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Core 7: Advanced concepts > Bioinorganic chemistry > Flashcards

Bioinorganic chemistry Flashcards

1
Q

What is the difference between a hard and soft ligand and give an example of each

A

Hard ligand= highly charged and has a small coordinating atom, eg RO- (very charge dense)
Soft ligand= low charge and large atom, eg RS- (not very charge dense)

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2
Q

What does the Irving Williams (I-W) series tell us about?

A

The relative stability of metal-ligand complexes for a given ligand and a +2 metal ion; tells us that for a simple ligand, the Cu2+ ligand complex will always be more stable (smallest ion).

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3
Q

How do proteins select the correct metal for the job?

A

The Cu-Zn superoxide dismutase: Zn displaces the Cu in the active site, countering the I-W series. This is due to PREORGANISATION- the amino acids at the zinc site are held in position by the protein structure such that the metal coordination is JUST THE RIGHT SIZE FOR Zn.

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4
Q

Describe the structure of tetra-aza macrocycles and how they are used in biochemistry

A

PORPHYRIN GROUP is used extensively in bioinorganic chem and is found in metalloproteins (proteins which contain a metal but don’t catalyse a reaction) and metalloenzymes (do catalyse a reaction)- COFACTORS.

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5
Q

List 4 examples of tetra-aza macrocycles in biochemistry

A

Haem, chlorin, corrin, protoporphyrin IX

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6
Q

List 5 methods of selective metal spectroscopy

A

Single X-ray diffraction, extended X-ray absorption fine structure (EXAFS), anisotropic electron paramagnetic resonance (EPR or ESR), Mossbauer spectrpscopy, resonance raman spectroscopy

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7
Q

What is single X-ray diffraction and what does it give you?

A

Grow a single crystal of a metalloprotein (/enzyme) and subject it to X-ray diffraction; gives a 3D map of electron density of the protein structure. This map is presented in the form of a contour map of the density and needs interpreting.

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8
Q

What are some disadvantages of single crystal X-ray diffraction?

A

The crystals are extremely difficult to grow and it is sometimes difficult to interpret the contour map so need to augment the crystal data with other techniques. The contour maps can also sometimes be at low resolution- hard to interpretate.

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9
Q

How does time resolved single crystal X-ray diffraction work and what does it give you?

A

Use an X-ray laser to photoexcite the crystals (suspended in aqueous solution, flowing down a funnel at a controlled rate) and record the time-resolved diffraction pattern (time-resolved photocrystallography). Can be used to study metalloproteins which absorb light (eg photosynthetic proteins); gives you time-resolved structure information.

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10
Q

How do EXAFS work and what are the big advantages of this technique?

A

Synchotron used to produce X-rays (tuned to the frequency which ionises only the metal) which ionise the metal, and we record the absorption. Produces a spectrum with an extended region of fine structure- effects of backscatter. These back-scattered waves interfere at the metal to change absorption of the incident rays; degree of interference depends on the size of the backscattered wave, DISTANCE of metal to each surrounding atom and the energy of the original X-ray. Do not need crystals for this technique and can be done in solution or in the solid phase.

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11
Q

What does the Fourier transformation of an EXAFS spectrum tell us and why does the size of the peak reduce?

A

Gives radial distribution plots which tells us about the distribution of electron density around the metal in all directions- ie what is surrounding the metal at particular distances. Size of peak reduces as the signal decays, lost electron density- can only see local environment of metal.

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12
Q

What type of compounds is anisotropic electron paramagnetic resonance (EPR or ESR) used for?

A

Compounds with unpaired electrons- RADICALS (rather than isotropic samples).

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13
Q

How does anisotropic electron paramagnetic resonance work and how is it metal selective?

A

Anisotropic EPR: freeze the sample to 20K- splits the g values (equiv to chemical shift in NMR) into x/y/z components (gx/gy/gz). This tells us about the coordination geometry (from g values) and the degree of splitting to the nucleus (hyperfine values). Can be metal selective when the metal has an unpaired electron.

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14
Q

Describe the 3 classes of copper enzymes in terms of EPR

A

Type 1: electron transfer enzymes (royal blue).
Type 2: enzymes involved in oxidation.
Type 3: EPR SILENT!!!

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15
Q

How does Mossbauer spectroscopy work?

A

Examining the energy transitions in the nucleus. The transitions are sometimes sensitive to oxidation state (Fe, Sn) because a change in oxidation state which is accompanied by a change in the s-character of the redox active orbital has some population at the nucleus.

Apply fixed wavelength X-rays to sample, which experiences the Doppler shift, and measure absorption as a function of sample speed- from this can determine an oxidation state.

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16
Q

What does Raman spectroscopy give us info about and when is this technique selective?

A

Gives info about vibrations: apply laser to metal (metalloprotein) sample and detect the enhanced scattering from the metal (due to the resonance with electronic absorptions in the visible region). RESONANCE Raman spectroscopy= selective.

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17
Q

What does resonance Raman spectroscopy tell us?

A

Obtain a Raman spectrum of the vibrations associated with a metal ion- - - bond order

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18
Q

What is a consensus sequence?

A

Conserved sequence of amino acids.

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19
Q

What is the consensus sequence for a Zinc finger protein?

A

-X-X-Cys-X-X-Cys-X-

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20
Q

What can amino acid sequences tell us?

A

Can look at sequences and align together to see which amino acids are conserved- can then try determine type of metalloprotein.

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21
Q

What is the consensus sequence found in type 1 copper proteins in electron transfer?

A

-Cys-X2-His-X4-Met-

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22
Q

What are siderophores?

A

Class of compounds used by bacteria to acquire iron.

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23
Q

Name 4 examples of siderophores

A

Enterobacrin, pyocheiin, pseudobactin, myobactin P

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24
Q

Describe 2 key features of enterobactin

A

The preorganisation of the serine groups (all the NH2 groups point down one side of the ring) and the ester bond linking the serine groups.

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25
Q

How does enterobactin form stable iron complexes?

A

Has 3 catechol groups which coordinate to the metal in a hexadentate manner, in a perfect octahedral geometry.
At the ‘top’ of the enterobactin is a ring of 3 serine residues linked via an ester bond.
The catechol groups are orientated via H-bonds towards the centre of the molecule- ie they are perfectly pre-organised for metal (Fe) chelation.

26
Q

How stable is the Fe(III) enterobactin complex?

A

Is the most stable Fe(III) complex known to man

27
Q

How does the bacterium then get the iron?

A

Hydrolyses the triserine (serine esterase) into 3 separate pieces- lose the chelate effect.

28
Q

What is one reason for siderophores forming stable complexes?

A

They are multidentate ligands (chelate effect).

29
Q

What is the role of transferrin (and lactoferrin) and what problems does this solve?

A

Transferrin= iron transport protein, lactoferrin= protein which transports iron from mother to baby (protects iron in the breast milk). Solves 2 problems: need to acquire and transport Fe securely against the threat of siderophores and need to store Fe securely for emergencies.

30
Q

How does the quaternary structure of transferrin allow for iron to be transported and discuss the complex stability

A

Has 4 lobes; lobes come together and the Fe is buried within the protein structure. The complex stability is lower than enterobactin, but because the Fe is buried within the protein structure, the siderophores can’t reach it (STERIC BULK)- ie stabilising the Fe KINETICALLY (rather than thermodynamically).

31
Q

Describe the active site characteristics of transferrin

A

Is composed of hard/borderline amino acids which will form strong and stable complexes with hard metal ions (like Fe3+). Fe is stably coordinated by the carbonate and the amino acids; the site is pre-organised to fit Fe3+ (selective).

32
Q

What is ferritin?

A

Fe storage protein

33
Q

Describe the structure of ferritin

A

4 alpha helical bundles which self assemble to give ferritin- shaped like a football, 70 Angstroms in diameter and hollow inside.

34
Q

What is the difference between apo- and holo-ferritin?

A

Apo- = empty, holo- = contains Fe

35
Q

How does Fe enter ferritin?

A

Through the channels in the protein coat.

36
Q

How is Fe stored inside ferritin?

A

Stored as rust (Fe3+) to keep bacteria away (stable). But mobilisation of the Fe is slow as takes time to liberate Fe from the ferritin.

37
Q

Discuss chrome tanning chemistry

A

Animal skins made of many components, particularly collagen. To soften the leather and remove much of the other materials we don’t want, the leather is treated with harsh chemicals. However, this reaction destroys the collagen structure so leather loses its elasticity; hence needs to be reconstructed. Cr gives leather back its elasticity by bridging collagen.

38
Q

Describe the uptake-reduction model

A

The tanneries use [CrO4]2- which hijacks sulfate pathways (isostructural). The [CrO4]2- gets reduced to Cr(III) inside the cell which is the stuck- CARCINOGENIC.

39
Q

Describe some properties of Zinc

A

Zn(II) is the only ox state- REDOX STABLE.
Zn(II) is d10= diamagnetic and colourless.
Kinetically labile (reacts quickly).
Zn can act as a Lewis acid.

40
Q

What are the problems with Zn?

A

Difficult to study spectroscopically

41
Q

Describe some similarities and differences between Zn(II) and Co(II) and what is the consequence of these?

A

Similarities:
No CFSE difference between the octahedral and tetrahedral Co(II), like for Zn(II).
Differences:
Zn(II)= d10, no CFSE
Co(II)= d7, coloured and magnetic, often has rich spectral features

Therefore Co(II) acts as a substitute for the spectroscopically silent Zn(II).

42
Q

What is carbonic anhydrase?

A

Zinc enzyme that converts the carbon dioxide; it is very efficient (catalyses every molecule of carbon dioxide it encounters).

43
Q

What compound do you use to remove spectroscopically silent Zn(II) from an enzyme (in order to replace with Co(II))?

A

EDTA

44
Q

What is the Beer-Lambert (B-L) law?

A

A= ε c l

45
Q

What is the metal in human carbonic anhydrase and its coordination geometry?

A

Zn, Td

46
Q

What is ethanol converted to in the liver and what is the enzyme that catalyses this process?

A

Ethanal, liver alcohol dehydrogenase

47
Q

Which 2 locations in the body have the highest concentration of zinc?

A

The prostate and parts of the eye

48
Q

Describe how the structure of zinc finger proteins allows it to bind to DNA

A

Has a defined structure; proteins with finger-like domains which fit into the grooves of DNA. Finger-like structure is a long run of amino acids with Zn(II) at the bottom.

49
Q

Why are the finger proteins dependent on zinc?

A

Without it the finger collapses; zinc is used as a switch to turn DNA recognition on/off.

50
Q

What could you replace zinc with in the finger proteins to give spectroscopic features?

A

Co(II)

51
Q

What is the consensus sequence for the zinc finger proteins?

A

-Cys-X2-Cys-Xn-His-X4-His-

Xn= long run of amino acids making up the ‘finger’

52
Q

What are the necessary features of electron transfer and what must be avoided?

A

FeS (iron protein) and Cyt (Fe cytochrome)

Must avoid the generation of partially reduced O2, so we must reduce oxygen in one go, to water (requires 4 electrons).

Must be able to transfer electrons quickly but, because electron transfer only happens one at a time (not 4), we must have 4 separate but very fast transfers.

53
Q

List the 3 main classes of electron transfer sites

A

Fe cytochromes, Fe/S proteins, Cu electron transfer proteins (Type 1 Cu).

54
Q

Describe how the structure of the Fe cytochrome allows it to perform its function

A

= tetra-aza macrocycles which coordinate to Fe (Fe is also coordinated by 2 further side chains).

Cytochromes transfer a single electron (FeII/FeIII), Fe is coordinately saturated (CN=6) therefore is unreactive to O2, the whole structure is very rigid ie very low reorganisation energy between the reduced and oxidised states.

55
Q

What is rubredoxin?

A

Example Fe/S protein which transfers electrons and has a single Fe at its active site.

56
Q

Why is electron transfer so rapid at rubredoxin active sites?

A

Because the protein structure holds the cysteinates in a fixed position so low reorganisation energy.

57
Q

How many Fe sites do ferredoxins have?

A

2

58
Q

Discuss copper proteins and the difference between Cu(I)/Cu(II)

A

Cupredoxin fol (blue copper proteins)= -Cys-Xn-His-Xn-Met….-His-

Cu is able to exist as Cu(I)/Cu(II) so can act as an electron transfer site.
Cu(I)= d10, no CFSE, prefers Td geometry
Cu(II)= d9, prefers sqaure planar or distorted octahedral geometries.
Large difference in structure between the 2 geometries hence large reorganisation energy therefore slow electron transfer (bad).

59
Q

What is the entactic state?

A

The protein holds the Cu coordination geometry halfway between Cu(I) Td and Cu(II) square planar- gives low reorganisation energy hence fast electron transfer

60
Q

What are the problems with the conversion of O2 to H2O in biology?

A

To get to H2O, have to go through superoxide (O2-), peroxide (O2 2-) and hydroxyl radical (.OH). All are toxic.

61
Q

What is the chemical reaction for the reduction of O2 to H2O?

A

O2 + 4H+ + 4e- –> 2H2O

Core 7: Advanced concepts (5 decks)

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