Lecture 12 - Nitrogen metabolism Notes | Study Plant Metabolism - Botany

Botany: Lecture 12 - Nitrogen metabolism Notes | Study Plant Metabolism - Botany

The document Lecture 12 - Nitrogen metabolism Notes | Study Plant Metabolism - Botany is a part of the Botany Course Plant Metabolism.
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 Page 1


Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            1 
 
                                                                            
 
Lesson Prepared Under MHRD project “National Mission on 
Education Through ICT” 
Discipline: Botany 
Paper: Plant Metabolism 
National Coordinator: Prof. S.C. Bhatla 
       Lesson: Nitrogen metabolism 
Lesson Developer: Dr. Sunita Yadav 
 Department/College: Department of Botany, Hansraj 
College
 
Lesson Reviewer: Prof. S.C. Bhatla 
Department/College: Department of Botany, University of 
Delhi 
Language Editor: Vinee Khanna 
Department/College: Department of Genetics, University 
of Delhi, South Campus 
Lesson Editor: Dr. Rama Sisodia, Fellow in Botany ILLL 
 
 
  
 
 
Page 2


Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            1 
 
                                                                            
 
Lesson Prepared Under MHRD project “National Mission on 
Education Through ICT” 
Discipline: Botany 
Paper: Plant Metabolism 
National Coordinator: Prof. S.C. Bhatla 
       Lesson: Nitrogen metabolism 
Lesson Developer: Dr. Sunita Yadav 
 Department/College: Department of Botany, Hansraj 
College
 
Lesson Reviewer: Prof. S.C. Bhatla 
Department/College: Department of Botany, University of 
Delhi 
Language Editor: Vinee Khanna 
Department/College: Department of Genetics, University 
of Delhi, South Campus 
Lesson Editor: Dr. Rama Sisodia, Fellow in Botany ILLL 
 
 
  
 
 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            2 
 
 
 
Table of Contents 
Nitrogen Metabolism 
? Introduction 
? Industrial Nitrogen Fixation 
? Atmospheric Nitrogen Fixation 
?   Lightning 
? Photochemical reactions 
? Biological Nitrogen Fixation 
? Historical aspects of nitrogen fixation 
? Biological nitrogen fixation 
? Asymbiotic nitrogen fixation 
? Aerobic nitrogen fixers 
? Facultative nitrogen fixers 
? Anaerobic nitrogen fixers 
? Symbiotic nitrogen fixation 
? Nitrogen fixation requires anaerobic conditions 
? Process of nodulation in legumes 
? Nodulin genes 
? Nodulation genes 
?  Leghemeglobin 
? Nitrogenase enzyme complex  
? General characteristics 
? Structure 
? Azoferredoxin 
? Azomolybdoferredoxin 
? Regulation of Nitrogenase 
? Unassimilated ammonium or nitrate may be dangerous 
? Nitrate assimilation 
? Nitrate reductase 
Page 3


Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            1 
 
                                                                            
 
Lesson Prepared Under MHRD project “National Mission on 
Education Through ICT” 
Discipline: Botany 
Paper: Plant Metabolism 
National Coordinator: Prof. S.C. Bhatla 
       Lesson: Nitrogen metabolism 
Lesson Developer: Dr. Sunita Yadav 
 Department/College: Department of Botany, Hansraj 
College
 
Lesson Reviewer: Prof. S.C. Bhatla 
Department/College: Department of Botany, University of 
Delhi 
Language Editor: Vinee Khanna 
Department/College: Department of Genetics, University 
of Delhi, South Campus 
Lesson Editor: Dr. Rama Sisodia, Fellow in Botany ILLL 
 
 
  
 
 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            2 
 
 
 
Table of Contents 
Nitrogen Metabolism 
? Introduction 
? Industrial Nitrogen Fixation 
? Atmospheric Nitrogen Fixation 
?   Lightning 
? Photochemical reactions 
? Biological Nitrogen Fixation 
? Historical aspects of nitrogen fixation 
? Biological nitrogen fixation 
? Asymbiotic nitrogen fixation 
? Aerobic nitrogen fixers 
? Facultative nitrogen fixers 
? Anaerobic nitrogen fixers 
? Symbiotic nitrogen fixation 
? Nitrogen fixation requires anaerobic conditions 
? Process of nodulation in legumes 
? Nodulin genes 
? Nodulation genes 
?  Leghemeglobin 
? Nitrogenase enzyme complex  
? General characteristics 
? Structure 
? Azoferredoxin 
? Azomolybdoferredoxin 
? Regulation of Nitrogenase 
? Unassimilated ammonium or nitrate may be dangerous 
? Nitrate assimilation 
? Nitrate reductase 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            3 
 
?  Structure 
? Regulation 
? Nitrite reductase 
? Ammonium assimilation 
? Introduction 
? Two alternative pathways 
? Reductive amination by GDH 
? Ammonia incorporation by GS 
? GOGAT or glutamate synthase 
? NADH-GOGAT 
? Fd-GOGAT 
? Transamination reactions 
? Aminotransferases 
? Amino acid biosynthesis 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Page 4


Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            1 
 
                                                                            
 
Lesson Prepared Under MHRD project “National Mission on 
Education Through ICT” 
Discipline: Botany 
Paper: Plant Metabolism 
National Coordinator: Prof. S.C. Bhatla 
       Lesson: Nitrogen metabolism 
Lesson Developer: Dr. Sunita Yadav 
 Department/College: Department of Botany, Hansraj 
College
 
Lesson Reviewer: Prof. S.C. Bhatla 
Department/College: Department of Botany, University of 
Delhi 
Language Editor: Vinee Khanna 
Department/College: Department of Genetics, University 
of Delhi, South Campus 
Lesson Editor: Dr. Rama Sisodia, Fellow in Botany ILLL 
 
 
  
 
 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            2 
 
 
 
Table of Contents 
Nitrogen Metabolism 
? Introduction 
? Industrial Nitrogen Fixation 
? Atmospheric Nitrogen Fixation 
?   Lightning 
? Photochemical reactions 
? Biological Nitrogen Fixation 
? Historical aspects of nitrogen fixation 
? Biological nitrogen fixation 
? Asymbiotic nitrogen fixation 
? Aerobic nitrogen fixers 
? Facultative nitrogen fixers 
? Anaerobic nitrogen fixers 
? Symbiotic nitrogen fixation 
? Nitrogen fixation requires anaerobic conditions 
? Process of nodulation in legumes 
? Nodulin genes 
? Nodulation genes 
?  Leghemeglobin 
? Nitrogenase enzyme complex  
? General characteristics 
? Structure 
? Azoferredoxin 
? Azomolybdoferredoxin 
? Regulation of Nitrogenase 
? Unassimilated ammonium or nitrate may be dangerous 
? Nitrate assimilation 
? Nitrate reductase 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            3 
 
?  Structure 
? Regulation 
? Nitrite reductase 
? Ammonium assimilation 
? Introduction 
? Two alternative pathways 
? Reductive amination by GDH 
? Ammonia incorporation by GS 
? GOGAT or glutamate synthase 
? NADH-GOGAT 
? Fd-GOGAT 
? Transamination reactions 
? Aminotransferases 
? Amino acid biosynthesis 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            4 
 
 
Introduction 
Nitrogen is present in many forms in the biosphere. Although vast quantities of molecular 
nitrogen is present in the atmosphere (77% by volume), it is not available for direct use by 
living organisms. Acquisition of this molecular nitrogen and it’s conversion to ammonium 
(NH
3
) and nitrate (NO
3
-
) accounts for nitrogen fixation. Conversion of inorganic to organic 
nitrogen is carried out by plants mainly. Nucleotides and amino acids (found in nucleic acids 
and proteins) mainly have nitrogen as their principal moiety constituting the prominent 
biochemical compounds in plant cells.  
The process of nitrogen fixation requires a large input of energy because it accounts to the 
production of NH
3 
and NO
3
-
 from nitrogen molecule by breakage of the stable triple covalent 
bond present in the dinitrogen molecule. Both natural and industrial processes contribute to 
the process of nitrogen fixation. 
 
1. Industrial Nitrogen Fixation: This type of fixation contributes to 20% of total 
nitrogen fixed. Nitrogen in combination with hydrogen forms ammonia in the presence of 
high temperature (about 200
?
C) and high pressure (about 200 atmospheres) and a metal 
catalyst (like iron). High activation energy of such a condensation reaction is overcomed by 
such extreme conditions i.e. high temperature and high pressure. 
  
                                  N
2
    +        H
2
                                              2 NH
3 
                            Nitrogen         Hydrogen                                    Ammonia 
 
This reaction is called Haber-Bosch process and serves as an initial trigger for the 
production of industrial and agricultural goods, as illustrated in the following equation:  
             
                                                                                                      O 
                                                                      
              2 NH
3
   +            CO
2
                                                  H
2
N-CO-NH
2 
              
Ammonia       Carbon dioxide                                                Urea 
 
2. Atmospheric nitrogen fixation: This can occur by any of the following two 
methods: 
 
i) Lightning: This form of nitrogen fixation amounts to about 8% of the total nitrogen fixed. 
In the presence of lightning, highly reactive OH
?
, H and O are formed from water vapour 
Page 5


Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            1 
 
                                                                            
 
Lesson Prepared Under MHRD project “National Mission on 
Education Through ICT” 
Discipline: Botany 
Paper: Plant Metabolism 
National Coordinator: Prof. S.C. Bhatla 
       Lesson: Nitrogen metabolism 
Lesson Developer: Dr. Sunita Yadav 
 Department/College: Department of Botany, Hansraj 
College
 
Lesson Reviewer: Prof. S.C. Bhatla 
Department/College: Department of Botany, University of 
Delhi 
Language Editor: Vinee Khanna 
Department/College: Department of Genetics, University 
of Delhi, South Campus 
Lesson Editor: Dr. Rama Sisodia, Fellow in Botany ILLL 
 
 
  
 
 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            2 
 
 
 
Table of Contents 
Nitrogen Metabolism 
? Introduction 
? Industrial Nitrogen Fixation 
? Atmospheric Nitrogen Fixation 
?   Lightning 
? Photochemical reactions 
? Biological Nitrogen Fixation 
? Historical aspects of nitrogen fixation 
? Biological nitrogen fixation 
? Asymbiotic nitrogen fixation 
? Aerobic nitrogen fixers 
? Facultative nitrogen fixers 
? Anaerobic nitrogen fixers 
? Symbiotic nitrogen fixation 
? Nitrogen fixation requires anaerobic conditions 
? Process of nodulation in legumes 
? Nodulin genes 
? Nodulation genes 
?  Leghemeglobin 
? Nitrogenase enzyme complex  
? General characteristics 
? Structure 
? Azoferredoxin 
? Azomolybdoferredoxin 
? Regulation of Nitrogenase 
? Unassimilated ammonium or nitrate may be dangerous 
? Nitrate assimilation 
? Nitrate reductase 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            3 
 
?  Structure 
? Regulation 
? Nitrite reductase 
? Ammonium assimilation 
? Introduction 
? Two alternative pathways 
? Reductive amination by GDH 
? Ammonia incorporation by GS 
? GOGAT or glutamate synthase 
? NADH-GOGAT 
? Fd-GOGAT 
? Transamination reactions 
? Aminotransferases 
? Amino acid biosynthesis 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            4 
 
 
Introduction 
Nitrogen is present in many forms in the biosphere. Although vast quantities of molecular 
nitrogen is present in the atmosphere (77% by volume), it is not available for direct use by 
living organisms. Acquisition of this molecular nitrogen and it’s conversion to ammonium 
(NH
3
) and nitrate (NO
3
-
) accounts for nitrogen fixation. Conversion of inorganic to organic 
nitrogen is carried out by plants mainly. Nucleotides and amino acids (found in nucleic acids 
and proteins) mainly have nitrogen as their principal moiety constituting the prominent 
biochemical compounds in plant cells.  
The process of nitrogen fixation requires a large input of energy because it accounts to the 
production of NH
3 
and NO
3
-
 from nitrogen molecule by breakage of the stable triple covalent 
bond present in the dinitrogen molecule. Both natural and industrial processes contribute to 
the process of nitrogen fixation. 
 
1. Industrial Nitrogen Fixation: This type of fixation contributes to 20% of total 
nitrogen fixed. Nitrogen in combination with hydrogen forms ammonia in the presence of 
high temperature (about 200
?
C) and high pressure (about 200 atmospheres) and a metal 
catalyst (like iron). High activation energy of such a condensation reaction is overcomed by 
such extreme conditions i.e. high temperature and high pressure. 
  
                                  N
2
    +        H
2
                                              2 NH
3 
                            Nitrogen         Hydrogen                                    Ammonia 
 
This reaction is called Haber-Bosch process and serves as an initial trigger for the 
production of industrial and agricultural goods, as illustrated in the following equation:  
             
                                                                                                      O 
                                                                      
              2 NH
3
   +            CO
2
                                                  H
2
N-CO-NH
2 
              
Ammonia       Carbon dioxide                                                Urea 
 
2. Atmospheric nitrogen fixation: This can occur by any of the following two 
methods: 
 
i) Lightning: This form of nitrogen fixation amounts to about 8% of the total nitrogen fixed. 
In the presence of lightning, highly reactive OH
?
, H and O are formed from water vapour 
Nitrogen Metabolism 
 
Institute of Lifelong Learning, University of Delhi                                            5 
 
and oxygen. These free H and O atoms subsequently form nitric acid (HNO
3
) when they 
come in contact with N
2
. HNO
3
 thus formed, falls along with rain on earth surface. 
 
    N
2
           +         O
2
                                            NO 
Nitrogen          Oxygen                                       Nitric oxide 
 
   NO          +        O
2
                                              NO
2 
 
                                                                                                 
H
2
O + O
2 
 
                                                                                                                  
 HNO
3 
                                                                                                               
Nitric acid 
 
 
                                                                   Falls along with rain 
 
ii) Photochemical reactions: This contributes to about 2% of the total nitrogen fixed. This 
kind of reaction leads to the production of nitric acid that subsequently falls along with rain.  
 
              NO          +        O
3
                                            HNO
3 
      Nitric oxide           Ozone                               Nitric acid (falls along with rain) 
 
3. Biological nitrogen fixation: This contributes to about 70% of the total nitrogen fixed. 
This process is carried out mainly by prokaryotic microorganisms like bacteria or blue green 
algae (cyanobacteria) which fix nitrogen into ammonia (NH
3
). This ammonia dissolves in 
water to form ammonium: 
 
          NH
3    
 +      H
2
O                                                      NH
4
+
   +   OH
- 
     Ammonia       Water                                                Ammonium 
 
This process of nitrogen fixation is very critical from agricultural point of view because 
nitrogen fertilizers produced through industrial means hardly ever meet agricultural 
requirements. 
This process can occur either asymbiotically or symbiotically which has been discussed in 
detail later in the chapter. 
 
 
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