Environmental Biochemistry CHEM 470

Below is a list of resources helpful in completing the lab assignments for CHEM 470. If you need help in using these resources, please contact the chemistry librarian.

When finding information sources on the internet, you must be selective and evaluate each source individually to ensure credibility and accuracy. Evaluating websites is a question of asking yourself 6 simple questions: Who? What? When? Where? Why? and How?

• How did you locate the information source? From a trusted website? Searching a library database?
• Who authored the source material? Are their qualifications given? Who is responsible for this information?
• What type of data does the source provide? Are the research methods provided?
• Why was the material published? Look for articles that aim to communicate results of scientific studies.
• When was the material published? Is it current?
• Where is the source data published? Is it the website of a respected organization or a commercial website?

Have a look at the How to Evaluate Information Sources handout for more guidelines on evaluating the appropriateness of your web resources.

Below are examples of inappropriate websites and alternative appropriate information sources:

• On the topic of cleaning up uranium contamination with Geobacter bacteria:
  • Inappropriate source of information: Mining bacteria's appetite for toxic waste.
  • Alternative article from PubMed: Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer.
• On the topic of cleaning up mercury spills with transgenic bacteria:
  • Inappropriate source of information: Engineered Bacteria Mop Up Mercury Spills.
  • Alternative article from PubMed: Characterization of mercury bioremediation by transgenic bacteria expressing metallothionein and polyphosphate kinase.

The process of Peer Review is when journals give submitted articles to a panel of experts to review and assess the merit and suitability of the research. This ensures that the conclusions and research methods are held to rigorous scholarly standards. Check out this video prepared by the University of Western Ontario for a more in-depth explanation.

PubMed (MEDLINE) contains abstracts to worldwide biomedical literature.

Medical Subject Headings (MeSH) can be searched to give the most relevant results:

• Choose MeSH Database from the Explore menu (found on the lower right side, below the search box on the home screen). 
• Type in your substance or topic and select Search.
• On the right hand side of the screen there is an Add to search builder button. Select this button, with AND selected from the dropdown menu.
• You can now type in other search terms with AND or hit Search PubMed.
  
  

Try limiting to review articles in PubMed. In the left hand column of the results page, under Article type, click on Review.

This database is provided freely from the National Library of Medicine but must be accessed from the Concordia Library website to see our holdings.

GreenFILE covers many aspects of environmental sciences.

When writing your assignments it is very important to document and cite your information sources properly. The citation style used in chemistry is The American Chemical Society citation style. Check out our ACS guide for examples and instructions.

The following books have been put on reserve at the Vanier Library:

• Alloway, B.J. and Ayres, D.C. Chemical Principles of Environmental Pollution, 2nd ed., 1997.
• Sterner, O. Chemistry, health and environment, 2nd ed., 2010.
• Alexander, M. Biodegradation and Bioremediation, 2nd ed., 1999.
• Manahan, S.E. Environmental Chemistry, 9th ed., 2010.

*All of these readings can be accessed using the Course Reserve System

Sulfotransferases

• Falany, C.N. 1997. Enzymology of Human Cytosolic Sulfotransferases. FASEB J. 11:206-216.
• Negish. M, et al. 2001. Structure and Function of Sulfotransferases. Arch. Biochem. Biophys. 390:149-157.

Glutathione-S-transferases

• Wang, Y. et al. 2008. Structure of an insect epsilon class glutathione S-transferase from the malaria vector Anopheles gambiae provides an explanation for the high DDT-detoxifying activity. Journal of Structural Biology, 164: 228-235.
• Deponte, M. and Becker, K. 2005. Glutathione S-transferase from Malarial Parasites: Structural and Functional Aspects. Methods in Enzymology, 401: 241-253.
• Armstrong, R.N. 1997. Structure, Catalytic Mechanism, and Evolution of the Glutathione Transferases. Chemical Research in Toxiciology 10:2-18.
• Sheehan, D. et al. 2001. Structure, Function and Evolution of Glutathione Transferases: Implications for Classification of Non-mammalian Members of an Ancient Enzyme Superfamily. Biochemical Journal 360:1-16.

Cytochrome P450

• Guengerich, F.P. 2001. Common and Uncommon Cytochrome P450 Reactions Related to Metabolism and Chemical Toxicology. Chemical Research in Toxicology 14:611-624.
• Williams, P.A. et al. 2004. Crystal Structures of Human Cytochrome P450 3A4 Bound to Metyrapone and Progesterone. Science 305:683-686.
• Yano, J.K. et al. 2004. The Structure of Human Microsomal Cytochrome P450 3A4 Determined by X-ray Crystallography to 2.05-ǺResolution. J. Biol. Chem. 279:38091-38094.

Aryl hydrocarbon receptor

• Soshilov, A. and Denison, M.S. 2008. Role of the Per/Arnt/Sim Domains in Ligand-dependent Transformation of the Aryl Hydrocarbon Receptor. J. Biol. Chem. 283:32995-33005.
• Moon, Y.J., Wang, X., and Morris, M.E. 2006. Dietary flavonoids: Effects on xenobiotic and carcinogen metabolism. Toxicology in Vitro. 20:187-210.
• Nguyen, L.P. and Bradfield, C.A. 2008. The Search for Endogenous Activators of the Aryl Hydrocarbon Receptor. Chem. Res. Toxicol. 21:102-116.

Mar regulon

• Barbosa, T.M and Levy, S.B. 2000. Differential expression of over 60 chromosomal genes in Escherichia coli by constitutive expression of MarA. J. Bacteriol. 182:3467-74.
• Vinué, L., McMurry, L.M., and Levy, S.B. 2013. The 216-bp marB gene of the marRAB operon in Escherichia coli encodes a periplasmic protein which reduces the transcription rate of marA. FEMS Microbiol. Lett. 345:49-55.

Drug resistance

• Aller, S.G. et al. 2009. Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding. Science. 323:1718-1722.
• Anderson, C., Hughes, C., Koronakis, V. 2000. Chunnel vision. Export and efflux through bacterial chunnel-tunnels. EMBO Reports. 1:313-8.
• Eswaran, J. et al. 2004. Three's company: component structures bring a closer view of tripartite drug efflux pumps. Current Opinion in Structural Biology. 14:741-747.
• Dawson, R.J.P. and Locher, K.P. 2006. Structure of a bacterial multidrug ABC transporter. Nature. 443:180-185.
• He, X. et al. 2010. Structure of a cation-bound multidrug and toxic compound extrusion transporter. Nature. 467:991-994.
• Pos, K.M. 2009. Drug transport mechanism of the AcrB efflux pump.. Biochimica et Biophysica Acta. 1794:782-793.
• Seeger, M.A. et al. 2006. Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism. Science. 313:1295-1298.
• Lu, M. et al. 2013. Structures of a Na+-coupled, substrate-bound MATE multidrug transporter. Proc. Natl. Acad. Sci. U.S.A. 110:2099-2104.
• Lu, M. et al. 2013. Structural insights into H+–coupled multidrug extrusion by a MATE transporter. Nat. Struct. Mol. Biol. 20:1310-1317.

Organic solvents

• J.L. Ramos, et al. 1997. Mechanisms for solvent tolerance in bacteria. J. Biol. Chem. 272:3887-3890.
• Kieboom, et al. 1998. Identification and molecular characterization of an efflux pump involved in Pseudomonas putida S12 solvent tolerance. J. Biol. Chem. 273:85-91.
• Isken S. and deBont, J.A.M. 1998. Bacteria tolerant to organic solvents. Extremophiles. 2:229-238.

Pathway engineering

• Timmis, K.N., Steffan, R.J., and Unterman, R. 1994. Designing microorganisms for the treatment of toxic wastes. Ann. Rev. Microbiol. 48:525-557.
• Lehrbach, et al. 1984. Enzyme recruitment in vitro: use of cloned genes to extend the range of haloaromatics degraded by Pseudomonas sp strain B13. J. Bacteriol. 158:1025-1032.

Xyl operon

• Marques, S. et al. 1994. Transcriptional induction kinetics from the promoters of the catabolic pathways of the TOL plasmid pWW0 of Pseudomonas putida for metabolism of aromatics. Journal of Bacteriology 176:2517-2524.
• Ramos, J.L., Marques, S., and Timmis, K.N. 1997. Transcriptional control of the Pseudomonas TOL plasmid catabolic operon is achieved through an interplay of host factors and plasmid-encoded regulators. Ann. Rev. Microbiol. 51:341-373.
• Troupel, D. and v.d.Meer, J.R. 2004. Bacterial Transcriptional Regulators for Degradation Pathways of Aromatic Compounds. Microbiology and Molecular Biology Reviews 68:474-500.

Mercury

• Barkay, T., Miller, S.M., and Summers, A.O. 2003. Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiology Reviews. 27:355-384.
• Miller, S.M., Moore, M.J., Massey, V., Williams, C.H., Distefano, M.D., Ballou, D.P., and Walsh, C.T. 1989. Evidence for the participation of Cys558 and Cys559 at the active site of mercuric reductase. Biochemistry. 28:1194-1205.
• Schiering, N., Kabsch, W., Moore, M.J., Distefano, M.D., Walsh, C.T., and Pai, E.F. 1991. Structure of the detoxification catalyst mercuric ion reductase from Bacillus sp. strain RC607. Nature. 352:168-72.
• Rugh, C.L., Wilde, H.D., Stack, N.M., Thompson, D.M., Summers, A.O., and Meagher, R.B. 1996. Mercuric ion reduction and resistance in transgenic Arabidopsis thaliana plants expressing a modified bacterial merA gene. PNAS. 93:3182-3187.
• Rugh, C.L., Senecoff, J.F., Meagher, R.B., and Merkle, S.A. 1998. Development of transgenic yellow poplar for mercury phytoremediation. Nature Biotechnology 16:925-928. 

Metallothionein

• Dallinger, R. et al. 1997. Metallothionein in snail Cd and Cu metabolism. Nature. 388:237-238.

Bioremediation, examples

• Lee, MD, et al. 1998. New perspectives on microbial dehalogenation of chlorinated solvents: Insights from the field. Annual Review of Microbiology. 52:423-452.

Radiation

• Daly, M.J. et al. 2004. Accumulation of Mn(II) in D. radiodurans Facilitates Gamma-Radiation Resistance. Science 306:1025-1028.
• Daly, M.J. 2000. Engineering radiation-resistant bacteria for environmental biotechnology. Current Opinion in Biotechnology. 11:280-285.
• Rajan, R. and Bell, C.E. 2004. Crystal Structure of RecA from  D. radiodurans: Insights into the Structural Basis of Extreme Radioresistance. J. Mol. Biol. 344:951-963.
• Narman, I. et al. 2004. PprA: a novel protein from D. radiodurans that stimulates DNA ligation. Mol. Microbiol. 54:278-285.

Dissimilatory metal reduction

• White, C., Sharman, A.K., and Gadd, G.M. 1998. An integrated microbial process for the bioremediation of soil contaminated with toxic metals. Nature Biotechnology. 16:572-575. 

Arsenic

• Kuroda, M. et al. 1997. Alternate Energy Coupling of ArsB, the Membrane Subunit of the Ars Anion-translocating ATPase. Journal of Biological Chemistry 272:326-331.
• Gladysheva, T.B., Oden, K.L., and Rosen, B.P. 1994. Properties of the Arsenate Reductase of Plasmid R773. Biochemistry. 33:7288-7293.

Antifreeze

• Harding, M.M., Anderberg, P.I., and Haymet, A.D.J. 2003. 'Antifreeze' glycoproteins from polar fish. Eur. J. Biochem. 270:1381-1392.
• Graether, S.P. and Sykes, B.D. 2004. Cold survival in freeze-intolerant insects. Eur. J. Biochem. 271:3285-3296.
• Griffith, M. and Yaish, M.W.F. 2004. Antifreeze proteins in overwintering plants: a tale of two activities. Trends in Plant Science. 9:399-405.

Plants

• Guerinot, M.L. and Yi, Y. 1994. Iron: Nutritious, Noxious, and Not Readily Available. Plant Physiology. 104:815-820.
• Eide, D., Broderius, M., Fett, J., and Guerinot, M.-L. 1996. A novel iron-regulated metal transporter from plants identified by functional expression in yeast. Proc. Nat. Acad. Sci. 93:5624-5628.
• Salt, D.E. et al. 1995. Mechanisms of Cadmium Mobility and Accumulation in Indian Mustard. Plant Physiology 109:1427-1433.
• Jones, D.L. and Kochian, L.V. 1997. Aluminum interaction with plasma membrane lipids and enzyme metal binding sites and its potential role in Al cytotoxicity.. FEBS Letters. 400:51-57.
• De la Fuente, J. M. et al. 1997. Aluminum Tolerance in Transgenic Plants by Alteration of Citrate Synthesis. Science. 276:1566-1568.

Here are a few journals that are important in the field of Environmental Biochemistry.

• Current Opinion in Biotechnology: The library is subscribed to the online version from 1995-today.
• Trends in Biotechnology: The library is subscribed to the online version from 1995-today.
• Nature Biotechnology: The library is subscribed to the online version from 1998-today.

Here is a list of websites useful for completing your assignments:

• Agricultural Network Information Centre
  
  
• ATSDR - Agency for Toxic Substances and Disease Registry
  ASTDR is a federal public health agency of the U.S. Department of Health and Human Services. The easiest way to navigate this site is to go to the A-Z Index in the menu to the left of the page. Also, take a look at the Toxicological Profiles from the Quick Links menu on the right hand side of the page. These are substantial profiles for hazardous substances.
  
  
• Biodegradation Database
  
  
• Directed Evolution
  
  
• Environmental Health Criteria Monographs (EHCs)
  Published by the World Health Organization, this website displays a list of hazardous compounds and their "physical and chemical properties; sources of environmental and industrial exposure and environmental transport, chemobiokinetics and metabolism including absorption, distribution, transformation and elimination; short and long term effects on animals (carcinogenicity, mutagenicity, and teratogenicity); and finally, an evaluation of risks for human health and the effects on the environment."
  
  
• Extension Toxicology Network
  
  
• Global Network of Environment and Technology
  
  
• Hazardous Waste Cleanup Information
  
  
• NIEHS - National Institute of Environmental Health Sciences
  Environmental information provided by one of the U.S. National Institutes of Health. The easiest way to navigate this site is to go to Environmental Health Topics in the Health & Education tab's dropdown menu, and take a look at the A to Z list.
  
  
• PubMed, Genbank, and Genome Resources
  
  
• U.S. Environmental Protection Agency
  This site is an authoritative source on the usage and regulation of compounds in the U.S. and includes links to outside sources of information. The easiest way to navigate this site is to browse through the topics listed under the different tabs at the top of the page (ex. Science & Technology - Substances and Toxics).
  
  
• World Wildlife Fund