Unit 5: The Nitrogen Cycle: Nitrification, Denitrification, And Fixation The nitrogen element possesses a variety of potential oxidation states. It could be +3 in compounds such ammonia, -5 in the nitrate ion, or any of the oxidation states in between. In the nitrogen cycle, nitrogen in the atmosphere enters the food chain through nitrogen-fixing bacteria in the soil and algae in the water. These bacteria then transform molecular nitrogen into ammonium ions (an 8-electron-transfer reaction!). These ammonium ions subsequently are oxidized into nitrites, and eventually these nitrites are oxidized into nitrates by bacteria present in the soil and water. Nitrates then are absorbed by plants through their roots and are used to produce proteins, which can in turn be disseminated through the food chain. Nitrogen also is released into the environment in various forms through the decomposition of dead organisms and through human and animal waste that subsequently are re-used by bacteria. In this unit, you will learn about the function of metal centers in the enzymes involved in the nitrogen cycle.
Unit 5 Time Advisory
This unit should take you approximately 3.5 hours to complete.
☐ Subunit 5.1: 2.5 hours
☐ Subunit 5.2: 0.5 hour
☐ Subunit 5.3: 1 hour
Unit5 Learning Outcomes
Upon successful completion of this unit, the student should be able to:
- Describe the nitrogen cycle, from uptake to the excretion of nitrogen-containing compounds. - Discuss the electron-transfer mechanisms involved in uptake and the incorporation that occurs during nitrogen fixation. - Identify the key enzymes involved in the nitrogen cycle, as well as their functions.
- Reading: The University of Waterloo: Dr. Colin Mayfield’s “Chapter
8: Microbial Ecology of the Nitrogen Cycle”
Link: The University of Waterloo: Dr. Colin Mayfield’s “Chapter 8:
Microbial Ecology of the Nitrogen
Instructions: Please click on the link above to access and read the entire webpage.
This reading discusses the entire nitrogen cycle, including the processes of nitrification, denitrification, and nitrogen fixation. The nitrification process converts ammonium to nitrate via a series of enzymatic steps; while denitrification involves a series of steps in which nitrate is reduced ultimately to N2. This material also provides an explanation for why nitrogen must undergo the nitrogen-fixation process and cannot just be utilized as is from the atmosphere.
Please note that this reading also covers material you need to know for subunits 5.2 and 5.3, found below. When you reach those subunits, you may find it helpful to refer back to this reading to review specific topics.
This reading, including note-taking, should take you approximately 2 hours and 30 minutes to complete.
5.2 Denitrification (Reductase) Note: The material you need to know for this subunit is covered in the reading assigned beneath subunit 5.1, found above. For this subunit, focus on the reading’s description of the processes and enzymes that convert nitrate into nitrogen or ammonia. Spend approximately 30 minutes reviewing this material before moving on to the next subunit of this course.
5.3 Nitrogen Fixation (Nitrogenase) Note: Some of the material you need to know for this subunit is covered in the reading assigned beneath subunit 5.1, found above—in particular, the reading’s description of the metal clusters used in different biological systems. In addition, material pertaining specifically to nitrogenases also has been covered in the readings assigned beneath sub-units 4.3 and 4.3.4 of this course. You may find it helpful to refer back to this previous material as you complete the web media assignment below.
Web Media: The University of Toronto Department of Chemistry: Robert H. Morris, Adrian Lee, and Alen Hadzovic’s “A Tour of Nitrogenase” Link: The University of Toronto Department of Chemistry: Robert H. Morris, Adrian Lee,and Alen Hadzovic’s “A Tour of Nitrogenase” (HTML and Java)
Instructions: Please click on the link above to access and read all the material presented in the online tour of nitrogenase. Please note that this tour requires Java to run; you may need to enable Java on your web browser or download a version of Java to your computer in order to complete this assignment.
This tour provides you with several models of the nitrogenase enzyme and its binding sites. Nitrogenase is actually composed of two enzymes, one Fe-based and the other FeMo-based. These two enzymes work in tandem to transfer electrons. Please proceed through the viewing exercise in order, reading the description for each of the models as you progress.
This web media assignment should take you approximately 1 hour to complete.