Bioinorganic catalysts Flashcards
What are the units of the rate constant?
s^-1
Michaelis-Menten kinetics
Model for enzyme kinetics
v = Vmax[S] / Km + [S]
v = rate of reaction Vmax = max. rate of reaction achieved by the system at saturating substrate concentration S = substrate Km = [S] at which rate of reaction is half of Vmax
Properties of Zn
Zn2+ = d10 = one common oxidation state = no redox activity
Intermediate
Bonding has more covalent character than Ca2+/Mg2+ (i.e. main group)
More labile than other TMs - fast water exchange, but kinetically inert when bound to His N
Easily variable coordination number - protein/substrate dictate geometry
Why is Zn employed by biological systems?
Not redox active
Good Lewis acid
Labile
Good coordination ability
Structural role of Zn
Zinc fingers
Zn(II) coordinated by 4 ‘permanent’ protein ligands
Functional role of Zn
As catalyst
Typical coordination of Zn(II) enzyme sites
3 ‘permanent’ protein ligands and 1 exchangeable ligand e.g. H2O
Zn2+ salts are…
…acidic in aqueous solution
Zn2+ + H2O Zn2+-OH- + H+
What is Zn2+-OH- used as in hydrolytic enzymes?
Activated water
Carbonic anhydrase
CO2 + H2O HCO3- + H+
Active site: one Zn2+ bound to 3 His and 1 exogenous H2O in an approximately tetrahedral geometry
How is pKa control in carbonic anhydrase achieved?
Neighbouring histidine and H-bonding network
The geometry the protein imposes on Zn
The lower polarity of the environment at Zn
Carboxylate shift
A mechanistic phenomenon characterised by the change in coordination mode of a carboxylate group (mono- to bidentate or vice versa) with ligand entrance/exit from the coordination sphere
This ability of the carboxylate group to rearrange in such a manner allows a constant/nearly constant coordination number to be maintained throughout an enzyme’s entire catalytic pathway
Example of carboxylate shift
In mononuclear Zn enzymes
The change is typically mono- to bidentate with ligand exit or bi- to monodentate with ligand entrance
Carboxypeptidase A
Catalyses peptide bond hydrolysis
Active site: Zn bound by 2 His, bidentate Glu and H2O
Unusual CN=5
Zn can be replaced by other metals e.g. Co(II), Mn(II) (but redox activity)
Alcohol dehydrogenase
Catalyses oxidation of alcohol in the liver
Dimer
Each subunit has 2 distinct tetrahedral Zn sites (i.e. 4 Zn per dimer)
Active site: Zn bound by 2 Cys, 1 His, 1 H2O
“Other” site: Zn bound by 4 Cys
Hydrogenase enzymes
Nature’s platinum
Responsible for uptake and evolution of molecular H2
Mostly found in anaerobic bacteria
Functions of hydrogenases
H+ acting as an oxidant (e.g. of sugars), leading to H2 evolution
Uptake of H2 to reduce CO2 to CH4/other methanogens
Uptake of H2 to reduce SO4^2-
Some aerobic organisms use H2 for energy:
2H2 + O2 —> 2H2O
Nitrogenase enzymes
A “special case” of hydrogenates
Molecular N2 is activated and H2 and NH3 are evolved
Four types of hydrogenases
- Iron hydrogenases
- NiFe hydrogenases
- NiFeSe hydrogenases
- Metal-free hydrogenase
Four types of hydrogenases
- Fe hydrogenases
- NiFe hydrogenases
- NiFeSe hydrogenases
- Metal-free hydrogenase
Fe hydrogenases
Function = H2 production
Core of FeS clusters
Mostly air sensitive (damaged by O2)
NiFe hydrogenases
Function = H2 consumption (activation)
Reversible process, dependent on pH/redox stimuli
FeS clusters combined with a Ni site
2 subunits:
Large = contains Ni-Fe catalytic site –> Ni involved in redox reactions, Fe(II) bound by 1 CO and 2 CN-
Small = contains FeS clusters, connects Ni active site of enzyme to surface of protein - i.e. serve as electron transport chain from NiFe redox site to cytochrome C3 (electron acceptor)
NiFeSe hydrogenase
Subset of the NiFe hydrogenase family, where a selenocysteine ligand coordinates the Ni atom in the active site
S in Met and Cys replaced by Se = more O2-tolerant
Higher catalytic activity than their Cys-containing homologues
Why is Ni considered the active catalytic centre in NiFe hydrogenases, rather than Fe?
Ni has the ability to stabilise weak agostic interactions with H2 in preference to Fe
Resulting in [M-H2]
The main role of the Fe centre is electron transfer and fine tuning of the redox chain
Haber Bosch process
N2 + 3H2 2NH3 + 92 kJ
300 atm
450 oC
Why is Ni considered the active catalytic centre in NiFe hydrogenases, rather than Fe?
Ni has the ability to stabilise weak agostic interactions with H2 in preference to Fe
Resulting in [M-H2]
The main role of the Fe centre is electron transfer and fine tuning of the redox chain
Structure of nitrogenase complex
Consists of 2 proteins
- Homodimeric Fe protein
- Heterotetrameric Fe-Mo protein
Homodimer Fe protein in nitrogenase complexes
Electron donor
60 kDa
[4Fe-4S] cluster
Receives electrons, stores electrons then donates electrons to the site when N2 is to be reduced
Heterotetrameric Fe-Mo protein
Where N2 binds and is reduced
2 alpha and 2 beta protein subunits
Also contains 2 FeS clusters (= P clusters) and 2 Fe-Mo cofactors
P clusters believed to be involved in electron transfer from the [4Fe-4S] cluster of the Fe protein to the Fe-Mo cofactor
Each Fe-Mo cofactor is covalently linked to the alpha subunit of the protein via 1 Cys (Fe) and 1 His (Mo) residue
Cofactor = redox centre = 1 Mo, 7 Fe, 9 S, also a central atom X of unknown identity (currency opinion X = C)
Nitrogenases in the absence of other substrates i.e. N2
Can function as hydrogenases 2H+ + 2e- —> H2
Can hydrogenate acetylene –> ethylene –> ethane
Intermediate M-H2 complexes can be substituted by N2
At least one H2 is released for each N2 fixation
Why is Mo considered the active catalytic centre in nitrogenases, rather than Fe?
Mo can form more stable [M-H2] agostic interactions
The main role of the Fe centre is electron transfer and fine tuning of the redox chain
Fe-V and Fe-only nitrogenases
Less efficient than Fe-Mo nitrogenases
Vitamin B12
Converted into 2 enzymes in the body:
5’-deoxyadenosylcobalamin, methylcobalamin
Humans require 1 mg per day
Structure of vitamin B12
Organometallic (Co-C bond)
A Co complex of corrin
Both Co(I) and Co(II) are stabilised
3 reactions that are B12-dependent
- Intramolecular rearrangements e.g. glutamate mutase, methylmalonyl-CoA mutase, L-beta-lysine mutase
- Reduction of ribonucleotides to deoxyribonucleotides e.g. ribonucleotide reductase
- Methyl group transfers (B12 acts as a “biological Grignard reagent”)
What does cleavage of the Co-C bond in vitamin B12 lead to?
Organometallic alkylations
Oxidation state of Co in vitamin B12
Co(III)
Co(I)
d8
Supernucleophile
Homolytic cleavage of the Co-C bond in vitamin B12
Forms radical species believed to be participate in several enzymatically catalysed hydrogen-transfer reactions
