Bio Inorganic

8/14/2019 Bio Inorganic

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D:

B C

/

/ &

/ /


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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

. race ements : e e+ e+ e+ , n n+ ,

Cu/Cu+/Cu+2/Cu+3

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+


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Percentage Composition of Selected Elements in Human Body


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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)


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Metal ions in multiple oxidation states serve as electron carriers. Ex. Cytochromes, Fe-S

clusters (Fe), Cytochrome C oxidase, azurin, plastocynin (Cu)


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Metal ions in multiple oxidation states also play role in dioxygen transportation. Ex.

Hemoglobin (Fe), hemocynin (Cu)


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


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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

Hard ligands are usually

the small highly

electronegative elements

or ligand atoms within a

hard polyatomic ion (exoxygen)


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B

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,

group NH2 (b) carboxylic group, -COOH (c) Hydrogenatom 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.


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Non polar hydrophobic amino acids


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polar neutral amino acids


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polar acidic amino acids


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polar basic amino acids


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Iron Containing Enzymes

Those containing aporphyrin ligand system

An iron - bearing heme

moiet

Those not containingporphyrin ligands

non - heme iron -

containin roteins

Iron Sulphur Clusters


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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)


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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.


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Heme Containing Iron Enzymes

Quaternary structure of

deoxyhemoglobin tetramer

subunits are in blue, and subunits in cyan


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Comparision of the deoxy Y and oxy R states highlighting the shifts associated with the

quaternary transitions.

Deoxy T statesubunits 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 inorange. The T state hemes are colored in black while the R state hemes in gray


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Cytochrome P 450cam

HH HH

D C 450

O

HH

O

HOH


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Catalytic Cycle of Cytochrome P450

R-H

e O2

FeII

SCys

Cys

Fe

S

OO

-

e

Fe

III

SCys

III

-

H2O

R-HR-H

R-OH

R-OHR-H

H+H2O

Cys

HH

Fe

S

O

III

Cys

+Fe

S

O

IV

Resting state

H+

Fe

SCys

O OH

III

Cys

-

Fe

S

OIII

R-H

R-HR-H

Second Oxidant

-


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450

(1) ,

,

(2) 450

AD 450

(3)

450 ,

(4) ()

(5)

(6) , ,

.

.


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Spectroscopic Signature of P450

State UV-vis EPR

Resting state Fe(III) 418 nm 2.45, 2.26, 1.91

Resting state Fe(III) + substrate 396 nm 7.85, 3.97, 1.78

Reduced state Fe(II) 408 nm

Reduced state Fe(II) + CO 450 nm

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


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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


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Spectroscopy


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Where Differences End

CPO P450

Polar hydrophilic distal site non polar hydrophobic distal site

Heme edge is available for substrate substrates need to bind closely to FeIV=O

Interaction and e- transfer 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


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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) Light absorption and energy delivery by antenna systems

(2) Primary electron transfer in reaction centers

(3) Energy stabilization by secondary processes

(4) 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

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.


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(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 ion-

pair 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, Aand C represent secondary electron donors, acceptors and carriers.


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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.


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D ( )

D ( )

D1 (), D2 (), C47 (), C43 (), C 559 (),

33 D (), C 550 (), 12 D ( ).

C : C (), (), ( ), A B ,

(), , C (), C ().


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C (), (), (), C (), & D ()

D1 D2


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,

0, 1, 2, 3 4.

, 0 1, 1 2, 2 3, 3 4,

4 0 .

D . 0.4

, 0.1 23 .

( )

, (0 : 1 : 2 : 3 = 25% : 25% :

25% : 25%).

B 2 3 1 30100 , .. 0 1

. , 35 0 : 1 = 25% :75%.


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