Bioinorganic Chemistry Flashcards
How has the concentration of Fe, Cu and Zn in sea water changed as life has evolved and what has this meant for life?
Concentration of Fe has dropped greatly which means life has adapted to be as successful as possible at scavenging (with siderophores).
Cu and Zn concentrations have increased meaning life has adapted to use them
If the pKa of a molecule is below the pH of the solution it is in, is that molecule likely to be protonated or deprotonated?
pKa is the pH where there is perfect equilibrium between protonated/deprotonated. If pKa is lower then the molecule is likely to be deprotonated.
What is the pKa of histidine, is it likely to be deprotonated in blood, what is its donor atom and does it bind hard or soft metal cations?
6.5 , likely to be deprotonated, nitrogen l.p. , binds hard and soft metal cations
What is the pKa of aspartate, is it likely to be deprotonated in blood, what is its donor atom and does it bind hard or soft metals?
4.5 , likely to be deprotonated, O- , binds hard metal cations
What is the pKa of glutamate, is it likely to be deprotonated in blood, what is its donor atom and does it bind hard or soft metals?
4.5 , likely to be deprotonated, O- , binds hard metal cations
What is the pKa of tyrosine, is it likely to be deprotonated in blood, what is its donor atom and does it bind hard or soft metals?
10 , unlikely to be deprotonated, OH, binds hard metal cations
What is the pKa of cysteine, is it likely to be deprotonated in blood, what is its donor atom and does it bind hard or soft metals?
8.5 , unlikely to be deprotonated, SH, binds soft metal cations
What is the pKa of methionine, is it likely to be deprotonated in blood, what is its donor atom and does it bind hard or soft metals?
no protons at donor site, S , binds to soft metal cations
What are the characteristics of soft metal ions and give some examples
Low oxidation state, large ionic radius: Cu+ Zn2+ Mn2+ Fe2+ Co2+
What are the characteristics of hard metal ions and give some examples
High oxidation state, small ionic radius: Na+ K+ Mg2+ Fe3+
Are theses cations hard or soft? Cu2+, Fe2+, Fe3+, Zn2+, Na+
Cu2+ - Soft
Fe2+ - Soft
Fe3+ - Hard
Zn2+ - Soft
Na+ - Hard
Which species does the Irving-Williams series concern itslft with?
+2 first row d-block elements
What is the general trend in the Irving-Williams series?
Which cation is an exception and why?
Stability of metal 2+ cations with a ligand generally increases along the first row of d-block elements.
Cu2+ is higher than expected due to geometries it forms in solution.
Refering to the Irving-William series, why is it surprising that in certain protein geometries Zn2+ replaces Cu2+? What is this phenomenon known as?
The Irving-Williams series says that [L-Cu]2+ complexes are more stable than [L-Zn]2+ complexes so we would expect Cu to be able to displace Zn. However the protein has amino acid residues that are at the EXACT distance to favour binding of Zn over Cu. The ability of a protein to do this is due to PREORGANISATION.
What groups bind Fe well and what characteristic of these types of molecules makes it difficult to remove Fe?
Tetra-aza macrocyles (4 N donors) like the haem group. Difficult to remove Fe as the group has to bend - providing kinetic stability
What metal cations does the porphyrin group bind?
Fe, Mg, Co and Ni
Why does the study of metalloproteins involve special techniques?
We want to know information at the active site (where chemistry occurs) - 1 metal cation with hundreds of atoms in the protein. Standard techniques (like IR) leads to too much information that can not easily be deconvoluted
What are 2 pros and 3 cons of single crystal x-ray diffraction?
Pros:
- Gives a full 3D map of electron density
- Useful if the structure is known but not geometry
Cons:
- Difficult to grow single crystals
- Structure is often not well resolved
- solid structure may be different to solution structure (where chemistry occurs)
Briefly describe how Extended X-ray Absorption Fine Structure (EXAFS) works
- specific x-ray wavelength excites metal cation of interest
- results in emission of 1s photoelectron
- excitation occurs multiple times resulting in “ripples” propagating from metal
- immediately surrounding atoms back scatter photoelectron ripples
- constructive and destructive interference causes metal ion to oscillate
- Modulation is measured and depends on M-X distance
What information does EXAFS give?
Distance between a metal ion and other atoms, M-X distance.
How is an EXAFS RDP plot predicted?
- Determine which atoms are closest to the metal centre and how many of them there are
- multiply the number of atoms with the number of electrons on the atom
- plot number of electrons against bond distance for each atom
- draw an average plot of all atoms taking into account decay
What is anisotropic electron paramagnetic resonance known as?
EPR
What must the metal cation have to be detected via EPR?
An unpaired electron
What is the EPR equivalent of ppm in NMR?
g-value
What is the EPR equivalent of J-constants in NMR?
Hyperfine coupling constant (a)
How is anisotropic EPR different to usually EPR?
Anisotropic EPR splits g-value and hyperfine coupling constants into directional components (e.g. gx, gy, gz)
What component is resolved in anisotropic EPR?
z-component (gz and az)
What is the equation for calculating multiplicity in EPR?
multiplicity = 2nI + 1
For type 1 Cu proteins; what are their functions and what are the gz and Az values?
Electron transfer proteins in plants. gz = 2.2 , az = 5 mT
For type 2 Cu proteins; what are their functions and what are the gz and Az values?
Carry out oxidation reactions. gz = 2.25 , az ~ 15-20 mT
For type 3 Cu proteins; what are the gz and Az values?
Both Cu2+ cations undergo ferromagnetic exchange - essentially no paramagnetic and so EPR silent
Briefly describe how Mossbauer spectroscopy works
gamma-rays at fixed wavelength irradiate a sample (Fe) that is moving
What information can be determined by Mossbauer spectroscopy?
Spin state of Fe or Sn which is due to:
- oxidation state
- ligand field strength
What elements does Mossbauer spectroscopy work for?
Fe or Sn
What are consensus sequences?
A particular pattern of amino acids that is indicative of a specific function
How can consensus sequences be used to identify protein function?
Consensus sequences are conserved across organisms, so identification of a particular sequence can be compared to a protein of known function
If oxygen is so reactive with organic molecules why doesnt it destroy us?
Oxygen is in the triplet state while our organic molecules are in the singlet state and so reaction is spin forbidden
What do we used metalloproteins for in oxygen reduction?
To slowly and carefully reduce oxygen without the generation of ROS
What is an ROS?
Reactive oxygen species - usually radicals that are very reactive and dangerous species
Where is cytochrome c oxidase located?
In the mitochondria
How are mitochondria adapted to have a high rate of cellular respiration?
They have a high surface : volume ratio
What happens inside the mitochondria?
Several enzymes take high energy electrons (from NADH) and through several redox reactions they lower the energy of the electron for O2 reduction. The last enzyme is cytochrome c oxidase
What is the job of cytochrome c oxidase? What are the active metal sites present?
Binding of O2 to a Cu and Fe site before reduction to H2O
How many electrons can cytochrome c oxidase hold?
4 electrons
Why is the reactivity of O2 with the metal ions in cyctochrome c oxidase fast and why is it important that this step is fast?
Its fast as the metal ions can swap their spins to accommodate spin changes in the O2 (spin-orbit coupling). Important to be quick to avoid generation of ROS
What is the role of superoxide dismutase?
Protects cytochrome c oxidase if/when an ROS is generated
What is the chemical equation for the reaction that occurs in superoxide dismutase?
2x O2- + 2x H+ –> O2 + H2O2
What are the metals present in superoxide dismutase?
Cu2+ (and Cu+ during reaction) and Zn2+
What is the role of Zn2+ in superoxide dismutase?
Not involved in reaction, tunes the reduction potential of Cu
Is photosynthesis highly exothermic or endothermic?
Highly endothermic: requires the input of (light) energy
What is the OEC and what is its role in photosynthesis?
Oxygen-evolving complex: a cluster or Mn and Ca ions that oxidise water to O2
What happens during each stage of the Kok cycle?
A tyrosine radical cation (produced via light absorption) oxides the OEC from S0 to S3, removing an electron each time. At S3 an oxyl species is bound. The highly oxidised S4 state oxidises 2 water molecules returning in to the S0 state
What is the empirical formula for the ion cluster in the OEC?
Mn4Ca
Why is Mn used by nature in the Kok cycle?
Mn has a range of stable oxidation states (0-7)
Why does biology need a range of reduction potentials?
So that electron transfer can be rapid
What is a reduction potential?
The measure of a tendency of a species to gain an electron (undergoing reduction)
What is Marcus theory?
It explains the rates of electron transfer reactions
What is the reorganisation energy?
The energy required to change the shape of the oxidised species so that it is ready for electron transfer (electron transfer has not occurred YET!)
What does a small reorangisation energy mean for the rate of electron transfer?
The smaller to reoragnisation energy the faster the rate of electron transfer
How do proteins achieve small reorganisation energies?
Active sites are rigid; resulting in fast electron transfer
What is the inverted Marcus region and what does it highlight?
Very small or large ΔG results in high reorganisation energy and a slow rate - there are limitations to how fast electron transfer can occur
What are the 3 main classes of electron transfer sites in biology?
1) Fe-S proteins
2) Fe cytochromes
3) Cu blue sites (Type 1 proteins)
What does the active site of a cytochrome contain?
Iron containing porphryn (e.g. haem group) and two amino acids
Why is electron transfer in cytochromes fast?
Structurally rigid active site means low reorganisation energy
Why cant oxygen bind to the metal centre in a cytochrome?
The Fe ion is coordinately saturated (e.g. cannot accept any more ligands)
What is the active site of Rubredoxin, and how does this affect the spin of the metal ion?
Fe ion coordinated to 4 cysteinates (4x Fe-S) which provide weak field splitting and a high spin Fe
What two features of Rubredoxin aid electron transfer?
1) The protein structure is rigid (low reorganisation energy)
2) Fe-S bond is largely covalent (delocalisation of charge aids electron transfer)
What does the consensus sequence of Rubredoxin look like?
4 Cys residues
What are the two different sites for Ferredoxins?
Fe2S2 unit and Fe4S4 cube
Why does the Fe4S4 cube have such a high reduction potential and is this a good thing?
The electron is fully delocalised across the whole cube - high reduction potential means very easy to accept an electron
Why isnt Fe used in electron transfer sites in plants, what is used instead?
Low Fe bioavailability - Cu used instead.
What is the issue with plants using Cu (instead of Fe) as electron transfer sites and how do proteins mitigate this difficulty?
Cu(I) and Cu(II) have different geometries (Td and D4h) resulting in large reorganisation energy - plat proteins hold Cu ions EXACTLY halfway between Td and D4h and use a mixture of hard and soft ligands (Cys and His) to stabilise neither Cu(I) or Cu(II). Cu-S also delocalised charge.
Define entatic state?
The distorted geometry of atoms in a protein to optimise its function
Type 1 Cu proteins have electron transfer rates that are too slow for high energy organisms, but how is Cu used in the CuA site of cyctochrom c oxidase?
CuA site contains 2 Cu centres with sulphur bridges that fully delocalise the electron allowing for rapid electron transfer
What are the three properties of Zn that make it useful in biology?
1) Redox inactvie (only exists as Zn2+)
2) Kinetically labile - rapid ligand exchange
3) Great Lewis acid - accepts lone pairs
Why is Zn2+ difficult to study and how do we get around this?
Zn2+ is d10, no CFSE with no preference for coordiantion geometry and therefore few spectroscopic features. (e.g. No EPR).
We replace Zn2+ with a spectroscopically non-silent ion (e.g. Co(II) d7)
What is the role of carbonic anhydrase
Catalyses the slow reaction of CO2 and H20 into a carbonate ion and a proton. An incredibly efficient enzyme
What is the ε value for Td geometry?
~ 500 M-1 cm-1
What are the steps in the catalytic cycle of Human carbonic anhydrase II?
Lewis acidity of Zn is transferred to Bronstead acidity of cooridanted H20:
- Bound H20 is deprotonated
- Bound OH- attacks CO2
- Ligand substitution of HCO3- with H20 restarting the cycle
What is the role of Liver alcohol dehydrogenase?
Converts ethanol to acetaldehyde with NAD+. Similar mechanism to human carbonic anhydrase II
What is the role of zinc finger proteins?
DNA recognition and DNA chemistry
What is the structure of a Zinc finger protein?
Zn bound to 2x S and 2x N.
How did the Great Oxygenation Event (GOE) and how did it kick off a global “arms race”.
The GOE led to the rapid decrease in Fe concentration in sea water due to the formation of insoluble Fe2O3 (rust). This started the competition between life for Fe
What is a siderophore?
A high affinity iron chelating compound usually excreted by an organism (e.g. bacteria)
What is enterobactin?
A siderophore molecules excreted by E.coli in our gut. Has a stability constant of 10^49 - nothing can bind Fe(III) better
What are the key features of enterobactin?
H-bond network forces rings inwards to form a pocket perfect for Fe(III).
What is the issue for E.coli with enterobactin having such a large stability constant? How does E.coli get solve this issue?
Very difficult to remove Fe(III) from enterobactin. Enterobactin is an ester and so is hydrolysed to give a less stable complex that can remove Fe.
Name 3 siderophores other than enterobactin. Which heteroatom in all of these molecules bind to Fe(III)?
catecholate, hydroxymate, carboxylate. Oxygen is the chelating atom
What two proteins do animals have to fight enterobactin and how do they do it?
Transferrin and lactoferrin - structure of the protein “snaps shut” to kinetically stabilise Fe(III) and to block enterobactin from stealing it
How is the binding pocket of transferrin (and lactoferrin) specialised for its purpose?
1) Contain hard amino acids for stable chelation to Fe(III)
2) Carbamate binding - protonation opens transferrin to allow release (pH change in endosome)
3) Amino acids are preorganised for the perfect fit
What is the role of ferritin
An Fe binding protein
How is the structure of ferritin specialised for its purpose?
Has a hollow centre for binding. Porous to allow Fe to pass through.
How does ferritin bind Fe?
Fe passes through wall and is oxidised from Fe(II) to Fe(III) and crystalised as Fe2O3 (rust)
Why is chromate used in leather tanning and why is it dangerous?
Chromate cross-links fibres (collagen) to make leather more durable but chromate is highly carinogenic
How is chromate taken into the body?
Has an isostructure with SO4- and enters via SO4- uptake channels. Then reduced to Cr3+ which interferes with DNA chemistry and causes cancer
