Definition: Interface of classical areas of inorganic chemistry with biology

Bio-Inorganic Chemistry

Study of naturally occurring inorganic elements

Introduction of metals into biological systems as probes/drugs

Storage/Transport & application of metals ions in biology

Nutrition / Toxicity / Pharmaceutical application

Classification of Chemical Elements 1. Bulk Elements : H/H+, C, N, O2-/O2 /O2-2, P, S/S-2 2. Macrominerals and Ions : Na/Na+, K/K+, Mg/Mg+, Ca/Ca+2, Cl-, PO4-3, SO4-2 3. Trace Elements Cu/Cu+/Cu+2/Cu+3 : Fe/Fe+2/Fe+3/Fe+4, Zn/Zn+2,

4. Ultra Trace Elements a. Nonmetal : F/F , I/I , Se/Se-2, Si/Si+4, As, B b. Metals : Mn/Mn+2/Mn+3/Mn+4/Mn+5, Mo/Mo+4/Mo+5/ Mo+6, Co/Co+2/Co+3, Cr/Cr+3/Cr+6, V/V+3/V+4/V+5, Ni+/Ni+2/Ni+3, Cd/Cd+2, Sn/Sn+2/Sn+4, Pb/Pb+2, Li/Li+

Percentage Composition of Selected Elements in Human Body

Role of Metal Ions in Biological Systems

Group I &II metals operate as structural elements or in maintenance of charge and osmotic balance

Metal ions that exist in single oxidation state functions as structural elements or as triggers. For ex. SOD, zinc fingers (Zn), Calmodulin or Troponin C (Ca+2)

Metal ions in multiple oxidation states serve as electron carriers. Ex. Cytochromes, Fe-S clusters (Fe), Cytochrome C oxidase, azurin, plastocynin (Cu)

Metal ions in multiple oxidation states also play role in dioxygen transportation. Ex. Hemoglobin (Fe), hemocynin (Cu)

Variable oxidation states of metals play vital role in enzymatic catalytic reactions.

Ligand preference and possible coordination geometries of the metal center are important bioinorganic principles. Metal ligand preference is closely related to the hard soft acid base nature of metals and their preferred ligands.

Hard cations can be thought of as small dense cores of positive charge Hard ligands are usually the small highly electronegative elements or ligand atoms within a hard polyatomic ion (ex oxygen)

Biochemistry Fundamentals

There are 20 naturally occurring amino acids In humans, 10 of these amino acids are essential Every amino acid contains a central carbon, called alpha
carbon, to which 4 substituent groups are attached (a) amine group NH2 (b) carboxylic group, -COOH (c) Hydrogen atom and (d) side chain (-R) group which is unique to each amino acid. This R group defines the nature (polar, acidic, basic) characteristics of the amino acid.

Non polar hydrophobic amino acids

polar neutral amino acids

polar acidic amino acids

polar basic amino acids

Iron Containing Enzymes

Those containing a porphyrin ligand system An iron - bearing heme moiety

Those not containing porphyrin ligands non - heme iron containing proteins

Iron Sulphur Clusters

IronSulfur proteins
Four basic core structures which have been characterized: Rubedoxins found only in bacteria, in which the [FeS] cluster consists of a single Fe atom bound to four Cys residuesthe iron atom can be in the +2 or +3 valency

Rhombic two-irontwo-sulfide [Fe2S2] clusterstypical stable cluster oxidation states are +1 and +2 (the charges of the coordinating cysteinate residues are not considered)

Cuboidal three-ironfour-sulfide [Fe3S4] clustersstable oxidation states are 0 and +1

Cubane four-ironfour-sulfide [Fe4S4] clustersstable oxidation states are +1 and +2 for ferredoxin-type clusters and +2 and +3 for HIPIP clusters.

Heme Containing Iron Enzymes

Quaternary structure of deoxyhemoglobin tetramer

subunits are in blue, and subunits in cyan

Comparision of the deoxy Y and oxy R states highlighting the shifts associated with the quaternary transitions. Deoxy T state subunits are shown in blue while the deoxy T state subunits are shown in cyan; oxy R state subunits are shown in red and oxy R state subunits are shown in orange. The T state hemes are colored in black while the R state hemes in gray

Cytochrome P 450cam
Ribbon Diagram of Cytochrome P450 with camphor

H H

OH

Catalytic Cycle of Cytochrome P450

R-H eR-H Fe Cys S Cys R-OH O H R-H O 2O R-H Fe III S
H+ III Fe II

O2 O O

Cys

R-H

FeIII S
e-

H2O R-H H

Fe III Resting state Cys S R-OH R-H O Fe IV S R-H + H2O Cys H+ Cys S O OH R-H Cys

Fe III

Second Oxidant

The principal features of the consensus mechanism of cytochrome P450 are (1) binding of substrate to the enzyme, sometimes accompanied by a spinstate change of the iron, to afford an enzyme-substrate adduct (2) reduction of the ferric cytochrome P450 by an associated reductase with an NADPH-derived electron to the ferrous cytochrome P450 (3) binding of molecular oxygen to the ferrous heme to produce a ferrous cytochrome P450-dioxygen complex, similar to the situation in oxymyoglobin (4) a second one-electron reduction and protonation to arrive at the Fe(III)hydroperoxy complex (5) protonation and heterolytic cleavage of the O-O bond in with concurrent production of a water molecule to form a reactive iron-oxo intermediate (6) and, finally, oxygen-atom transfer from this iron-oxo complex to the bound substrate to form the oxygenated product complex. Product dissociation completes the cycle.

Spectroscopic Signature of P450

State Resting state Fe(III) Resting state Fe(III) + substrate Reduced state Fe(II) Reduced state Fe(II) + CO

UV-vis 418 nm 396 nm 408 nm 450 nm

EPR 2.45, 2.26, 1.91 7.85, 3.97, 1.78

Change of spin is due to change in coordination around Fe from hexa coordinate (with H2O) to pentacordinate

Haloperoxidases / Chloroperoxidase
Chloroperoxidase catalyse the formation of C-X bonds (X = I, Br, Cl) in the presence of H2O2. But it cannot catalyse the formation of C-F bond. Why??????? This is a 2 e- process. They are classified as peroxide dependent oxidases. Structurally quite similar to P450 class with a thiolate axial ligation

Biosynthesis of Caldariomycin

Spectroscopy
The spectroscopic signatures of CPO is very similar to that of P450 class The only difference from P450 is they show temp dependent spin transition

Where Differences End

CPO Polar hydrophilic distal site Heme edge is available for substrate Interaction and e- transfer

P450 non polar hydrophobic distal site substrates need to bind closely to FeIV=O site.

P450 structure contains deep substrate binding pockets surrounding by hydrophobic residues for stereo specific hydroxylations. CPO active site combines the features of enzymes with polar active site and a channel leading to FeIV=O pocket partly lines with hydrophobic residues

Photosynthesis (Historical Background)

The first expansion bubble shows a crosssection of a leaf, with the different types of cells; the dark spots are the chloroplasts. The second bubble is a chloroplast; the thylakoid membranes are the dark lines, the stroma is the stippled area. The third bubble shows a grana stack of thylakoids. The fourth bubble shows a schematic picture of the molecular structure of the thylakoid membrane,with a reaction center flanked by antenna complexes.

Phases of Energy Storage in Photosynthesis

Beginning with photon absorption and ending with the export of stable carbon products from the chloroplast can be sub classified into 4 phases: (1) (2) (3) (4) Light absorption and energy delivery by antenna systems Primary electron transfer in reaction centers Energy stabilization by secondary processes Synthesis and export of stable products.

Antennas and Energy Transfer Processes

For light energy to be stored by photosynthesis, it must first be absorbed by one of the pigments associated with the photosynthetic apparatus. Photon absorption creates an excited state that eventually leads to charge separation in the reaction center. The antenna system does not do any chemistry; it works by an energy transfer process that involves the migration of electronic excited states from one molecule to another. This is a purely physical process,which depends on a weak energetic coupling of the antenna pigments. In almost all cases, the pigments are bound to proteins in highly specific associations. In addition to chlorophylls, common antenna pigments include carotenoids and open-chain tetrapyrrole bilin pigments found in phycobilisome antenna complexes.

(a) General electron transfer scheme in photosynthetic reaction centers. Light excitation promotes a pigment (P) to an excited state (P*),where it loses an electron to an acceptor molecule (A) to form an ionpair state P+A-. Secondary reactions separate the charges, by transfer of an electron from an electron donor (D) and from the initial acceptor A to a secondary acceptor (A). This spatial separation prevents the recombination reaction. (b) Schematic diagram of cyclic electron transfer pathway found in many anoxygenic photosynthetic bacteria. The vertical arrow signifies photon absorption: P represents the primary electron donor:D, A and C represent secondary electron donors, acceptors and carriers.

Stabilization by Secondary Reactions

The more familiar oxygen-evolving photosynthetic organisms have a different pattern of electron transfer. They have two photochemical reaction center complexes that work together in a noncyclic electron transfer chain. The two reaction center complexes are known as photosystems I and II. Electrons are removed from water by photosystem II,oxidizing it to molecular oxygen, which is released as a waste product. The electrons extracted from water are donated to photosystem I and, after a second light-driven electron transfer step, eventually reduce an intermediate electron acceptor, NADPH. Protons are also transported across the membrane and into the thylakoid lumen during the process of the noncyclic electron transfer,creating a pH difference. The energy in this pH gradient is used to make ATP.

Photosystem II

Dimer structure of PSII (top view)

Dimer structure of PSII (side view)

D1 (green), D2 (red), CP47 (orange), CP43 (purple), - and subunits of Cyt b 559 (cyan), and the three extrinsic proteins 33 kDa (cyan), Cyt c 550 (pink), 12 kDa (deep blue). Cofactors are shown as: Chls (green), carotenoids (yellow), lipids (deep blue), Q A and Q B , Pheo (blue), Mn, Fe and heam ring of Cyt (red), and Ca (yellow).

D1 and D2 structure in PSII

Chls (green), Pheo (blue), Mn (red), Ca (yellow), Tyr Z & Tyr D (orange)

According to Kok model, the water splitting complex cycles through five charge storing states which correspond to different redox states of the four catalytic manganese ions denoted by S0, S1, S2, S3 and S4. In this process there are light induced transions, namely S0 S1, S1 S2, S2 S3, S3 S4, and the spontaneous S4 S0 conversion. During this last step a molecular oxygen molecule is released. Half-times for the first two transitions are around 0.4 ms, for the third is 0.1 ms and for the last is 2-3 ms. If one exposes photosynthetic apparatus (thylakoid membranes) to continuous photon exposure or to a large number of consecutive light flashes, the distribution of Sstates shows an equilibrium (S0 : S1 : S2 : S3 = 25% : 25% : 25% : 25%). But in dark S2 and S3 states relax back to the S1 state with a half-time of 30-100 s, i.e. only S0 and S1 states are stable in dark. Obviously, after 3-5 minutes of dark adaptation the distribution of S-states will be close to S0 : S1 = 25% : 75%.

Mechanisms of Water Oxidation

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