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CH 339L Literature Search: Enzymes


Spring 2009 ASSIGNMENT 2: Submit References

Find at least 3 reputable references besides your textbook, 2 of which must be from scientific journals. Cite them using the CSE name-year format and submit with PDF copies of all articles (at least two).

What is a research article?

Background Information

Before starting a literature search on an enzyme, you need basic background information about that enzyme. This is not easily found in the primary journal literature, where authors assume you already know the basic facts. So you first need to consult other sources for details such as nomenclature, EC Number, source, reactions catalyzed, etc.

A number of reputable Web resources of enzyme data are available. They are listed on the Biochemical Information page, including BRENDA and IUBMB's ENZYME.

Literature Searching

To search the scientific literature, you need to use a quality index database that covers the literature of your field. DO NOT USE GOOGLE! (Why not?)

The primary literature database for the biomedical sciences is Medline, or its free, public equivalent PubMed. (There are other databases that also cover the life sciences very well, but for the purposes of this assignment PubMed will suffice.)

Sample Search

  1. The enzyme you've chosen for your topic is hexokinase.

  2. You might begin by searching your enzyme in the IUBMB Enzyme Nomenclature database to obtain basic information about its names, classification, and EC number, which is 2.7.1.1. The BRENDA database provides even more extensive information and data about thousands of enzymes. This kind of basic background information is not easily found in journal articles. Articles are much more specific and narrowly focused.

  3. Connect to the PubMed database (or its proprietary Medline equivalents).

    http://www.ncbi.nlm.nih.gov/sites/entrez

  4. Enter "hexokinase" as a search term. Note that you retrieve nearly 8000 articles, listed in reverse-chronological order. Obviously you will need to narrow this down. What aspects of this enzyme are you going to cover in your presentation? Say for instance you're interested in this enzyme's role in colon cancer.

  5. Narrow your search by entering:
    hexokinase and (colon cancer)
    and you're down to 23 hits, which is more focused and easy to browse for interesting articles.

  6. Browse the results, or do further searches to broaden or refocus your search as you go. Note that PubMed provides many ways to browse and link to related articles and reviews. Click on an article title to see its abstract, a summary of what the article covers. Read the abstract carefully first to determine if the article is worth obtaining for your work.

Getting the Articles

PubMed like most index databases provides links to the full text of articles it indexes. The functionality of these links depends on two factors: 1) digital full text must exist, and 2) the article must be covered by UT-Austin's electronic journal subscriptions, or otherwise freely available. If one of these factors is not true, then you won't be able to get the article online. Older articles (often before the mid-1990s) are often not available to us, and of course there are thousands of journals that UT does not subscribe to in any way.

  1. Say this article is of interest:

    1: J Bioenerg Biomembr. 2008 Jun;40(3):183-91.
    Uncovering the role of VDAC in the regulation of cell life and death.
    Shoshan-Barmatz V, Keinan N, Zaid H.
    Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel. vardasb@bgu.ac.il
    Proper cell activity requires an efficient exchange of molecules between mitochondria and cytoplasm. Lying in the outer mitochondrial membrane, VDAC assumes a crucial position in the cell, forming the main interface between the mitochondrial and the cellular metabolisms. ..... etc.

    The reference is on top: journal, year, volume, pages. Then come the paper's title and authors, followed by the abstract.

  2. In PubMed for example, the link to full text is in the upper right corner of the window. In this example the link is to SpringerLink, the publisher of this particular journal. Click on this link.

  3. You are taken to the publisher's page for this article. Here you also find the abstract and available full text options. If you click on the PDF link you will view and/or download the PDF file of the article.

  4. IMPORTANT! If you are doing this work off-campus, outside of UT's IP address range, you will need to go through the Libraries' proxy server before you can see full text of licensed journals. To establish a proxy session, look up the desired journal title in our E-Journals Database and link to it that way. You will be asked for your UT EID and password, and thereafter you'll be OK until you close your browser.

What if it's not available online?

Don't panic. Not everything is online! Researchers often have to - gasp - come into the Library to get a copy of a journal article or book that we have only in print. It's not the end of the world, just a little slower. Researchers and students ignore print material at their peril -- never limit yourself to what's available online.

  1. Say this reference is of interest for your project:
    Br J Exp Pathol. 1987 Jun;68(3):331-41.
    Hexokinase and adenylate kinase activities in aorta, heart muscle and skeletal muscle from uraemic rats.
    Krog M, Ejerblad S, Johansson H, Wilander E, Agren A.

    Note that it's from 1987, pretty old by medical journal standards but possibly still very relevant. PubMed provides no link to full text. Now what?

  2. Go to the Library Catalog and select the Journal Title search. Enter "british journal of experimental pathology". Don't use abbreviations, use full titles.

  3. The journal pops right up, and you see from the volume list that volume 68 (1987) is available at the Life Science Library.
    Life Science Library RB 1 B7 V.68 1987 AVAILABLE

  4. Go over to the Life Science Library (MAI 220), into the stacks, and find the volume at its call number. Find the article and photocopy it with your Libraries copy card. If you have trouble locating the volume, ask library staff for help.

If a journal is not held at UT at all, in the context of this assignment it's best to just find another one. But almost any article is available to you via Interlibrary Services, free of charge, if you can wait a few days to a couple of weeks for it to arrive.

Citing the Articles

When citing an article in the text of your presentation or papers, use the CSE Name-Year System (formerly CBE). Examples can be found at this site. A copy of the most recent edition of the style manual is available in the Life Science Library's reference collection (T 11 S386 2006). See the Style Guides page for additional information.

Need Help?

For more information about searching Medline and PubMed, see the Tutorials offered by the Life Science Library.

Or contact the Chemistry Library using our email form.