lecture 5-bioinorganic chemistry
TRANSCRIPT
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