5. Bioinorganics Flashcards
What are the essential metal groups in biology?
- Bulk metals
- Trace metals
What are the roles of bulk metals in biology?
- Charge carriers: Na+/K+ pump
- Cofactors: Mg2+ in rubisco active site
- Signalling molecules: Ca2+ in synapsis, myosin action
What are the roles of trace metals in biology?
- Catalysts: Mo+ in N2 fixation
- Cofactors: Mn+ for water splitting enzyme, Zn+ in zinc fingers
- Electron transfer: Fe+ in heme, ferritin; Cu+ in hemocyanin
What is a ligand?
Ligand - ion / molecule which attaches to a Me by a dative covalent / coordinate bond - ligand has a lone e pair
Which two amino acid have identical ligand properties?
Asp and Glu - can form bidentate ligands
Why is lysine not a good ligand?
Lys is too negative to be a ligand - gets protonated in solutions
What group is a good sigma and pi e donor?
Sulphur:
- Thiol (Cys): good π donor
- Methylated thiol (Met): good σ donor to ‘soft’ metals
Why cofactors can be classified as ligands?
Cofactors form bonds with Me+ by donating e pairs
What is a common mechanism some ligands undergo to act like ligands?
Deprotonation - free e pair for bond formation with Me+
Define what is a Lewis acid
Lewis acid - e pair acceptor
Me+ in ligand bond formation - Lewis acids
How metal ion binding to oxygen influences carbonyl group?
Me+ bound by free e pair of O - charge transferred - C more positive => carbonyl activation for Nuc- attack
Which enzyme regulates pH in blood?
Carbonic anhydrase
Describe the active site of carbonic anhydrase + its function
Carbonic anhydrase active site:
- 3 His residues
- tetrahedral arrangement
- Zn+
Carbonic anhydrase present in blood - converts CO2 into soluble H2CO3 / insoluble form to regulate blood pH (catalyses reaction both ways)
In muscle CO2 -> H2CO3
In blood H2CO3 -> CO2 (if blood pH is too low/acidic)
What is Zn+ mechanism of action in carbonic anhydrase active site?
Carbonic anhydrase catalysis cycle:
1) Zn+ activates H2O: for deprotonation: Zn+ binds H2O: - draws charge from O: lone pair (Zn+ - Lewis acid) -> H2O deprotonation
2) O- neg charge - acts as good Nuc - attacks CO2 -> CO2 bound to O at active site
3) Another H2O: attacks Zn+ - HCO3- leaves the active site
(Zn+ forms max tetrahedral structure)
=> main carbonic anhydrase catalysis - H2O deprotonation (rate determining step - slowest)
What enzyme cleaves peptide bonds?
Peptidases perform proteolysis - peptide bond cleavage
Describe the active site of peptidases + its function
Peptidase active site:
- Glu, His, His residues
- Zn+ / Mn+ / Cu+
Breaks peptide bonds in polypeptides to produce carboxylic acid + amine
Ex: Thermolysin - in bacteria released out for protein breakdown
What is Me+ mechanism of action in cpeptidase active site?
Peptidase / protease catalysis mechanism:
1) Me+ binds with C=O and H2O at active site
2) H2O: attacks C=O - O added to C=O -> peptide bond cleavage
3) COO- held by Me+ at peptidase active site - NH2 amine released
=> new C / N termini formed
How can peptidase / protease mechanism be prevented in protein purification?
Remove Me+ needed for peptidase / protease active site - use EDTA to chelate the Me+ => proteolysis prevented
What metal ion acts in ATP hydrolysis? What function it performs?
Mg2+ in ATP -> ADP + Pi:
- polarises two terminal phosphate groups - facilitates H2O attack for ATP hydrolysis
- after the reaction stabilises phosphates after bond cleavage
What is ATP hydrolysis mechanism? An example location of this reaction
ATP -> ATP + Pi
1) Mg2+ draws charge from O- in phosphates - P+ more positive for H2O: attack
2) H2O: attacks 3rd P+ - covalent bond celavage
3) Mg2+ stabilises the detached and 2nd phosphate on ADP
Ex: ATP hydrolysis by myosin during muscle action - reaction coupled to motion - E released from ATP for contraction
In what other reaction involving ATP hydrolysis reaction does Mg2+ act?
ATP hydrolysis in DNA / RNA adenosine nucleotide synthesis by DNA / RNA polymerases:
1) Mg2+ stabilises phosphates
2) DNA-Ribose attacks 1st phosphate - pyrophosphate cleaved off
3) Mg2+ holds both pyrophosphate and new RNA/DNA A nucleotide
What is Mg2+ function in myosin action?
- Mg2+ stabilises neg charges of active site residues
- As Mg2+ moved to the left - charge moved -> different interactions between active site residues => change in myosin conformation - MOTION
What are the common metal deficiency / excess diseases?
Cu (mutations in Cu transport proteins):
- Cu deficiency - Menkes disease
- Cu excess - Wilson’s disease
Fe:
- Fe deficiency - anaemia (pooor O2 transport)
- Fe excess - liver failure
What is the iron storage protein?
Ferritin - binds Fe2+ inside the hollow cavity - stores
What are the different reactive oxygen species (ROS) in biology? How are they created?
Triplet oxygen -> Singlet oxygen -> Super-oxide -> Peroxide
Define what are oxygen reactive species (ROS)?
Oxygen reactive species (ROS) - radical / non-radical oxygen molecules formed by partial reductions
What is the electron configuration of triplet O2?
What is the electron configuration of superoxide?
What is the electron configuration of peroxide?
How does triplet oxygen form a diradical?
What is the electron configuration of O2 singlet?
How are ROS created? What are the effect of ROS in organisms?
What are the dangerous reaction mechanisms of ROS in organisms?
- Superoxide attcked by π systems => DNA disruption -> cancer
- Peroxide acts in Nuc attack at carbonyl => further oxidation
What is the hydrogen peroxide catalytic cycle in presence of Fe / Cu ions?
Fenton chemistry:
free Fe / Cu ions can cause free radical production - catalytic cycle - produce hydroxyl radicals (.OH) + peroxy radicals (.OOH)
What catalytic cycle is perfomed by superoxide dismutase?
- .O2H superoxide from immune response
- Cu2+ / Cu+ in active site -> 2 reactions for ROS degeneration
What enzyme catalyses hydrogen peroxide degeneration?
Catalase
Explain the active site of catalase enzyme
Catalase active site:
- His residue - stabilises H, Tyr - ligates Fe3+
- heme - Fe3+ / Fe4+
- reaction: peroxide reduction to H2O + O2
- peroxide acts as Nuc - attacks Fe3+
Explain the reaction mechanism catalysed by catalase
Catalase catalyses peroxide reduction to water and oxygen:
1) Tyr hold Fe3+, His residue holds H, H2O2 attacks Fe3+
2) 2e- transferred to peroxide -> Fe4+ and radical on heme (compound 1), oxide ion formed
3) Second H2O2 attacks Fe4+ -> gives 2e- -> Fe3+ and H2O+O2 => catalytic cycle again as Fe at heme is Fe3+ again
What is compound 1?
Compound 1 - Fe4+ oxo radical cation
Which metabolic process uses oxygen reduction to water?
Cellular respiration
What is a respirasome?
Respirasome - a supramolecular protein complex in oxidative phosphorylation that accomplishes electron transfers and ATP synthesis (cytochrome c + NADH dehydrogenase)
Which enzyme acts in oxygen reduction in respiration?
Cytochrome oxidase
- O2 -> H2O
- Heme I + Heme II can store 4e-
- enzyme attached to inner mitochondrial membrane facing intermembrane mitochondrial space
What is electron transfer needed for in cells?
Electron transfer (ET) - chain of e- transfers through mitochondrial / photosynthetic membrane proteins - fall in E - E used for ATP generation
What is the final acceptor of electron in electron transfer (ET)?
Oxygen
What are the possible factors influencing rate of electron transfer (ET)?
- distance
- intervening medium
- driving force
- reorganisation of cofactors
Explain how distance influences the rate of electron transfer (TF)
Distance:
- rate decreases exponentially with increasing distance - jump between e- clouds not possible
Explain how intervening medium influences the rate of electron transfer (ET)
Intervening medium (thtough what e- will have to go through):
- fully conjugated: molecular orbitals are connected - easu e- jump
- through atoms: slower
- typical pasked protein: even slower
- vacuum: insulating environment
What is the optimum value of intervening medium of ET for a typical packed protein?
β = 1.4
Optimised ET
Not maximised ET rate - average rate in nature
Explain how driving force influences rate of ET
Doesn’t affect the rate - affects equilibrium position (K) of ET - difference in reduction potential determined if the e- will jump or not
Explain how reorganisation of cofactors influences ET rate
Reorganisation of cofactors - before reaction bond length / coordination geometry / spin state changes - e- must tunnel between donor and acceptor
Reorganisation of cofactors:
rate constant HEAVILY dependent on reorganisation energy
Explain plastocyanin in ET
Plastocyanin:
- e- carrier in photosynthesis
- Cu2+ + e -><- Cu+
- Cu2+ favours sq planar - geometry change - Cu+ favours Td
Explain cytochrome c in ET
Cytochrome c:
- Fe heme in active site
- octahedral coordination of Fe3+ -> Fe2+
- below - His, above - Met (axial ligation)
- no spin state change
Explain iron-sulphur clusters in ET
Explain NADPH / quinones in ET
Explain flavins in ET
What is the active site of myoglobin (Mb)? Explain the function of components
Active site binds O2:
- Proximal His: holds heme
- Distal His: holds O2, polarises O2 and strengthens Fe-O2 bond
- Fe2+
Explain O2 binding to myoglobin controversy
Pauling / Weiss
Does the spin state change when O2 binds to myoglobin?
Yes, high spin Fe2+ (unbound) -> high spin Fe2+ / Fe3+ (binding controversy Pauling / Weiss)
Myoglobin vs hemoglobin O2 binding curves
What molecule is used for O2 transport in invertebrates?
Hemocyanin
- Cu+ -> Cu2+
- 6 His at active site
