Enzymes in inorganic
biochemistry
Calmodulin
A lot of the Calcium in biology à hydroxyapatite: bone, tooth.
Ca2+ mainly outside cell ß Ca2+-ATPase (Na+/Ca2+ exchange)
Ca2+ high in ER/SR, Golgi apparatus and mitochondria ß SERCA
(sarco(endo)plasmic reticulum ATP-ase)
Ca2+ intracellular second messenger à binding to calmodulin
large flexible (irregular) coordination sphere
coordination to seven oxygen atoms: 5 from the amino acid side
chains (including a bidentate carboxylate), one from the peptide
backbone, and one of H2O
fast exchange rates
short lived strong signal à Ca2+ binding to calmodulin à EF-hand
conformation to activate kinases + activation of nitric oxide synthases
nitric oxide: cellular messenger for widening of blood vessels
NADPH H + Arg + O2 à citrulline + H2O + NO
Jack bean urease
Catalyses:
Used by plants for urea recycling à ammonia for growth, obtained from animal urea (part of nitrogen
cycle)
Reaction speed up 3 x 1015
Two Ni ions in active site
Lewis acid à acid base catalysis
Polarize C=O bond to make C more susceptible to nucleophilic attack by OH
Stabilizing formed C-O-
Electron withdrawal from H2O à makes it more like hydronium ion à water
more easily dehydrated à stronger base à faster reaction
NH2 proton donation (more like NH3/NH4) à better leaving group
Brings reactants closer together
,Rubisco
Mg2+ enzyme à must important enzyme in nature
Mg2+
smallest of all bulk biological elements
Octahedral coordination geometry
Coordinates to H2O
Coordinated to ATP, DNA, RNA à counter ion for
charge stabilization
Lewis acid in enzymes: stabilizes (formed) enols
and enolates ß electron withdrawal
Less polarizing (electron withdrawing) than Zn 2+
Catalyses part of the carbon cycle
Fixation of CO2 in Calvin cycle (photosynthesis dark reaction)
Ribulose 1,5-bisphosphate carboxylase/oxygenase
Oxygen + ribulose-1,5-bisphosphate phosphoglycerate + 2-phosphoglycol
Carbonic anhydrase
Zn2+ enzyme
Zn borderline
High in Irving Williams
Structural role: Zn fingers, biomineralization
Catalytic role: acid base catalysis à lewis acid
Neutral ligand coordination to Zn2+ promotes dissociation of one H from
coordinated water
Zn carbonyl mechanism (increasing susceptibility for nucleophilic attack
by enol stabilization/carbonyl polarization)
Zn hydroxide mechanism (activation water to OH as nucleophile)
Present in blood circulation system
à avoids formation of gas bubbles
Facilitates reversable dissolution of CO2 as HCO3-
Catalyses reversibly:
CO2 + H2O à HCO3- + H+
In lungs: diffusion of CO2 to the air + lower pH à reaction balance shifts to left side
In tissues à respiration à CO2 formation à reaction balance shifts to the right side
, Supplies CO2 to photosynthetic organisms to compensate for poor rubisco efficiency
Alpha CA: animals, Beta CA: plants, Gamma CA: bacteria à unrelated but Zn
Cd variant in marine phytoplankton
via
biochemistry
Calmodulin
A lot of the Calcium in biology à hydroxyapatite: bone, tooth.
Ca2+ mainly outside cell ß Ca2+-ATPase (Na+/Ca2+ exchange)
Ca2+ high in ER/SR, Golgi apparatus and mitochondria ß SERCA
(sarco(endo)plasmic reticulum ATP-ase)
Ca2+ intracellular second messenger à binding to calmodulin
large flexible (irregular) coordination sphere
coordination to seven oxygen atoms: 5 from the amino acid side
chains (including a bidentate carboxylate), one from the peptide
backbone, and one of H2O
fast exchange rates
short lived strong signal à Ca2+ binding to calmodulin à EF-hand
conformation to activate kinases + activation of nitric oxide synthases
nitric oxide: cellular messenger for widening of blood vessels
NADPH H + Arg + O2 à citrulline + H2O + NO
Jack bean urease
Catalyses:
Used by plants for urea recycling à ammonia for growth, obtained from animal urea (part of nitrogen
cycle)
Reaction speed up 3 x 1015
Two Ni ions in active site
Lewis acid à acid base catalysis
Polarize C=O bond to make C more susceptible to nucleophilic attack by OH
Stabilizing formed C-O-
Electron withdrawal from H2O à makes it more like hydronium ion à water
more easily dehydrated à stronger base à faster reaction
NH2 proton donation (more like NH3/NH4) à better leaving group
Brings reactants closer together
,Rubisco
Mg2+ enzyme à must important enzyme in nature
Mg2+
smallest of all bulk biological elements
Octahedral coordination geometry
Coordinates to H2O
Coordinated to ATP, DNA, RNA à counter ion for
charge stabilization
Lewis acid in enzymes: stabilizes (formed) enols
and enolates ß electron withdrawal
Less polarizing (electron withdrawing) than Zn 2+
Catalyses part of the carbon cycle
Fixation of CO2 in Calvin cycle (photosynthesis dark reaction)
Ribulose 1,5-bisphosphate carboxylase/oxygenase
Oxygen + ribulose-1,5-bisphosphate phosphoglycerate + 2-phosphoglycol
Carbonic anhydrase
Zn2+ enzyme
Zn borderline
High in Irving Williams
Structural role: Zn fingers, biomineralization
Catalytic role: acid base catalysis à lewis acid
Neutral ligand coordination to Zn2+ promotes dissociation of one H from
coordinated water
Zn carbonyl mechanism (increasing susceptibility for nucleophilic attack
by enol stabilization/carbonyl polarization)
Zn hydroxide mechanism (activation water to OH as nucleophile)
Present in blood circulation system
à avoids formation of gas bubbles
Facilitates reversable dissolution of CO2 as HCO3-
Catalyses reversibly:
CO2 + H2O à HCO3- + H+
In lungs: diffusion of CO2 to the air + lower pH à reaction balance shifts to left side
In tissues à respiration à CO2 formation à reaction balance shifts to the right side
, Supplies CO2 to photosynthetic organisms to compensate for poor rubisco efficiency
Alpha CA: animals, Beta CA: plants, Gamma CA: bacteria à unrelated but Zn
Cd variant in marine phytoplankton
via
