BCH 467: Analytical Biochemistry Library Lab

In this section we'll see the difference between primary and secondary literature, what type of information may be found in each and which resources to use to find this type of literature. 

In biochemistry, the primary literature reports on experimental results and almost always appears in scholarly journals.  

Identifying a primary article is fairly easy, in addition to article reporting on the results of an experiment, the format of the article follows the typical pattern of most of the scientific literature. The article will contain, in this order:

1. Bibliographic Information plus an Abstract
   Bibliographic information includes the title of the article, authors, journal title and journal volume, pages and date, followed by an abstract or summary of the article.  This format has been used since the mid-20th century; previously, journal articles did not have an abstract and the bibliographic information usually consisted of just the article title and the author names (the journal title, if it appeared at all, was a "running title" in either an upper or bottom corner of the page). 
    
2. Introduction and Literature Review
   Explanation of what has been studied and why. In some cases the introduction also includes the literature review in which the authors describe what has been previously published on this topic; in other cases, literature review is placed right after the introduction under its own heading.  
    
3. Methodology and Instrumentation
   Description of the experiment's protocol or process; if a specific instrument was used the make/model of the device might also be included.  
    
4. Data Presentation
   The experiment's results and the analysis thereof.  Could also include discussion of problems encountered during the experiment and possible solutions. 
    
5. Conclusions
   Summary of what was discovered and what additional studies are needed.
    
6. References 
   Previously published literature, mentioned within the article, is listed in the preferred citation style of the journal . 
    

Examples of primary biochemical literature; note that each is reporting on an experiment and each is outlined as described above: 

• Ros, A., Faupel, M., Mees, H., van Oostrum, J., Ferrigno, R., Reymond, F., Michel, P., Rossir J.S., and Girault, H.H. (2002)  Protein purification by off-gel electrophoresis. Proteomics 2, 151-156
   
• Tokarski, C., Fillet, M., and Rolando, C. (2011) Improved gel electrophoresis matrix for hydrophobic protein separation and identification. Anal. Biochem. 410, 98-109
   
• Pumma, S., Kaltgrad, E., and Finn, M.G. (2005)  “Clickable” Agarose for Affinity Chromatography. Bioconjugate Chem. 16, 1536-1541

To find the primary literature, use the  "Literature Indexes" page listed under  Section 4: Resources.  

The term "secondary literature" refers to a variety of document types.  For the purposes of this course,  we'll define secondary literature as documents that contain commentary about, or analysis of, the primary literature or documents that summarize the knowledge of a specific topic.   The secondary literature does not present new knowledge, instead it takes existing knowledge (aka the primary literature), determines the relationships and reworks the information into a single, cohesive and understandable document.    

Examples of secondary literature includes encyclopedia articles, handbooks and scholarly review articles: 

• Encyclopedia article
  • McGregor, E., and Dunn, M.J. (January 15, 2005) Basic Techniques and approaches: Two-dimensional gel electrophoresis (2-DE).   Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics.  10.1002/047001153X.g30240
     
• Handbook 
  • Hardin, C.C., and Knopp, J.A. (2013) Biochemistry - Essential Concepts. Oxford University Press, N.Y.
     
• Review Articles
  • Jones, S., and Thornton, J.M. (1995)  Protein-protein interactions: A review of protein dimer structures. Prog. Biophys. Mol. Biol. 63,  31–59, 61–65
     
  • Mateo, C., Palomo, J.M., Fuentes, M., Betancor, L., Grazu, V., Lopez-Gallego, F., Pessela, B.C.C., Hidalgo, A., Fernandez-Lorente, G., Fernandez-Lafuente, R., and Guisan, J.M. (2006) Glyozyl agarose: a fully inert and hydrophilic suport for immobilization and high stabilization of proteins. Enzyme Microb. Technol. 39, 274–280
    Note that even though the word "review" is not in the title of the article, the content of the article is indeed a review.  

To find secondary literature, use the "Background Information" and "Literature Indexes" pages under Section 4: Resources..

Click on the titles of the following references to view the full text. Answer the following questions about each article:

• Is the article a primary source (knowlege gained through direct observation) or a secondary source (knowledge gained from other sources) and why?
• Is the article scholarly or a news item about the industry? 

Articles: 

1. Ahn, T., Yim, S.K., Choi, H.I., and Yun, C.H. (2001)  Polyacrylamide gel electrophoresis without a stacking gel: use of amino acids as electrolytes.  Anal. Bioch. 291, 300-303
    
2. Anon.(Sept 2005) Replacing electrophoresis.  R&D 47.9, 41  
    
3. Maddox, J. (1990) Understanding gel electrophoresis. Nature 345, 381
    
4. Meldolesi, J., and Covo, D. (1972)  Composition of cellular membranes in the pancreas of the guinea pig. IV: Polyacrylamide gel electrophoresis and amino acid composition of Membrane Proteins.  J. Cell Biol. 55, 1-18
    
5. Tran, N.T., Ayed, I., Pallandre, A., and Taverna, M. (2010) Recent innovations in protein separation on microchips by electrophoretic methods: an update. Electrophoresis 31, 147-173

Move on to Section 4: Resources