BIO-INORGANIC CHEMISTRY

This book covers material that could be included in a one-quarter or one-semester course in bioinorganic chemistry for graduate students and advanced undergraduate students in chemistry or biochemistry. We believe that such a course should provide students with the background required to follow the research literature in the field. The topics were chosen to represent those areas of bioinorganic chemistry that are mature enough for textbook presentation. Although each chapter presents material at a more advanced level than that of bioinorganic textbooks published previously, the chapters are not specialized review articles. What we have attempted to do in each chapter is to teach the underlying principles of bioinorganic chemistry as well as outlining the state of knowledge in selected areas. ​ ​ We have chosen not to include abbreviated summaries of the inorganic chemistry, biochemistry, and spectroscopy that students may need as background in order to master the material presented. We instead assume that the instructor using this book will assign reading from relevant sources that is appropriate to the background of the students taking the course. ​ ​ For the convenience of the instructors, students, and other readers of this book, we have included an appendix that lists references to reviews of the research literature that we have found to be particularly useful in our courses on bioinorganic chemistry.

4. Ionophores are low molecular weight natural products which dissolve in the plasma membrane or intracellular membranes of cells and make the membrane permeable to specific ions. 5. Once, the ionophore senses the presence of a cation a cycle of operations is initiated as shown in the following table.
Where I -refer the ionophore MI+-cation-carrier complex 1. The first stage is the formation of complex between cation and ion carrier.
a. In complex formation, the ion forms are co-ordination complex with the ionophore in which there is a well-defined ratio (typically 1:1) of ion to ionophore.
b. The ionophore wraps around the ion so that the ion exists in the polar interior of the complex, while the exterior is predominantly hydrophobic in character.
c. The ionophore molecule essentially acts as the solvent for the ion, replacing the aqueous salvation cell (H 2 O molecule) that normally surrounds the ion.
2. In the second stage, diffusion of the cation-carrier complex through the membrane is carried out.
3. In the third stage, the cation is released. This step regulates the free ionophore for further cation transport.
Transport of K + by Monensin ionophore is shown below. The transport of K + from a lower concentration side to a higher concentration side (active transport) of Monensin is visualized as below. The process involves cation transport coupled with proton transport. Ionophores are a class of compounds that form complexes with specific ions and facilitate their transport across cell membranes.
An ionophore typically has a hydrophilic pocket (or hole) that forms a binding site specific for a particular ion. Some, ionophores are synthesized by microorganisms to import ions into their cells.
2. The Na/K pump's job is to move potassium ions into the cell while simultaneously moving sodium ions out of the cell. (The sodium potassium pump uses active transport to move molecules from a high concentration to a low concentration).
3. This pump is powered by ATP (Adenosine triphosphate). For each ATP that is broken down, 3 sodium ions move out and 2 potassium ions move in. In order to move the ions (Na + /K + ) against their gradients, energy is needed. This energy is supplied by ATP. 4. Sodium ions bind to the pump and a phosphate group from ATP attaches to the pump, causing it to change its shape. 5. In this new shape, the pump releases the three sodium ions and now binds two potassium ions. Once the potassium ions are bound to the pump, the phosphate group detaches. 6. This in turn causes the pump to release the two potassium ions into the cytoplasm. The sodium-potassium pump is an anti-porter transport protein. 7. The sodium potassium pump is vital to numerous bodily processes, such as nerve cell signaling, heart contractions and kidney functions. The Na/K pump is a specialized type of transport protein found in your cell membranes.
8. The sodium -potassium pump is the integral in maintaining the acid-base balance as well as in healthy kidney function. Energy is derived from pumping sodium outside the cell, where it becomes concentrated, wanting to push its way back in. This energy is used to remove acid from the body.
9. The sodium-potassium pump is an important contributor to action potential produced by nerve cells.
10. This pump is called a P-type ion pump because the ATP interaction phosphorylates the transport protein and causes a change in its conformation.

Metallo Porphyrins:
Porphyrins are a group of heterocyclic macrocycle organic compounds composed of four pyrrole subunits with conjugated double bonds interconnected at their α carbon atoms via methane bridge (=CH-).
1. It is the combination of metal ion with porphyrin ring.
2. In general, the porphyrins complex with dipositive metal ions to form metal porphyrin complexes.
3. The hole in the centre of the porphyrin ring is ideal for accommodating metals of the first transition series.
4. The porphyrin system is fairly rigid, because of the delocalization of the π electrons in the pyrrole rings. 5. The metal (Ni) -N bond distance is approximately 193-196 pm in Ni porphyrin. 6. In Fe2 + porphyrins the bond distance is about 2 pm (picometer).
7. If the size of the metal is too small, the ring becomes ruffled to allow closer approach of the nitrogen atoms to the metal.
8. If the size of the metal is too large, it cannot fit into the hole and since it is above the plane of the ring.

Physical And Chemical Properties:
1. Small variations in properties of the compound are possible by varying the substituents on the periphery.

2.
Porphyrin is a good σ donor and also an effective π acceptor.
3. Fe can undergo redox reaction depending on the environment. The trace minerals are iron, manganese, copper, iodine, zinc, cobalt, fluoride, and selenium. These minerals play important nutritional role. The deficiency of these elements causes disease and it can even result in death. The excess concentration of these elements in the body will produce toxic effect.

Biological Importance Of Iron (Fe):
• Iron plays a central role in almost all living cells.
• Iron is used in red blood cells to carry oxygen to the tissues and is also a critical component of many metabolic proteins and enzymes.
• A healthy adult needs 10 to 18 mg of iron each day in the intake of food. The RDA of iron for men is 8 mg, for women 18 mg, and for pregnant women 27 mg.
• Iron is found in the body in the form of heme iron and non-heme iron.
• Heme iron is bound within a ring-like molecule called porphyrin. Heme iron is present in red blood cells.
• Non-heme iron such as iron-sulfur cluster proteins are used in energy production and other metabolic functions.
• Iron deficiency anemia is a condition where a lack of iron in the body leads to a reduction in the number of red blood cells.

The Most Common Symptoms Include:
• tiredness and lack of energy (lethargy) • shortness of breath • noticeable heartbeats (heart palpitations) • a pale complexion

Less Common Symptoms Include:
• headache • an altered sense of taste • feeling itchy • hair loss Ferrous gluconate used in the treatment of anemia. It has a significant role in respiration and photosynthesis.

Biological Importance Of Zinc (Zn):
• Zinc plays multiple roles in the body. It is involved in many cellular metabolic processes and is used in growth and development, the immune system, neurological function, and reproduction.
• It is a trace element and an adult should have 10 to 15 mg in the body.
• It also forms a structural part of cell membranes and is a component of the zinc finger proteins, which act as transcription factors.
• Zinc also supports normal growth and development during pregnancy, childhood, and adolescence and is required for proper sense of taste and smell.
• A daily intake of zinc is required to maintain a steady state because the body has no specialized zinc storage system.
• Zinc deficiency is characterized by growth retardation, loss of appetite, and impaired immune function.

Biological Importance Of Magnesium (Mg):
• Magnesium is an essential mineral and electrolyte that plays a role in many bodily processes, including energy production, bone and teeth structure, muscle function, nerve function, DNA replication and RNA and protein synthesis.
• These ions activate many of the enzymes that control the addition and removal of phosphate groups from compounds in the cell.
• Magnesium ions forms the central metal ion of the chlorophyll molecule, which traps the energy from the sunlight in the process of photosynthesis and which gives green colour to the plants.
• Early symptoms of magnesium deficiency can include nausea and vomiting, loss of appetite, tiredness, and weakness.
• Although many people are not getting enough magnesium, deficiency is rare, and symptoms usually indicate an underlying health condition.
• Too much of magnesium in the body decreases muscle and nerve response, and high levels can produce local or general anesthesia and paralysis.

Biological Importance Of Cobalt (Co):
• Cobalt is an essential trace element that is an integral part of vitamin B12, which is essential in the metabolism of folic acid and fatty acids.
• Cobalt is involved in the production of red blood cells and is important for the proper functioning of the nervous system as it can help in creating a myelin sheath.
• It is the component of vitamin B12 includes the metabolism of carbohydrates, fats, etc., • Cobalt that we need is obtained from dairy products and meat.
• A lack of cobalt in the diet results in a disease called pernicious anemia which produces symptom of fatigue and general weakness.
• Too much vitamin B12, in the diet will stimulate the production of too many erythrocytes, producing a condition called polycythemia.

Biological Importance Of Molybdenum (Mo):
• Molybdenum is an essential nutrient. Its main function is in removing toxins particularly from the metabolism of sulfur containing amino acids.
• Molybdenum participates in the energy transfer reactions in the cell.
• Molybdenum helps with: energy production, by breaking down some of the amino acids; cell protection, by activating antioxidants; and waste removal, by metabolizing toxins that can be excreted in urine.
• It is necessary for the function of certain intestinal enzymes.
• The chief role of molybdenum is to activate nitrate reductase enzyme during nitrogen metabolism.
• Molybdenum participates in the energy transfer reactions in the cell.

The Role Of Sodium (Na) In Biological Activity:
• Sodium plays a key role in the regulation of blood volume, blood pressure, osmotic balance and maintains a constant pH.
• It is main base of the body.
• Sodium is an essential electrolyte that helps maintain the balance of water in and around your cells.
• It is important for proper muscle and nerve function.
• It also helps maintain stable blood pressure levels.
• Insufficient sodium in your blood is also known as hyponatremia.
• It's regulated in the body by your kidneys, and it helps control your body's fluid balance.
• A person needs 1-2 grams of sodium daily in his diet.
• It helps in maintaining the peripheral resistance of blood vessels.

The Role Of Potassium (K) In Biological Activity:
• Potassium is a mineral that plays many important roles in the body.
• Potassium is most commonly used for treating and preventing low potassium levels, treating high blood pressure, and preventing stroke.
• Potassium helps your nerves and a muscle "talk" to each other, moves nutrients into and waste out of your cells, and helps your heart function.
• Food sources of potassium include fruits (especially dried fruits), cereals, beans, milk, and vegetables.
• Average daily requirement of potassium in an adult is 4 g.
• It helps your kidneys to control your blood pressure by controlling the amount of fluid stored in your body. The more fluid, the higher your blood pressure.
• Potassium deficiency is known as hypokalemia.
• Neutralize the effect of organic acids.

The Role Of Calcium (Ca) In Biological Activity:
• Calcium is an essential element in living organisms. It plays an important role in the metabolism of nitrogen in some plants where a deficiency of calcium leads to poor absorption of nitrogen.
• Calcium is the fifth most common element in the body.
• Its major function in building and maintaining bones and teeth, calcium is important in the activity of many enzymes in the body.
• The regulation of heartbeat and clotting of blood are all dependent on calcium.
• They play an important role in signal transduction pathways, where they act as a second messenger, in neurotransmitter release from neurons, in contraction of all muscle cell types, and in fertilization.
• Almost all of the calcium in the body is stored in bone.
• Calcium is used to help blood vessels move blood throughout the body and to help release hormones and enzymes that affect almost every function in the human body.
• It gives nutrients to the development of root hairs.
• Average daily requirement of calcium in an adult is 1000 mg.
• Calcium is found in dairy products, broccoli, cabbage, kale, tofu, sardines and salmon.
The Role Of Phosphorus (P) In Biological Activity: • Potassium forms the sugar-phosphate backbone of DNA and RNA. It is important for energy transfer in cells as part of ATP (adenosine triphosphate) and is found in many other biologically important molecules.
• Phosphorus also has an important role in vertebrates, whose bones and teeth contain apatite, a highly stable phosphate mineral.
• It plays an important role in how the body uses carbohydrates and fats.
• It is also needed for the body to make protein for the growth, maintenance, and repair of cells and tissues.
• Phosphorus is found in high amounts in protein foods such as milk and milk products and meat and alternatives, such as beans, lentils and nuts.
• Phosphorus also plays an important structural role in nucleic acids and cell membranes.
• It is involved in the body's energy production.
• Our body absorbs less phosphorus when calcium levels are too high, and vice versa.
• Together with calcium, phosphorus provides structure and strength.

Electron Transfer In Iron-Sulphur Proteins:
There are several non heme iron sulphur proteins that are involved in electron transfer reactions. They contain distinct iron-sulphur clusters composed of iron atoms, sulfhydryl group from cysteine residues and inorganic sulphur atoms.
Sulphur clusters are found in a variety of metalloproteins, such as the ferredoxins, NADH dehydrogenase and etc. Iron-sulphur clusters are best known for their role in the oxidation-reduction reactions of electron transport in mitochondria and chloroplasts. Both Complex I and Complex II of oxidative phosphorylation have multiple Fe-S clusters. There are several types of non-heme protein involved in electron transfer.

Rubredoxin:
1. Rubredoxins are low molecular weight iron containing proteins found in anaerobic bacteria.
2. These contain only one Fe atom; this single Fe atom is at the centre of tetrahedron of 4 cysteine sulphur atoms.
3. It does not contain inorganic sulphur atom. It is abbreviated Fe (I) so where S stands for inorganic sulphur.
4. Rubredoxins perform one-electron transfer processes. The central iron atom changes between the +2 and +3 oxidation states. In both oxidation states, the metal remains high spin, which helps to minimize structural changes.
5. This iron-sulphur protein is an electron carrier, and it is easy to distinguish its metallic centre changes, the oxidized state is red in colour (due to a ligand metal charge transfer), while the reduced state is colour less.

Ferredoxin:
Ferredoxins are small proteins containing iron and sulphur atoms organized as iron-sulphur clusters. These biological "capacitors" can accept or discharge electrons, with the effect of a change in the oxidation state of the iron atoms between +2 and +3. In this way, ferredoxin acts as an electron transfer agent in biological redox reactions. Ferredoxins can be classified according to the nature of their iron-sulphur clusters.

Plant type:
1. A group of ferredoxins, originally found in chloroplast membranes, has been termed "chloroplast-type" or "plant-type". 5. It has a bridged structure FeIIS 2 as shown below.

Its active center is a [Fe
6. It acts as the electron acceptor associated with Photosystem I in photosynthesis. It accepts an electron and is reduced, giving it the capacity to pass on those electrons as part of the electron transport process.

Bacterial type:
1. A group of Fe 4 S 4 ferredoxins originally found in bacteria has been called as bacterial type.
2. It consists of a cubane like clusters of 4 iron atoms, 4 inorganic sulphur atom and 4 cysteine ligands.

The [Fe 4 S 4 ] ferredoxins may be further subdivided into low-potential and
high-potential ferredoxins.
Dioxygen Binding: 1. Hemoglobin is a tetrameric protein; mb is a monomeric protein having a polypeptide chain where as it has one heme group which consists of four subunits 2α-subunit and 2β-subunit.
2. The capacity of hemoglobin to bind the oxygen depends on the prosthetic (non-protein component) group called heme.
3. The heme group is responsible for the distinctive red colour of blood.
4. The heme group consists of an organic component and a central iron atom.

The organic component called porphyrin is made up of 4 pyrrole rings linked
by methane bridges to form a tetrapyrrole ring.
6. The iron atom lies in the centre of the porphyrin, bonded to the four pyrrole nitrogen atoms.
7. The iron can form two additional bonds, one on each side of the heme plane.
These binding sites are called 5 th and 6 th co-ordination sites.
8. The 5 th co-ordination site is occupied by the imidazole ring of a histidine residue from the protein.
9. The deoxy hemoglobin present in the 6 th co-ordination site remains unoccupied.
10. The Fe 2+ -N bond length is 2.18 Ǻ which is much greater than the mean radius 12. This movement of Fe (II) causes the coordinated histidine to move towards the porphyrin plane.
13. Four methyl groups, 2 vinyl groups and 2 iso propionate side chains are attached.
14. The active sites of both hemoglobin and Myoglobin contain the heme group.
Oxygen Transport And Utilisation: 1. The oxygen that we need for survival is transported from the lungs to peripheral tissues by hemoglobin.
2. Hemoglobin is densely packed in our red blood cells. 6. The pigment with molecular oxygen is called oxy hemoglobin.
7. As the blood circulates to the periphery, the small amount of dissolved oxygen is consumed first by cells, organs and tissues which begin a sequential release of heme bound oxygen.
8. The pigment without oxygen is called as deoxy hemoglobin.
9. During the release of oxygen, the hemoglobin tetramer undergoes some intramolecular conformational changes, called co-operativity.
10. As a result of co-operativity once the 1 st oxygen has been released, the releasing of the 2 nd oxygen is facilitated.
11. After the release of the 2 nd oxygen it undergoes some conformation changes which facilitate the release of 3 rd oxygen.
12. Co-operativity is an important phenomenon that permits the occupying and releasing of large amounts of oxygen.

Biological Dioxygen Carriers: (Other Than Hemoglobin And Myoglobin)
Hemerythrin: 1. Hemerythrin is an oligomeric non-heme protein responsible for oxygen transport in the marine invertebrates.
2. Myohemerythrin is a monomeric O 2 -binding protein found in the muscles of marine invertebrates. 9. Another oxygen containing pigment is hemocyanin. It is found in many marine species.

Hemerythrin and
10. The polypeptide chain must have a molecular weight between 50000 -75000.
11. The Cu is in +1 oxidation state in the deoxy form and it is diamagnetic in nature and so it is colour less.
12. The Cu is in +2 oxidation state in the oxy form and it is paramagnetic in nature and so it is blue in colour.
13. The dioxygen binding site appears to be a pair of copper atoms, each bound by 3 histidine residues.
14. It means oxy hemocyanin binds with oxygen because of which the Cu gets oxidized from +1 to +2. An empty cavity exists between the Cu atoms.
15. If the hemocyanin contains n number of Cu centres then it will contain n/2 of O 2 molecules. It is also called as oxo species.

Structure And Function Of Hemoglobin:
1. Hemoglobin is a tetramer with a molecular weight of 64,000 Daltons (64,458 g/mol) and contains 4 heme groups bound to protein chains.
2. Two of the chains are labeled as β -have 146 amino acids and the other two are labelled as α which have 141 amino acids.
3. As per Perutz mechanism the iron in deoxy heme having high spin Fe (II) configuration.
4. The radius of high spin Fe 2+ is too large to fit within the plane of the porphyrin nitrogen atoms. Also, the Fe (II) -N bond length in high spin is 218pm which is much greater than the mean radius 205 pm of the porphyrin cavity.
5. Hence, the iron atom is forced to sit about 80 pm above the centre of the heme group towards the apically coordinated histidine ring.
6. Oxygenation of hemoglobin results in two of the heme groups moving about 100 pm towards each other while two others separate themselves by about 700 pm. It means that one αβ half of the molecule rotates 15° relative to the other half. This movement is responsible for the co-operative effects observed.

7.
The deoxy form is called as 'T' state and that of oxy form is 'R' state.
8. The co-ordination of the dioxygen molecule as a sixth ligand causes spin pairing to take place on the iron atom. Since the radius of the low spin Fe (II) is about 17 pm smaller than high spin Fe (II). The Fe-N bond distance will relatively show a reduction in distance to an extent of 200 pm and hence the low spin iron atom in the porphyrin cavity. Hence, co-ordination with oxygen will therefore cause the iron atom to pull about 80 pm into the plane of the heme group.
9. Due to the movement of the iron atom into the cavity, which also pull the imidazole group of the histidine residue attached to the iron atom and the tertiary structure of the protein chain of which it takes part will be rather drastically altered.
10. The above movement of the protein chain of another heme group to react.
When the fully saturated hemoglobin molecule with four O 2 molecules reaches the tissues, the whole sequence of reactions discussed above will be reversed.

Comparison Of Myoglobin (Mb) And Hemoglobin (Hb)
Myoglobin Hemoglobin

Physiology Of Myoglobin And Hemoglobin:
1. Hemoglobin and Myoglobin are two important biomolecules which are involved in oxygen transport and storage in bio systems.

Hemoglobin transports oxygen from lungs and the oxygen are transferred to
Myoglobin for use in respiration. 11. If one oxygen molecule is present in general, it will dissociate more readily than from a highly oxygenated species. So, this results in a sigmoid curve for oxygenation of hemoglobin from the above figure. 12. This effect favours oxygen transport and it helps the hemoglobin gets saturated in the lungs and deoxygenated in the capillaries.

Photosynthesis:
1. Photosynthesis is the synthesis of carbohydrates by the green organs of a plant in the presence of sunlight.
2. CO 2 and H 2 O are taken from the air and soil respectively, oxygen being the by-product.
3. Electrons for the reduction of CO 2 are obtained from water (i.e.) a reduced (NaDPH 2 ) substance is produced which later reduces CO 2 .

Process In Photosystem II:
The copy warned the Little Blind Text, that where it came from it would have been rewritten a thousand times and everything that was left from its origin would be the word.

Process In Photosystem I:
• In the Photosystem I, by absorbing energy of photon, p-700 gets excited.
• High energy electrons released from photo system I, are accepted by the substance iron-sulphur protein complex designed at A (FeS).
• From the reduced A (FeS) these electrons are accepted by oxidised ferredoxin (Fd) by accepting this electrons Fd is reduced.
• From reduced Fd electrons are taken by FAD which is reduced to FAD 2 from the reduced FAD electrons are accepted by NADP and it is reduced to NADPH 2 .
• The hydrogen attached to NADPH 2 is used for converting CO 2 to carbohydrates. This process is repeated.

Chlorophyll And Photosynthetic Reaction Centre:
1. In photosynthetic reaction, the reaction centre is a protein with a molecular weight of about 1, 50,000.
2. The heart of the reaction centre is a pair of chlorophyll molecules referred as spectral pair.
3. The special pair on conduct with one other through the overlap of one of the pyrrole rings in each molecule.
4. In addition, an acetyl group on each molecule co-ordinates to the magnesium atom of the other.
5. All photosynthetic systems contain one or more of the green pigments called chlorophyll.
6. Chlorophyll's are tetra pyrroles of the porphyrin family.

7.
In the active sites of the chlorophyll pigment, a Mg 2+ ion is co-ordinated by the 4 pyrrole Nitrogen atoms of the porphyrin ring system at a distance of about 0.3 to 0.5 A° above the macrocycle plane.
8. The methylidine carbon atom between the pyrrole rings III and IV is connected with the C 6 carbon atom of the pyrrole ring III through HC [COOCH 3 ] (C=O) moiety to form a cyclopentanone ring.
9. The long phytyl chain attached to the C 7 carbon atom of the pyrrole ring IV.
10. The complete parent system I to IV is called porphyrin.
11. Chlorophyll absorbs light of low energy in the far-red region near 700.
12. The exact wavelength of maximum absorption depends upon the nature of substituents on chlorophyll.

Chapter 4 Advanced Bio-Inorganic Chemistry
Enzymes: 1. Enzymes are in general globular proteins.
2. It is a macromolecular biological catalyst. They are responsible for thousands of metabolic processes that sustain life.
3. Enzymes are generally accelerating both the rate and specify the metabolic chemical reaction.

4.
Enzymes are specific to their substrate. Specificity is determined by their active site.
5. Normally increasing the temperature make molecules to react faster.
6. Biological systems are very sensitive to temperature changes.
7. Enzymes can increase the rate of a reaction without increasing temperature.
8. They do this by lowering the activation energy. They create a new reaction pathway a "Short-Cut".
9. Enzymes controlled reactions 108 to 1011 times faster than corresponding non-enzymatic reaction.

Lock and key Hypothesis:
1. The Lock and key model of enzyme action, proposed earlier this century, proposed that the substrate was simply drawn into a closely matching cleft on the enzyme molecule.
2. Fit between the substrate and the active site of the enzyme is exact. Like a key fit into a lock precisely. This temporary structure is called the enzymesubstrate complex formed.
3. The substrate shape must be compatible with the enzymes active site in order to fit and be reacted upon.
4. The enzyme modifies the substrate. In this instance the substrate is broken down, releasing two products.
Enzymes are catalysts. Most are proteins. Enzymes bind temporarily to one or more of the reactants, the substrate of the reaction they catalyze. In doing so, they lower the amount of activation energy needed and thus speed up the reaction.

Examples:
Catalase: It catalyzes the decomposition of hydrogen peroxide into water and oxygen.
Vitamin B12: 1. Vitamin B 12 is a water-soluble vitamin involved in the metabolism of every cell of the human body. It is a co-factor in DNA synthesis and in both fatty acid and amino acid metabolism.
2. Vitamin B 12 is also known as cobalamin, cyanocobalamin, methyl cobalamin etc., used for all compounds containing a corrin nucleus.
3. The structure of vitamin B 12 is based on a corrin ring, which is nearly planar, macrocyclic ring like the porphyrin system found in hemes, chlorophylls and cytochromes.

Metalloproteins:
Proteins which contain a metal atom such as iron, copper, magnesium, zinc etc as an integral part of the structure are called metalloproteins. There are two types of metalloproteins:

Heme Proteins:
These are metalloproteins containing the heme group. Heme is the prosthetic group consisting of a porphyrin ring chelated to an iron atom. The heme proteins are coloured and hence called chromo proteins.

Blue copper proteins:
These are metalloproteins which contain copper as the active site. Examples are stellacyanin, platocyanin and azurin. These are Cu (II) complexes which functions as electron transfer redox systems. Each of these has pseudo tetrahedral (between tetrahedral and square-planar) geometry. The Cu (I)/ Cu (II) centre in these systems is ideally adapted for electron exchange as it involves no change in spin state.
The blue copper proteins occur in some bacteria known as cyanobacteria (also called blue-green algae). Some of these species are free-living, others live in close association with plants. Some of them convert the atmospheric nitrogen into nitrogen compounds hence used as biofertilizers.

Metalloenzymes:
1 Carboxy Peptidase: 1. Carboxy peptidase is a pancreatic enzyme that cleaves carboxyl terminal amino acid from a peptide chain by hydrolysing the amide linkage.
2. The zinc ion is bound in a distorted tetrahedral environment by two histidine nitrogen atoms and one atom of oxygen from a glutamic carbonyl group.
3. The fourth co-ordination site is free to accept a pair of electrons from the donor atom in the substrate to be cleaved.
4. Co-ordination of water to Zn 2+ may enhance the rate of equilibrium between H 2 O and the OHnucleophile. 5. Zn 2+ may serve as a Lewis acid catalyst by co-ordination to peptide carbonyl group and thereby reduce the electron density at its carbon atom and promotes hydrolysis.
6. The carbonyl oxygen atom of the peptide linkage that is to be broken has replaced the water molecule in the co-ordination sphere of the zinc ion.
7. On addition, a nearby hydrophobic pocket envelops the organic group of the amino acid to be cleaved and those amino acids with aromatic side groups react most readily. 12. This illustrates the basic key and lock theory first proposed by Fischer in which the enzyme and substrate fit each other sterically.
13. There is a good evidence at the enzyme also encourages the reaction by placing strain on the bond to be broken.
14. From the evidence of spectroscopic studies in enzymes containing metal ions that, unlike Zn 2+ shows d-d transitions. The spectrum of the enzymes containing such as a metal ion provides information on the micro symmetry of the site of the metal.
15. For example, Co 2+ can replace Zn 2+ and the enzyme retains the activity. The spectrum of carboxy peptidase A (Co II ) is irregular and has a high absorptivity, indicating that a regular tetrahedron is not present.
16. The distortion is due to the metal in the enzyme is peculiarly poised for action and that this lowers the energy of the transition state.
Carbonic Anhydrase: 1. Carbonic anhydrase is a Zn -enzyme. This enzyme occurs in red blood cells.
2. It catalyses hydration of CO 2 below pH 7 and dehydration of the bicarbonate ion according to the following reaction.
3. It has one zinc atom per molecule; it has co-ordinated to three histidine 9. In some mechanisms, the CO 2 co-ordinated directly to the Zn-atom, this is highly not possible. It catalyzes hydration of CO 2 below pH 7 and dehydration of the bicarbonate ion according to the following reaction.
10. The IR asymmetric stretching frequency for CO 2 is found to be 2343.5 cm -1 for the free molecule, which shows good interaction of one O2 atom and not the other.
11. The visible spectrum of Co 2+ substituted enzyme shows very small shiftsupon binding CO 2 , again incompatible with strong O 2 -metal interactions.
12. The Zn atom is thought to be considerably more acidic in carbonic anhydrase than in carboxy peptidase.

Mechanism Of Reversible Hydration Of CO2 To Carbonic Acid:
1. The substitution of a third, neutral and basic histidine in place of glutamate anion contributes the greater acidity.
2. The three histidines are pulled back making the Zn more electronegative and more acidic towards the fourth position.

This polarises an attached H 2 O molecule, to the point of loss of an H + ion to
form a co-ordinated hydroxo group. The above diagram shows the pathway of the reversible hydration of CO 2 to carbonic acid (HCO 3 -).
4. It is a closed loop; it may be carried out either clockwise to hydrate CO 2 or anti-clockwise to release CO 2 from ion from HCO 3bloodto the lungs.
5. The rates of the forward and reverse reactions in the hydration of CO 2 equilibrium increases as the pH are raised. 9. The above mechanism, relates a part on the x-ray and crystal studies proved that the structure of carbonic anhydrase, which indicates the presence of a hydrophobic nature adjacent to the site of CO 2 . This rapid hydration or dehydration by carbonic anhydrase appears to occur at a site near Zn 2+ .
10. Ligands that can co-ordinate to an active centre in an enzyme and prevent coordination by the substrate will tend to inhibit the action of that enzyme.
Nitrogen Fixation: 1. Nitrogen fixation is the process by which nitrogen is taken from its relatively inert molecular form (N 2 ) in the atmosphere and converted into nitrogen compounds useful for other chemical processes.
2. Fixation of atmospheric nitrogen is an important step in the nitrogen cycle, providing nitrogen for plant nutrition. Nitrogen present in these nitrogenous compounds is called fixed or combined nitrogen.
Fixation of Atmospheric Nitrogen:

Fixation of N2 as NH3 by Haber's Process:
A mixture of nitrogen (manufactured by liquefaction of air) and hydrogen in the ratio 1:3 is compressed to a presence of 200-500 atmospheres and is passed over a catalyst (finely divided iron + molybdenum) heated to about 550 • c. This forms the Haber's process for the manufacture of ammonia which then can be converted into ammonium salts by treatment with suitable acids.

Fixation of N2 as HNO3 by Ostwald's Process:
NH 3 manufactured by Haber's process is oxidised to nitric oxide (NO) by passing a mixture of NH 3 (1 volume) and air (8 volumes) over heated Pt gauze at 1070K.
NO combines with more of O 2 to give nitrogen dioxide (NO 2 ) which when absorbed in water in the presence of excess of air, gives HNO 3 .

Fixation of N2 as HNO3 by Birkland-Eyde Process:
Under the influence of high-tension electric arc where the temperature is high, nitrogen of the air combines with oxygen to form nitric oxide. It combines with more of oxygen to form nitrogen peroxide. This may be absorbed in water in presence of excess of air to give nitric acid which may be used for the manufacture of nitrogenous fertilizer.

NH 3 obtained by Haber's process and HNO3 obtained by Ostwald's process and
Brikland-Eyde process can be used for the preparation of ammonium salts and nitrates which are used as fertilizers.

Fixation of Nitrogen as Calcium Cyanamide:
Nitrogen gas obtained by the evaporation of liquid air is passed over calcium carbide heated to 800-1000 • c. A mixture of calcium cyanamide and carbon is obtained which is extensively used as a fertiliser under the name of nitrolim. In Vivo Nitrogen Fixation: reactions. There are also a number of substances that act to store and transport iron itself.

Fixation of Nitrogen as Nitrides
Cobalt is understood to be an essential trace element in animal nutrition, the only  commonly known as Cis-platin, has a wide spectrum of anticancer activity.

Applications of Bio-Inorganics in Medicine
Trans-platin has no effect on Escherichia coli. conditions establish that bridging occurs to quinine, cytosine and adenine but not to thymine.
Cis-platin must hydrolyse in the right place. If it hydrolyses in the blood before it gets in to the chromosomes within the cell, it will be more likely to react with a non-target species.
A related chemotherapeutic agent, diamine (1,1-cyclobutanedicarboxylato) platinum (II) is known as Cis-platin. This compound undergoes equation more slowly and produces less severe side effects than Cis-platin.

Mode of Action:
The exact mode of action of the platinum complexes is not known. It is only the cis isomer, which is active at low concentrations, not the trans isomer. Therefore, it is presumed that the two cis groups in the complex are replaced by some other groups in the cancer cell, forming a chelate ring. Such an association helps destroying cancerous cells. The replacement of the groups in the trans position by a chelating reagent is not easy and hence, the trans isomers of platinum complexes do not have therapeutic property.

Copper Complexes:
Some of the copper complexes are found to have anti-inflammatory activities.
Therefore, these complexes are used for the treatment of arthritis. Examples:

Advanced Tools
Docking: Schematic illustration of docking a small molecule ligand (green) to a protein target (black) producing a stable complex.
In molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions.
The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism).
Therefore, docking is useful for predicting both the strength and type of signal produced.
Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site. Characterization of the binding behaviour plays an important role in rational design of drugs as well as to elucidate fundamental biochemical processes.

Molecular Docking:
Molecular Docking is a valuable tool in structural biology and computer-aided drug design. Docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. The chief goal of ligand-protein docking is to predict the predominant binding modes of a ligand with a protein of known three-dimensional structure. It also predicts the strength of the binding, the energy of the complex; the types of signal produced and calculate the binding affinity between the two molecules using scoring functions. Successful docking methods do search for the high-dimensional spaces effectively and use a scoring function that correctly ranks the dockings.
To provide information about the interactions between the human cytochrome protein and the novel compounds theoretically, docking studies were carried out using the Schrödinger software. Characterization of the binding behaviour plays an important role in the rational design of drugs as well as to elucidate the fundamental biochemical processes.
Molecular docking can be divided into two separate sections.

Search Algorithm:
The algorithm should create an optimum number of configurations that include the experimentally ─ determined binding modes. The following are the various algorithms used for docking analysis.

Types of Docking:
The following are the chief methods used for docking

Lock and Key or Rigid Docking:
In rigid docking, both the internal geometry of the receptor and the ligand is kept fixed and the docking is performed.
Induced Fit or Flexible Docking: An enumeration on the rotations of one of the molecules (usually smaller one) is performed. For every rotation, the surface cell occupancy and the energy are calculated; later the most optimum pose is selected.