - product safety, availability, protocols, etc., include:

• American Chemical Society
• SciFinder

Many chemical companies have on-line catalogues, as well as MSDS sheets, protocols, technical information, etc.

• Sigma-Aldrich
• Bio-Rad
• Fischer Scientific
• Roche Applied Science

Some more general sources of information about science include:

• Nature Journal Online
• Science Magazine
• Information about careers in science