Bioinorganic ChemistryBioinorganic ChemistryStudy of metal species in biological systems

•metal ion transport and storage,

•Metallohydrolase enzymes,

•metal-containing electron transfer proteins,

•oxygen transport and activation proteins,

•bioorganometallic systems such as hydrogenases and alkyltransferases,

•enzymes involved in nitrogen metabolism pathways.

Biological functions of selected metal ionsBiological functions of selected metal ions

hydrogenase, hydrolaseNi

Dioxygen transport and storage, electron transfer, oxidase

Fe, Cu

Photosynthesis, structural, oxidaseMn

Nitrogen fixation, oxidaseV, Mo

Structural, charge carrierCa

Structural, hydrolase, isomeraseMg, Zn

Charge carrier, osmotic balanceNa, K

FunctionMetal

Na Mg

K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn

Y Zr Nb Mo Tc Ru Rh Pd Ag Cd

La Hf Ta W Re Os Ir Pt Au Hg

Naturally occurring in biologyNaturally occurring in biology

Used as probesUsed as probes

Chemical elements essential to life forms can be divided into the following

(i) Bulk elements: C, H, N, O, P, S

(ii) Macrominerals and ions: Na, K, Mg, Ca, Cl, PO43-, SO4

2-

(iii) Trace elements: Fe, Zn, Cu

(iv) Ultratrace elements comprises of

(a) non-metals: F, I, Se, Si, As, B

(b) metals: Mn, Mo, Co, Cr, V, Ni, Cd, Sn, Pb, Li

Essentiality of elements is defined by

(1) A physiological deficiency appears when the element is removed from the diet

(2) The deficiency is relieved by the addition of that elementto the diet

(3) A specific biological function is associated with the element

Every essential element follows a Every essential element follows a dosedose--response curve response curve

At lowest dosages organism does not survive

In deficiency regions, the organism exists with less than optimal functions

After optimal dosage (plateau region), higher dosage cause toxic effects in the organism eventually leading to lethality

Active Site and Enzyme Substrate ComplexActive Site and Enzyme Substrate Complex

The active site of an enzyme is the region that binds the substrate and contributes the amino acid residues that directly participates in the making and breaking of chemical bonds

GeneralizationsGeneralizations

1) Enzymes are usually very large compared to the substrate

Only a small portion is involved in ES complex

Rest portion is involved in control and maintaining of structure

2) The substrate is bound by relatively weak forces

ΔG E-S complex = (12 to 36) KJ mol-1

(strength of a covalent bond is upto ~ 450 KJ mol-1)

3) Active sites are designed to exclude H2O

Surrounded with non-polar amino acids to create a hydrophobic environment

Essential for substrate binding and product formation (Catalysis)

SpecificitySpecificity

Active site provides specificity for its particular substrate

Substrate has a matching shape to fit into the active site (Lock and Key mechanism)

Formation of Enzyme-Substrate Complex is thus crucial to the product formation

Evidence for EnzymeEvidence for Enzyme--Substrate ComplexSubstrate Complex

(1) At constant [E], increasing the [S] will increase the reaction rate until a maximum velocity is reached,

(2) Isolation of E-S complex

(3) X-ray diffraction studies of E-S complex

(4) Spectroscopic studies of E-S complex

Active sites of EnzymesActive sites of Enzymes

Zn

His(N)

OH2

His(N)

Glu(O)

peptide hydrolysis(removes terminal aminoacids from proteins)

Carboxy peptidase

Zn

His(N)

OH2

His(N)

His (N)H2O + CO

Carboxy anhydrase

H2CO3 H+ + HCO3-

Zn

Cys(S)

OH2

His(N)

Cys(S)

Liver Alcohol dehydrogenase

CH3CHOCH3CH2OH

NAD+ NADH

ActiveActive--Sites of EnzymesSites of Enzymes

N

N

N

N FeII

CO2-

CO2-

N

N

N

N FeII

CO2-

CO2-

OO

O2

Hemoglobin

N

NH

N

HN

N

NH

N

HN

N

NH

N

NH

N

HN

N

NH

NH

N

Nh

N

NH

N

NH

CuI CuI

CuII

O

O

CuII

N

O2

Hemocyanin

NNH

N

HN

O2FeII

O

FeII

O O

O O

NNH

N

NH

H

NHN

NHN

N

HN

FeII

O

FeIII

O O

O O N

NH

NHN

NHN

H O

O

Hemerythyrin

PorphyrinsPorphyrins

Porphyrins are tetrapyrrole macrocycles with conjugated double bonds and various groups attached to the perimeter

N

HN

N

NH

R R

R

R

R R

R

R

variation of substituents facilitates the tuning of electron-donating and electron-withdrawing ability of the ligand

The porphyrins can accept two hydrogen ions to form+2 diacids or donate two protons to form -2 dianions

Porphyrins are found in many metalloenzyme

photosynthesisChlorophyll Mg-porphyrin

dioxygen carrierHemoglobin

MyoglobinFe-porphyrin

electron transferCytochromeFe-porphyrin

FunctionEnzyme

CytochromesCytochromes

Cytochromes are electron transfer proteins

There are three types of cytochromes depending upon the porphyrin types

cytochrome a, cytochrome b, cytochrome c

N N

NN

Fe

HO

OOH

OHO

O

H

a

N N

NN

Fe

HO

OOH

OHO

b

N N

NN

Fe

s-cys protein

OOH

OHO

c

s-cys protein

The prosthetic group in all cytochromes comprises of four heme units

They have a molecular weight of about 12,400

Active site differences between Hemoglobin and Cytochrome

FeN N

N N

O

N

O

(His)

Hemoglobin

FeN N

N N

S (cys)

N(His)

Cytochromes

Depending upon the ligand, the redox potential of a given cytochromecan be tailored to meet specific need in electron transfer schemes (photosynthetic versus respiration)(photosynthetic versus respiration)

The potentials are such that the electron flow is from

b c a O2

Cytochrome a is capable of binding O2 and reducing them

Cytochrome a is responsible for severe toxicity of CN-

CN- binds to the 6th site and stabilize FeIII to such an extent that it cannot participate in electron transfer schuttle

HemoglobinHemoglobin

FeN N

N N

N(His)

High Spinparamagnetic

t2g4 eg2

FeN N

N N

O

N(His)

II II

O

Low Spindiamagnetic

t2g6 eg0

DeoxyhemoglobinDeoxyhemoglobin OxyhemoglobinOxyhemoglobin

Deoxyhemoglobin is the form of hemoglobin without the bound oxygen. The oxyhemoglobin has significantly lower absorption (660 nm) than deoxyhemoglobin (940 nm). This difference is used for measurement of the amount of oxygen in patient's blood by pulse oximeter.

The size of Fe2+ increase by 28% on going from

Low spin (oxyhemoglobin) (0.61 Å)

to

High spin (Deoxyhemoglobin) (0.78 Å)

The Fe2+ in deoxyhemoglobin is too large to fit in the ring and is situated (0.7-0.8)Ao above the ring

Thus, presence of O2 changes the electronic arrangement of Fe2+ and distorts the shape of the complex

The globular protein prevents the irreversible oxidation of Fe(II) to Fe(III)

CooperativityCooperativityWhen O2 binds to

one sub-unit Fe2+ contracts, moves into plane

of porphyrin ring

moves the histidine attached to ittriggers conformational

changes in the globin chain

translated through H-bond network

Enhances the ability of other three units to bind O2

This phenomenon is This phenomenon is called cooperative effect called cooperative effect

In a similar way when the blood reaches the muscle, only one O2 is released, the others are released even more easily due to the cooperative effect in reverse

picket fence porphyrin