Cofactors Flashcards
What is a cofactor
Organic molecules or ions that are required by an enzyme for activity
Where does TPP come from
Thiamine
Where does TPP come from
Thiamine
Where does PLP come from
Pyridoxine
Biotin structure
Valerete side chain (CH2x4 then COO-) holds it into active site as prosthetic group as it is covalently attached to enzyme
Imidazoline ring cis fused to tetrahydrothiophene ring
Imidazoline ring has an NH group that combines with CO2
Reaction mechanism of pyruvate carboxylase (biotin)
ATP + bicarbonate —> carboxyphosphate
Leaving group is phosphate so CO2 released
Biotinyl enzyme NH group does nucleophilic attack on CO2
Forms carboxybiotinyl enzyme
CO2 lost from carboxybiotinyl enzyme as e- move from O- to C=O in ring (next to NH)
Attack of H on pyruvate to form a C=CH2
Attack onto CO2
Forms OAA
What cofactors are in pyruvate dehydrogenase
TPP (thiamine pyrophosphate)
FAD
Lipoamide
Coenzyme A
NAD
TPP structure
Has thiazole group
Key feature s relative acidity of H due to stabilising effect of N+ and S
The carbanion of TPP is stabilised by the thiazole ring because of the electron withdrawing properties of the S and +ve charge on the N
5 member ring with 5 group on N and opposite c
Role of TPP
In E1 of pyruvate dehydrogenase
Forms covalent bond with alpha keto acid by attacking the carbonyl group
Attaches temporary electron sink (schiff base)
Mechanism of TPP
Carbon can deprotonated to form carbanion
Fairly stable because of neighbouring +ve N and S
Very good nucleophile
Carbanion attacks electrophilic centre (carbonyl of alpha keto acid)
Prontate oxyanion species
N+ acts as e- sink to stabilise charge on c
Hydroxyethyl-TPP intermediate when in protonated form can form a resonance hybrid (double bond shifts from N=C to C=C-OH) can pick up a proton and be rapidly deprotonated
Lipoamide group role in pyruvate dehydrogenase
Captures 2C molecule formed after decarboxylation
Oxidised hydroxyethyl TPP on E1
Transfers acetyl to CoA on e2
On swinging arm to move betweenE1 and E3 (regenerated in E3)
Lipoamide structure
5 member ring containing disulphide bridge (S-S)
Next to disulphide bridge it is joined to lipoid acid
Joined to enzyme by amide linkage
Lipoamide mechanism in E2
Attack of hydroxyethyl TPP carbanion onto S of disulphide bridge
E- transferred to second S, ring broken and 1S protonated
Base attacks proton on OH group, e- move to c then to c of ring
Forms oxyanion then decomposes
1 sulphur has acetyl group
-ve TPP is good leaving group
CoA-sh attacks carbonyl and e- move to s
Forms acetyl - coA and fully reduced Lipoamide
FeS cluster in aconitase
3Fe4S
Binds substrate, pins in appropriate geometry
Fe acts as Lewis acid ad accepts lone pair of e-
PLP structure
Has reactive aldehyde group and acidic phenolic group
6 member ring with a nitrogen
N lone pair not delocalised into ring so N can act as a base
Reactive aldehyde reacts with amino groups to form a schiff base
Acidic phenol has lower pKa so can be deprotonated (can H bond intermediates)
Forms tautomer when H from phenol moves onto N
NH+ can then act as temporary e- sink to stabilise carbanions
