Bioinorganic catalysts

Question 1

What are the units of the rate constant?

Answer 1

s^-1

Question 2

Michaelis-Menten kinetics

Answer 2

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

Question 3

Properties of Zn

Answer 3

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

Question 4

Why is Zn employed by biological systems?

Answer 4

Not redox active
Good Lewis acid
Labile
Good coordination ability

Question 5

Structural role of Zn

Answer 5

Zinc fingers

Zn(II) coordinated by 4 ‘permanent’ protein ligands

Question 6

Functional role of Zn

Answer 6

As catalyst

Question 7

Typical coordination of Zn(II) enzyme sites

Answer 7

3 ‘permanent’ protein ligands and 1 exchangeable ligand e.g. H2O

Question 8

Zn2+ salts are…

Answer 8

…acidic in aqueous solution

Zn2+ + H2O Zn2+-OH- + H+

Question 9

What is Zn2+-OH- used as in hydrolytic enzymes?

Answer 9

Activated water

Question 10

Carbonic anhydrase

Answer 10

CO2 + H2O HCO3- + H+

Active site: one Zn2+ bound to 3 His and 1 exogenous H2O in an approximately tetrahedral geometry

Question 11

How is pKa control in carbonic anhydrase achieved?

Answer 11

Neighbouring histidine and H-bonding network
The geometry the protein imposes on Zn
The lower polarity of the environment at Zn

Question 12

Carboxylate shift

Answer 12

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

Question 13

Example of carboxylate shift

Answer 13

In mononuclear Zn enzymes

The change is typically mono- to bidentate with ligand exit or bi- to monodentate with ligand entrance

Question 14

Carboxypeptidase A

Answer 14

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)

Question 15

Alcohol dehydrogenase

Answer 15

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

Question 16

Hydrogenase enzymes

Answer 16

Nature’s platinum
Responsible for uptake and evolution of molecular H2
Mostly found in anaerobic bacteria

Question 17

Functions of hydrogenases

Answer 17

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

Question 18

Nitrogenase enzymes

Answer 18

A “special case” of hydrogenates

Molecular N2 is activated and H2 and NH3 are evolved

Question 19

Four types of hydrogenases

Answer 19

1. Iron hydrogenases
2. NiFe hydrogenases
3. NiFeSe hydrogenases
4. Metal-free hydrogenase

Question 20

Four types of hydrogenases

Answer 20

1. Fe hydrogenases
2. NiFe hydrogenases
3. NiFeSe hydrogenases
4. Metal-free hydrogenase

Question 21

Fe hydrogenases

Answer 21

Function = H2 production
Core of FeS clusters
Mostly air sensitive (damaged by O2)

Question 22

NiFe hydrogenases

Answer 22

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)

Question 23

NiFeSe hydrogenase

Answer 23

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

Question 24

Why is Ni considered the active catalytic centre in NiFe hydrogenases, rather than Fe?

Answer 24

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

Question 25

Haber Bosch process

Answer 25

N2 + 3H2 2NH3 + 92 kJ

300 atm
450 oC

Question 26

Why is Ni considered the active catalytic centre in NiFe hydrogenases, rather than Fe?

Answer 26

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

Question 27

Structure of nitrogenase complex

Answer 27

Consists of 2 proteins

1. Homodimeric Fe protein
2. Heterotetrameric Fe-Mo protein

Question 28

Homodimer Fe protein in nitrogenase complexes

Answer 28

Electron donor
60 kDa
[4Fe-4S] cluster
Receives electrons, stores electrons then donates electrons to the site when N2 is to be reduced

Question 29

Heterotetrameric Fe-Mo protein

Answer 29

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)

Question 30

Nitrogenases in the absence of other substrates i.e. N2

Answer 30

Can function as hydrogenases 2H+ + 2e- —> H2

Can hydrogenate acetylene –> ethylene –> ethane

Question 31

Intermediate M-H2 complexes can be substituted by N2

Answer 31

At least one H2 is released for each N2 fixation

Question 32

Why is Mo considered the active catalytic centre in nitrogenases, rather than Fe?

Answer 32

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

Question 33

Fe-V and Fe-only nitrogenases

Answer 33

Less efficient than Fe-Mo nitrogenases

Question 34

Vitamin B12

Answer 34

Converted into 2 enzymes in the body:
5’-deoxyadenosylcobalamin, methylcobalamin
Humans require 1 mg per day

Question 35

Structure of vitamin B12

Answer 35

Organometallic (Co-C bond)
A Co complex of corrin
Both Co(I) and Co(II) are stabilised

Question 36

3 reactions that are B12-dependent

Answer 36

1. Intramolecular rearrangements e.g. glutamate mutase, methylmalonyl-CoA mutase, L-beta-lysine mutase
2. Reduction of ribonucleotides to deoxyribonucleotides e.g. ribonucleotide reductase
3. Methyl group transfers (B12 acts as a “biological Grignard reagent”)

Question 37

What does cleavage of the Co-C bond in vitamin B12 lead to?

Answer 37

Organometallic alkylations

Question 38

Oxidation state of Co in vitamin B12

Answer 38

Co(III)

Question 39

Co(I)

Answer 39

d8

Supernucleophile

Question 40

Homolytic cleavage of the Co-C bond in vitamin B12

Answer 40

Forms radical species believed to be participate in several enzymatically catalysed hydrogen-transfer reactions