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Year 3 - Chemistry > Bioinorganic > Flashcards

Bioinorganic Flashcards

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1
Q

How does cis-platin work?

A

In blood plasma has 2x Cl ligands as high [Cl-]
In cytosol low [Cl-] so replaced by OH2 to make charged complex which can coordinate

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2
Q

What are the characteristics of Na+ and K+ complexes?

A

Weak interactions

Hard ligands

Selectivity from size match and hydrophobicity

No redox chemistry

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3
Q

How are Na+ and K+ used in cells?

A

Controlling osmotic pressured

Transported in and out of cells - weak, reversible coordination chemistry

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4
Q

What are the characteristics of Mg2+ and Ca2+ complexes?

A

Hard ligands

Strong ionic interactions - charge dense ions

Selectivity from size match and hydrophobicity

Ca - fast ligand exchange kinetics

No redox chemistry

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5
Q

How is Mg and Ca used in biology?

A

Mg - ATP catalysis, structural role in enzymes

Ca - signalling (as fast ligand exchange with hard ligands), and structural (Ca phosphates/carbonates are insoluble)

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6
Q

Define compartmentalisation

A

Distribution of elements in and out of a cell, between organelles

Barriers formed by lipid bilayers - impermeable to ions

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7
Q

What is the concentration of Na+ and K+ in and outside a cell?

A

Inside - high [K+] and low [Na+]

Outside - low [K+] and high [Na+]

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8
Q

Define passive transport

A

Channel or ionophore facilitates diffusion of ion down its conc gradient

No energy required

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9
Q

How do K+ protein channels function?

A

K+ conducted down electrochem gradient

Selective against Na+

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10
Q

What is a ionophore?

A

Small molecule with polar interior and lipophilic exterior

Allows for reversible binding of ions for membrane transport

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11
Q

What is the use of an ionophore?

A

Antibiotic targeting the K+ membrane transport

Selectively transports K+ and disrupts ion gradients to destroy bacteria

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12
Q

What is active transport?

A

Ion pump transports ions against conc gradient using energy from ATP hydrolysis

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13
Q

How do ion pumps work?

A

Free energy of ATP hydrolysis used to interconvert between two conformations of ion pump

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14
Q

Why is Ca2+ suitable for signalling?

A

Large & flexible coordination geometry

Intermediate binding constants

Fast ligand exchange kinetics

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15
Q

What is Calmodulin?

A

Ca2+ sensor - protein

Changes conformer upon 4x Ca2+ binding

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16
Q

How is iron often stored in animals and why?

A

Essential but difficult to obtain and v toxic in XS

Haemoglobin and myoglobin as Fe-porphyrins

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17
Q

How is Fe(III) transported in mammals?

A

Transferrin proteins

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18
Q

What are the properties of transferins?

A

Hard donors

Multi-dentate, chelate effect

High binding constant - to obtain Fe(III) at low conc

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19
Q

How can bacteria get a source of Fe?

A

Cannot absorb directly - precipitates as Fe(OH)3

Multi-dentate O-donor ligands called siderophores used to scavenge

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20
Q

Describe how myoglobin works

A

Fe protein that coordinates O2 reversibly

Protein has several alpha-helices, haem is between them

Helix E stabilises coordinated O2

Helix F provides proximal histidine ligand

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21
Q

What is haem?

A

Fe(II) - porphyrin

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22
Q

How does O2 bind to myoglobin?

A

Works as O2 is a strong field pi-acceptor ligand

Fe(II) LS has no e- in antibonding orbitals so small radiuseff and moves into porphyrin plane

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23
Q

How can the binding of O2 in myoglobin be shown as an MO diagram?

A
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24
Q

Where is myoglobin found?

A

Found in tissue

Controls [O2] in the tissue

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25
Q

What is haemoglobins purpose and basic structure?

A

O2 transport protein in RBCs

α2β2 Tetramer - each subunit being similar to myoglobin

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26
Q

How does the oxygen binding affinity of myoglobin and haemoglobin compare?

A
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27
Q

Why is myoglobin not used for oxygen transport?

A

Myoglobin - 98% saturated in lungs and 91% in tissue so only 7% of sites can be used for transport

Haem - 66 % of sites can be used for transport, due to cooperative binding and release

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28
Q

What does the basic term cooperativity of haem mean?

A

Change of shape of the haem structure as binding of oxygen changes

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29
Q

What is the model of allosteric cooperativity in haemoglobin?

A
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30
Q

What prevents the oxidation of haem to Fe(III)?

A

Steric bulk prevents this thermo tendency

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31
Q

What is hemocyanin?

A

Cu protein used in anthropods for O2 transport

In the blood plasma directly

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32
Q

Define energy in electrochem terms

A

Flow of e- from fuel to an oxidant

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33
Q

What are the three electron transfer centre classes?

A

All found in proteins, and adapted for long-range transfer

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34
Q

What factors affect reduction potentials of metals in proteins?

A

Coordination chem: ionisation energy, ligands

Influence of active site: relative permittivity, neighbouring charges on AA, H-bonding

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35
Q

How does the influence of the active site affect reduction potential?

A

Permittivity - stabilises low charge centres

H bonding - stabilise reduced states

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36
Q

What is Marcus’ theory on the rate of ET?

A

ET rate depends on:

ΔG0 - of reaction

ΔG - activation

λ - reorganization energy

HAD - overlap of electron donor and acceptors

Temperature

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37
Q

What is commonly seen in ET centres in proteins?

A

Redox active metal centres

Small r(M-L) change between oxn states

Close donor and acceptors

Ability to delocalise e-

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38
Q

How does ET work in Fe porphyrins?

(type of cytochromes)

A

6-coordinate and low spin

Cytochrome has edge exposed to solvent - can interact with other proteins to allow for e- transfer

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39
Q

How is Cu coordinated in transfer centres?

A

N imidazole (histidine)

Thiolate S (cysteine)

More oxidising by cytochromes

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40
Q

Why and when are cu centres blue?

A

Small e- transfer proteins

Ligand to metal charge transfer transitions

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41
Q

What is the entactic state?

A

State of an atom/group which has geometric or electronic condition adapted for function

Due to binding in a protein

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42
Q

How does ET occur in mono-Cu centred proteins?

A

Rigid coordination sphere from protein

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43
Q

Why is ET fast in Cu centred proteins?

A

Rigid coordination sphere prevents r(M-L) change

Small reorganisation energy

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44
Q

When are bi-nuclear Cu e- transfer centres used?

A

Long range e- transfer in some enzymes

Similar coordination environment to mono

e- delocalised which lowers reorganisation energy

45
Q

What are the roles and abundance of metal-S/O clusters?

A

Found in nearly all organisms

Used for: ET, redox catalysis, acid-base catalysis, sensing

46
Q

What is the structure of Fe-S centres?

A
47
Q

Why are FeS centres good for doing fast ET?

A

Can delocalise the extra e-

Minimises bond length change

Decreased reorganisation energy

48
Q

What are the structures of the three most common FeS centres?

A
49
Q

What are the features of FeS structures wrt electronic factors?

A

Generally single ET

Reduced form is a good reducing agent (in general)

Fe atoms are high spin (tet. geometry of thiolate ligands)

50
Q

What is the reduction half-equations for FeS?

A
51
Q

What affects the redox potential of FeS clusters?

A

Ligands bonded to Fe: His coordination stabilises Fe(II) and raises reduction potential (more +ve)

Protein environment: proteins raise redox potential (more +ve) due to H-bonding and local dielectric environment

52
Q

What is an electron relay?

A

Chain of FeS clusters in proteins

e- tunnels between clusters, to redox partners in mitochondrial membranes

Causes H+ pumping, O2 reduction to H2O

E.g. NADH-hydrogenase

53
Q

What is a hydrogenase?

A

Metalloenzymes which catalyse interconversion of H2 and H+

High turnover enzymes

All contain Fe, some also contain Ni in active site

54
Q

What does the active site of a hydrogenase look like?

A

Features: bi-metallic, coordinated to protein via cysteine S ligands, one CO or CN ligand

55
Q

How is H2 oxidised by [FeFe] hydrogenase?

A
56
Q

How is H2 oxidised by [NiFe] hydrogenase?

A

Arginine pockets acts as a base

57
Q

How does H2 oxidation by hydrogenase compare with classical oxidation?

A

Classical: oxidative addition by TM complex

Hydrogenase: H2 split heterolytically by “Frustrated Lewis Pair”

58
Q

How can catalysts working similar to hydrogenases be synthesised?

A

Frustrated lewis pair compounds synthesised

Compound has lewis acid and base that cannot combine to form an adduct

59
Q

What is the structure of the Dubois catalyst?

A

Frustrated lewis pair catalyst

60
Q

What is carbon monoxide dehydrogenase?

A

CO2 conversion to CO

Uses FeS clusters, with Ni

[Ni4Fe-4S] clusters

61
Q

What is the shape of clusters in CO2 dehydrogenase?

A
62
Q

What are nitrogenases?

A

Reduction of N2 to NH3

Found in nitrogen fixing bacteria on root nodules of legumes

Active process - uses ATP, but does at RTP which usually difficult as high activation cost

63
Q

What is the overall equation of nitrogen fixation?

A

Uses nitrogenase

N2 + 8 H+ + 16 ATP → 2 NH3 + H2 + 16 PO3(OH)2- + 16 ADP

64
Q

What is the structure of nitrogenase enzymes?

A

Two proteins: MoFe and Fe protein

65
Q

What is the structure of the P cluster in nitrogenases?

A
66
Q

What is the structure of the FeMo-cofactor in nitrogenases?

A
67
Q

What does FeMo-cofactor (FeMoco) do in nitrogenase?

A

Site responsible for N2 to NH3

Mechanism not understood

68
Q

What is the function of Cytochrome c peroxidase?

A

Reduction of H2O2 using e- from cytochrome c

Uses Ferryl complex

69
Q

What is the structure of cytochrome c peroxidase?

A

Fe(III) cytochrome

70
Q

What is the catalytic cycle for reduction using cytochrome c peroxidase?

A
71
Q

What is a ferryl complex?

A

FeIV=O complex

oxide ligand stabilises high oxidation state

72
Q

What is cytochrome P450?

A

Mono-oxygenase → catalyses regiospecific O-insertion into C-H bonds

Essential in biosynthesis

73
Q

What is the mechanism of Cytochrome P450?

A
74
Q

When are ferryl intermediates found in non-haem oxygenases?

A

Fe(II),coordinated by AA, reacts with O2 → ferryl species

Ferryl species used to oxidise organic compounds

Fe(II) low in Irving-Williams series, so ion not bound tightly and difficult to study spectroscopically

75
Q

What is corrin?

A

Cobalt in a complex with macrocyclic ligand

Used as a cofactor

76
Q

What is cobalamin?

A

When 5th ligand on corrin complex is benzimidazole

77
Q

What is a cofactor?

A

Non-protein compound or metal ion required for enzyme’s activity as a catalyst

78
Q

What is the structure of coenzyme B12?

A
79
Q

What is the structure of coenzyme B12?

A
80
Q

What oxidation states of cobalt can exist in macrocycles?

A
81
Q

What is the mechanism of the methyl transfer by coenzyme B12?

A
82
Q

What is the mechanism of radical-based rearrangements by coenzyme B12?

A

Co(II) is low spin and JT distortion occurs

Even powerful σ-donors not bound, so weak N- or O- donors do not bind to Co and inhibit catalysis

83
Q

What are the steps in radical-based rearrangement by coenzyme B12?

A

Co(III) - C bond in resting state

Homolytic cleavage

C radical performs hydride abstraction

Radical rearrangement to form 1,2 transfer

84
Q

What forms of radical rearrangements do coenzyme B12 catalyse?

A

Isomerisation by mutases

Dehydration or deamination by lyases

85
Q

What is the name of enzymes which use FeS clusters for radical-based rearrangements?

A

Radical S-adenosylmethionines (radical SAMs)

Same as B12 - uses a 5’-deoxyadenosyl radical, but generated by reductive cleavage of SAM cation using [4Fe-4S] cluster

86
Q

What is the mechanism for radical SAM production of 5’-deoxyadenosyl radical?

A
87
Q

Learn the radical SAM rearrangement with lysine zwitterion?

A
88
Q

What is the purpose of cytochrome c oxidase?

A

Proton pump reduces O2 to H2O

Found in mitochondrial membranes

89
Q

What is the equation and mechanism of cytochrome c oxidase?

A

O2(g) + 4e- + 8H+ → 2H2O(l) + 4H+

Proton in reactants from inside, in products outside

Protons pumped across mitochondrial membrane against conc gradient

Gradient formed used to make ATP (via ATP synthase), so is an energy store

90
Q

What is the structure of metal centres in cytochrome c oxidase?

A
91
Q

What is the mechanism of cytochrome c oxidase?

A

O2 binding to Fe(II) porphyrin (like haemoglobin)

Radical formation (on nearby tyrosine – like cytochrome c peroxidase)

Formation of an Fe(IV) ferryl intermediate (like peroxidase and P450)

92
Q

How is O2 produced in photosynthesis?

A

2H2O → 4H+ + 4e- + O2

2H2O → 2H2 + O2

Solar energy captures & stores energy as chemical bonds via oxidation, occurs in chloroplasts

H2 stored as NADPH

93
Q

What metal is found in chloroplasts?

A

Manganese-oxo species

94
Q

What is the cycle for photosynthesis?

A
95
Q

What is the Mn complex structure in chloroplast?

A
96
Q

What are the main mechanisms in enzyme catalysis?

A

Ferryl intermediates

Oxygen rebound mech - cytochrome P450

Radical - coenzyme B12

Radical SAM

97
Q

How do metalloenzymes typically act as lewis acid-base catalyst?

A

Metal acts as lewis acid

Surrounding ligand (side chains) or water acts as lewis base

Often Zn as no accessible redox chem (high on IW series) and FeS clusters

98
Q

What is the difference between structural or catalytic zinc?

A

Structural - coordinatively saturated (4 coordinate)

Catalytic - metal ion in active site (3 coordinate), coordinatively unsaturated

99
Q

What are zinc fingers?

A

Small proteins using Zn(II) ions in a structural role

Many play roles in DNA recognition - regulates transcription and translation

100
Q

What are some features of catalytic Zn?

A

3-coordinate, 4th is exchangeable with H2O

Fast H2O and ligand exchange rates

Flexible coordination geometry

Acts as a Lewis acid

101
Q

How can Zn catalyse amide/ester hydrolysis?

A

Aided by coordinating ligand in proteins (His)

Large effective [OH-] in active site

102
Q

What is the mono Zn-carbonyl mechanism for amide/ester hydrolysis?

A
103
Q

What is the Zn-carbonyl mechanism for amide/ester hydrolysis with 2xZn?

A
104
Q

What is the alcohol dehydrogenase mechanism using Zn-carbonyl?

A
105
Q

What is the mechanism of carbonic anhydrase?

A

Hydrolysis of CO2

Produces carbonic acid

106
Q

How are FeS centres used in lewis acid-base catalysis?

A

In aconitase which is included in the Krebs cycle

107
Q

What does aconitase catalyse?

A
108
Q

What is the cycle in aconitase catalysis of citrate?

A

Year 3 - Chemistry (12 decks)

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