1. Unit II Metal ions in Biological systems
Dr. SS. Vutukuru, M.Tech., Ph.D, PG DEM

2. Nitrogen Fixation

3. Sources Lightning Inorganic fertilizers Nitrogen Fixation
Animal Residues
Crop residues
Organic fertilizers

4. Encyclopaedia Britannica, Encyclopaedia Britannica (1998)

5. Forms of Nitrogen Urea  CO(NH2)2 Ammonia  NH3 (gaseous)
Ammonium  NH4
Nitrate  NO3
Nitrite  NO2
Atmospheric Dinitrogen N2
Organic N

6. Global Nitrogen Reservoirs
Metric tons nitrogen
Actively cycled
Atmosphere
3.9*1015 No
Ocean  soluble salts
Biomass
6.9*1011
5.2*108
Yes
Land  organic matter
 Biota
1.1*1011
2.5*1010
Slow

7. Roles of Nitrogen
Plants and bacteria use nitrogen in the form of NH4+ or NO3-
It serves as an electron acceptor in anaerobic environment
Nitrogen is often the most limiting nutrient in soil and water

8. Nitrogen is a key element for
amino acids
nucleic acids (purine, pyrimidine)
cell wall components of bacteria (NAM)

9. Nitrogen Cycle Ammonification/mineralization Immobilization
Nitrogen Fixation
Nitrification
Denitrification

10. Ammonification or Mineralization
NH4
NO2
R-NH2 NO
NO2
NO3

11. Mineralization or Ammonification
Decomposers: earthworms, termites, slugs, snails, bacteria, and fungi
Uses extracellular enzymes  initiate degradation of plant polymers
Microorganisms uses:
Proteases,lysozymes, nucleases to degrade nitrogen containing molecules

12. Plants die or bacterial cells lyse  release of organic nitrogen
Organic nitrogen is converted to inorganic nitrogen (NH3)
When pH<7.5, converted rapidly to NH4
Example:
Urea NH3 + 2 CO2

13. Immobilization The opposite of mineralization
Happens when nitrogen is limiting in the environment
Nitrogen limitation is governed by C/N ratio
C/N typical for soil microbial biomass is 20
C/N < 20 Mineralization
C/N > 20 Immobilization

14. Nitrogen Fixation Energy intensive process :
N2 + 8H+ + 8e ATP = 2NH3 + H2 + 16ADP + 16 Pi
Performed only by selected bacteria and actinomycetes
Performed in nitrogen fixing crops
(ex: soybeans)

15. Microorganisms fixing
Azobacter
Beijerinckia
Azospirillum
Clostridium
Cyanobacteria
Require the enzyme nitrogenase
Inhibited by oxygen
Inhibited by ammonia (end product)

16. Rates of Nitrogen Fixation
N2 fixing system
Nitrogen Fixation (kg N/hect/year)
Rhizobium-legume
Cyanobacteria- moss
30-40
Rhizosphere associations
2-25
Free- living
1-2

17. Bacterial Fixation Occurs mostly in salt marshes
Is absent from low pH peat of northern bogs
Cyanobacteria found in waterlogged soils

18. Nitrification Two step reactions that occur together :
1rst step catalyzed by Nitrosomonas
2 NH O2  2 NO2- +2 H2O+ 4 H+
2nd step catalyzed by Nitrobacter
2 NO2- + O2  2 NO3-

19. Optimal pH is between
If pH < 6.0  rate is slowed
If pH < 4.5  reaction is inhibited

20. Denitrification Removes a limiting nutrient from the environment
4NO3- + C6H12O6 2N2 + 6 H20
Inhibited by O2
Not inhibited by ammonia
Microbial reaction
Nitrate is the terminal electron acceptor

21. Metal ions
Many metal ions have role in biological processes of the body
The ions have different physical and chemical properties
Complex formation
Oxidation states
Minerals in food

22. The most important ions
Ca2+
Mg2+
Fe2+
Cu2+
Zn2+
Co3+
Na+ K+
Role:
1.5-2% of body mass, bones, teeth
Bones and teeth, intracellular activity
Hemoglobin, O2 transfer
Cofactor in enzymes
Cofactor in enzymes,growth, healing
In vitamin B12
Water balance, nerve impulses, fluids inside and outside cells

23. Oxygen transport proteins hemoglobin
Hemoglobin is a tetramer composed of two α and two β subunits
Each subunit contains an iron-porphyrin ring that binds oxygen
Oxygen binding is highly cooperative between each subunit

24. Oxygen transport

25. Hemoglobin as oxygen carrier
In each hemoglobin molecule there are four heme groups
Heme = Fe2+ surrounded by phorphyrin group,
As O2 carrier: O2 binds to Fe2+ as a ligand
Reversible process

26. The transport of oxygen in blood - Haemoglobin

27. Oxygen Transport The resting body requires 250ml of O2 per minute.
We have four to six billion haemoglobin containing red blood cells.
The haemoglobin allows nearly 70 times more O2 than dissolved in plasma.

28. Hemoglobin
Binding of O2 alters the structure

29. Haemoglobin
4 x Haem group
x Polypeptide chain

30. Hemoglobin Oxygen carrier protein 4 subunits = 2 alpha + 2 beta
Normal adult = HbA = a2b2
Four heme groups - iron-porphyrin compound at O2 binding site
Iron containing porphyrin rings, only Fe2+ can bind O2
Each heme combines with one globin protein chain
Molecular weight of hemoglobin is 64,000
Each gm of Hb can carry up to 1.31ml of O2, theoretically up to ml/gm

31. Chemical Binding of Hemoglobin & Oxygen
Hemoglobin combines reversibly with O2
Hemoglobin is the unoxygenated form
Oxyhemoglobin is when O2 combined
Association and dissociation of Hb & O2 occurs within milliseconds
Critically fast reaction important for O2 exchange
Very loose coordination bonds between Fe2+ and O2, easily reversible
Oxygen carried in molecular state (O2) not ionic O2-

32. Haemoglobin Saturation
Haemoglobin saturation is the amount of oxygen bound by each molecule of haemoglobin
Each molecule of haemoglobin can carry four molecules of O2.
When oxygen binds to haemoglobin, it forms OXYHAEMOGLOBIN;
Haemoglobin that is not bound to oxygen is referred to as DEOXYHAEMOGLOBIN.

33. Pathological Ligands of Hemoglobin
Ligands form covalent bonds to the ferrous iron in Hb
These bonds have more affinity to iron than oxygen which binds weakly to Hb
Carbon Monoxide
250 times the affinity than oxygen
Does not dissociate readily
Requires hours to rid body of CO
Nitric Oxide
Binds to Hb 200,000 times more strongly
Hemoglobin binds irreversibly to NO
Used to treat pulmonary hypertension

34. Hemoglobin & Myoglobin
Myoglobin is single chained heme pigment found in skeletal muscle
Myoglobin has an increased affinity for O2 (binds O2 at lower Po2)
Mb stores O2 temporarily in muscle

35. Myoglobin and Hemoglobin
Increases O2 solubility in tissues (muscle)
Facilitates O2 diffusion
Stores O2 in tissues
Hemoglobin
Transports O2 from lungs to peripheral tissues (erythrocytes)

36. Figure 7-17a

37. Sickle-cell

38. Capillary Blockage

39. Porphyrin
Porphyrin rings are biological molecules used in a variety of essential chemical processes
The two most well-known porphyrins are heme and chlorophyll

40. Heme
Because of their large conjugated double bond system, porphyrins typically absorb visible light
Chlorophyll’s green color, heme’s red, and the blue blood of some sea creatures are all a result of this absorbance
Additionally, the 4 nitrogen atoms at the center of the ring are excellent at conjugating metals because of their lone pairs
As a result, porphyrins are a common way to attach metals to proteins

41. Chlorophyll –porphyrins are important in plants, too!
Chlorophyll as a Photoreceptor
Chlorophyll is the molecule that traps this 'most elusive of all powers' - and is called a photoreceptor. It is found in the chloroplasts of green plants, and is what makes green plants, green. The basic structure of a chlorophyll molecule is a porphyrin ring, coordinated to a central atom. This is very similar in structure to the heme group found in hemoglobin, except that in heme the central atom is iron, whereas in chlorophyll it is magnesium.

42. Chrophyll
Porphyrin is also part of the chlorophyll, the key substance for the photosynthesis of green plants, some algae and some bacteria.
Chlorophyll absorbs mainly violet-blue and orange-red light and reflect green colour which give plants their green colour
Several kinds of chlorophyll exist (chl a,chl b etc.). They differ from each other in details of their molecular structure and absorb slightly different wavelengths of light.

44.   Chlorophyll is composed of two parts; the first is a porphyrin ring with magnesium at its center, the second is a hyrophobic phytol tail.
  The ring has many delocalized electrons that are shared between several of the C, N, and H atoms; these delocalized electrons are very important for the function of chlorophyll. 
The tail is a 20 carbon chain stabilizes the molecule in the hydrophobic core of the thylakoid membrane.

45. Copyright © 2005 Pearson Education, Inc
Copyright © 2005 Pearson Education, Inc., publishing as Benjamin Cummings

46. Photosynthesis Overview
Two processes - each with multiple steps
Light reactions
convert solar energy to chemical energy
light energy drives transfer of electrons to NADP+ forming NADPH
ATP generated by photophosphorylation
occur at the thylakoids

47. Photosynthesis Overview
Two processes - each with multiple stages
Calvin cycle
Named for Melvin Calvin who worked out many of the steps in the 1940s
incorporates CO2 from the atmosphere into an organic molecule (carbon fixation)
uses energy from the light reaction to reduce the new carbon to a sugar
occurs in the stroma of the chloroplast

48. Interactions of light with chloroplast matter
Light may be reflected, absorbed, or transmitted by matter
Pigments such as chlorophyll absorb photons of different wavelengths (energy)
Plants are green because red and blue light are absorbed and green light is transmitted and reflected
Light
Reflected
Light
Absorbed
Light
Grana
Transmitted
Light
Chloroplast
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49. Light is composed of particles called photons that act like waves. 
Visible light is also called photosynthetically available radiation (PAR) .
Changes in the wavelength of visible light (PAR) result in a change of color. 
Light with a wavelength of 450 nm is blue while light with a wavelength of 650 nm is red. 

50. 2. Each Cluster of Pigment Molecules is referred to as a PHOTOSYSTEM.
COVERTING LIGHT ENERGY TO CHEMICAL ENERGY
1. The Chlorophylls and Carotenoids are grouped in Cluster of a Few Hundred Pigment Molecules in the Thylakoid Membranes.
2. Each Cluster of Pigment Molecules is referred to as a PHOTOSYSTEM. 
There are Two Types of Photosystems known as PHOTOSYSTEM I AND PHOTOSYSTEM II.
3. Photosystem I and Photosystem II are similar in terms of pigments, but they have Different Roles in the Light reactions.
4. The Light Reactions BEGIN when Accessory Pigment molecules of BOTH Photosystems Absorb Light.
5. By Absorbing Light, those Molecules Acquire some of the Energy that was carried by the Light Waves.
6. In each Photosystem, the Acquired Energy is Passed to other Pigment Molecules until it reaches a Specific Pair of CHLOROPHYLL a Molecules. .

51. Photosystem
Photosystem is composed of the Light Harvesting Complex (LHC) and the reaction center.  The LHC is composed of hundreds of molecules of chlorophylls and accessory pigments.

52. How a photosystem harvests light
When any antenna molecule absorbs a photon, transferred to a particular chlorophyll a in the reaction center
At the reaction center is a primary electron acceptor which removes an excited electron from the reaction center chlorophyll a
Copyright © 2005 Pearson Education, Inc., publishing as Benjamin Cummings

53. Reaction Center Closeup
Absorption of
light boosts
energy of an
electron.
Energy is passed
from molecule to
molecule in the
light-harvesting
complex until it
reaches the
reaction center
Primary
electron
acceptor
Chlorophyll a
molecules
Copyright © 2005 Pearson Education, Inc., publishing as Benjamin Cummings

54. Two Types of Photosystems
Photosystem I
reaction center chlorophyll a molecule
P absorption peak at 700nm
Photosystem II
P680

55. Noncyclic Electron Flow
PS II
PS I
Copyright © 2005 Pearson Education, Inc., publishing as Benjamin Cummings

56. A mechanical analogy for the light reactions
1) Photons of light boost
energy of electrons.
2) Energy is extracted from
electrons in the electron
transport chain and
used for ATP synthesis.
3) Another photon boosts
energy of an electron
which ultimately is
transferred to NADPH 1) 2) 3)
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57. Cyclic electron flow P700 Ferridoxin • No O2 generated
• No NADH generated
• Only ATP generated
P700
cyclic photophosphorylation
Copyright © 2005 Pearson Education, Inc., publishing as Benjamin Cummings

58. Light (dependent)Reactions
Happen ONLY in sunlight
Hence they depend on light!
Light is absorbed by chlorophyll molecules
The energy generates molecules of ATP
Image from: Biology 11: College Preparation. Pg 74. Nelson, Toronto

59. Summary
Image from: Biology 11: College Preparation. Pg 74. Nelson, Toronto