5. Bioinorganics Flashcards by Barbora Buc

What are the essential metal groups in biology?

Bulk metals
Trace metals

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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

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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

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What is a ligand?

Ligand - ion / molecule which attaches to a Me by a dative covalent / coordinate bond - ligand has a lone e pair

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Which two amino acid have identical ligand properties?

Asp and Glu - can form bidentate ligands

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Why is lysine not a good ligand?

Lys is too negative to be a ligand - gets protonated in solutions

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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

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Why cofactors can be classified as ligands?

Cofactors form bonds with Me+ by donating e pairs

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What is a common mechanism some ligands undergo to act like ligands?

Deprotonation - free e pair for bond formation with Me+

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Define what is a Lewis acid

Lewis acid - e pair acceptor
Me+ in ligand bond formation - Lewis acids

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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

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Which enzyme regulates pH in blood?

Carbonic anhydrase

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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)

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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)

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What enzyme cleaves peptide bonds?

Peptidases perform proteolysis - peptide bond cleavage

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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

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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

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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

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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

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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

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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

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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

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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

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What is the iron storage protein?

Ferritin - binds Fe2+ inside the hollow cavity - stores

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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 Fenton chemistry?

Fenton chemistry - peroxide reactions with Fe / Cu ions that produce ROS

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 enzyme catalyses degeneration of superoxide?

Superoxide dismutase

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

Which enzyme can convert dioxygen into water without ROS?

Cytochrome oxidase

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

What is the driving force in ET?

Driving force - difference in reduction potentials of donor / acceptor

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

From all factors which are the most rate determining in ET?

Biggest influence on rate of ET: - distance between donor and acceptor - reorganisation of cofactors

What are the studied examples for electron transfer (ET)?

- plastocyanin - Cu complexes - cytochrome c - iron-sulfur clusters - NADPH / quinones / flavins

Explain plastocyanin in ET

Plastocyanin: - e- carrier in photosynthesis - Cu2+ + e -><- Cu+ - Cu2+ favours sq planar - geometry change - Cu+ favours Td

What is teh major change when Cu2+ -> Cu+?

Geometric change: Cu2+ sq planar - Cu+ 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

Explain hemoglobin active site components and thier functions

What molecule is used for O2 transport in invertebrates?

Hemocyanin - Cu+ -> Cu2+ - 6 His at active site