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Year 3 - Chemistry > Bioinorganic > Flashcards

Bioinorganic Flashcards

(108 cards)

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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
What is haemoglobins purpose and basic structure?
O2 transport protein in RBCs α2β2 Tetramer - each subunit being similar to myoglobin
26
How does the oxygen binding affinity of myoglobin and haemoglobin compare?
27
Why is myoglobin not used for oxygen transport?
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
28
What does the basic term cooperativity of haem mean?
Change of shape of the haem structure as binding of oxygen changes
29
What is the model of allosteric cooperativity in haemoglobin?
30
What prevents the oxidation of haem to Fe(III)?
Steric bulk prevents this thermo tendency
31
What is hemocyanin?
Cu protein used in anthropods for O2 transport In the blood plasma directly
32
Define energy in electrochem terms
Flow of e- from fuel to an oxidant
33
What are the three electron transfer centre classes?
All found in proteins, and adapted for long-range transfer
34
What factors affect reduction potentials of metals in proteins?
Coordination chem: ionisation energy, ligands Influence of active site: relative permittivity, neighbouring charges on AA, H-bonding
35
How does the influence of the active site affect reduction potential?
Permittivity - stabilises low charge centres H bonding - stabilise reduced states
36
What is Marcus' theory on the rate of ET?
ET rate depends on: ΔG0 - of reaction ΔG - activation λ - reorganization energy HAD - overlap of electron donor and acceptors Temperature
37
What is commonly seen in ET centres in proteins?
Redox active metal centres Small r(M-L) change between oxn states Close donor and acceptors Ability to delocalise e-
38
How does ET work in Fe porphyrins? | (type of cytochromes)
6-coordinate and low spin Cytochrome has edge exposed to solvent - can interact with other proteins to allow for e- transfer
39
How is Cu coordinated in transfer centres?
N imidazole (histidine) Thiolate S (cysteine) More oxidising by cytochromes
40
Why and when are cu centres blue?
Small e- transfer proteins Ligand to metal charge transfer transitions
41
What is the entactic state?
State of an atom/group which has geometric or electronic condition adapted for function Due to binding in a protein
42
How does ET occur in mono-Cu centred proteins?
Rigid coordination sphere from protein
43
Why is ET fast in Cu centred proteins?
Rigid coordination sphere prevents r(M-L) change Small reorganisation energy
44
When are bi-nuclear Cu e- transfer centres used?
Long range e- transfer in some enzymes Similar coordination environment to mono e- delocalised which lowers reorganisation energy
45
What are the roles and abundance of metal-S/O clusters?
Found in nearly all organisms Used for: ET, redox catalysis, acid-base catalysis, sensing
46
What is the structure of Fe-S centres?
47
Why are FeS centres good for doing fast ET?
Can delocalise the extra e- Minimises bond length change Decreased reorganisation energy
48
What are the structures of the three most common FeS centres?
49
What are the features of FeS structures wrt electronic factors?
Generally single ET Reduced form is a good reducing agent (in general) Fe atoms are high spin (tet. geometry of thiolate ligands)
50
What is the reduction half-equations for FeS?
51
What affects the redox potential of FeS clusters?
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
What is an electron relay?
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
What is a hydrogenase?
Metalloenzymes which catalyse interconversion of H2 and H+ High turnover enzymes All contain Fe, some also contain Ni in active site
54
What does the active site of a hydrogenase look like?
Features: bi-metallic, coordinated to protein via cysteine S ligands, one CO or CN ligand
55
How is H2 oxidised by [FeFe] hydrogenase?
56
How is H2 oxidised by [NiFe] hydrogenase?
Arginine pockets acts as a base
57
How does H2 oxidation by hydrogenase compare with classical oxidation?
Classical: oxidative addition by TM complex Hydrogenase: H2 split heterolytically by “Frustrated Lewis Pair”
58
How can catalysts working similar to hydrogenases be synthesised?
Frustrated lewis pair compounds synthesised Compound has lewis acid and base that cannot combine to form an adduct
59
What is the structure of the Dubois catalyst?
Frustrated lewis pair catalyst
60
What is carbon monoxide dehydrogenase?
CO2 conversion to CO Uses FeS clusters, with Ni [Ni4Fe-4S] clusters
61
What is the shape of clusters in CO2 dehydrogenase?
62
What are nitrogenases?
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
What is the overall equation of nitrogen fixation?
Uses nitrogenase N2 + 8 H+ + 16 ATP → 2 NH3 + H2 + 16 PO3(OH)2- + 16 ADP
64
What is the structure of nitrogenase enzymes?
Two proteins: MoFe and Fe protein
65
What is the structure of the P cluster in nitrogenases?
66
What is the structure of the FeMo-cofactor in nitrogenases?
67
What does FeMo-cofactor (FeMoco) do in nitrogenase?
Site responsible for N2 to NH3 Mechanism not understood
68
What is the function of Cytochrome c peroxidase?
Reduction of H2O2 using e- from cytochrome c Uses Ferryl complex
69
What is the structure of cytochrome c peroxidase?
Fe(III) cytochrome
70
What is the catalytic cycle for reduction using cytochrome c peroxidase?
71
What is a ferryl complex?
FeIV=O complex oxide ligand stabilises high oxidation state
72
What is cytochrome P450?
Mono-oxygenase → catalyses regiospecific O-insertion into C-H bonds Essential in biosynthesis
73
What is the mechanism of Cytochrome P450?
74
When are ferryl intermediates found in non-haem oxygenases?
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
What is corrin?
Cobalt in a complex with macrocyclic ligand Used as a cofactor
76
What is cobalamin?
When 5th ligand on corrin complex is benzimidazole
77
What is a cofactor?
Non-protein compound or metal ion required for enzyme's activity as a catalyst
78
What is the structure of coenzyme B12?
79
What is the structure of coenzyme B12?
80
What oxidation states of cobalt can exist in macrocycles?
81
What is the mechanism of the methyl transfer by coenzyme B12?
82
What is the mechanism of radical-based rearrangements by coenzyme B12?
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
What are the steps in radical-based rearrangement by coenzyme B12?
Co(III) - C bond in resting state Homolytic cleavage C radical performs hydride abstraction Radical rearrangement to form 1,2 transfer
84
What forms of radical rearrangements do coenzyme B12 catalyse?
Isomerisation by mutases Dehydration or deamination by lyases
85
What is the name of enzymes which use FeS clusters for radical-based rearrangements?
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
What is the mechanism for radical SAM production of 5'-deoxyadenosyl radical?
87
Learn the radical SAM rearrangement with lysine zwitterion?
88
What is the purpose of cytochrome c oxidase?
Proton pump reduces O2 to H2O Found in mitochondrial membranes
89
What is the equation and mechanism of cytochrome c oxidase?
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
What is the structure of metal centres in cytochrome c oxidase?
91
What is the mechanism of cytochrome c oxidase?
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
How is O2 produced in photosynthesis?
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
What metal is found in chloroplasts?
Manganese-oxo species
94
What is the cycle for photosynthesis?
95
What is the Mn complex structure in chloroplast?
96
What are the main mechanisms in enzyme catalysis?
Ferryl intermediates Oxygen rebound mech - cytochrome P450 Radical - coenzyme B12 Radical SAM
97
How do metalloenzymes typically act as lewis acid-base catalyst?
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
What is the difference between structural or catalytic zinc?
Structural - coordinatively saturated (4 coordinate) Catalytic - metal ion in active site (3 coordinate), coordinatively unsaturated
99
What are zinc fingers?
Small proteins using Zn(II) ions in a structural role Many play roles in DNA recognition - regulates transcription and translation
100
What are some features of catalytic Zn?
3-coordinate, 4th is exchangeable with H2O Fast H2O and ligand exchange rates Flexible coordination geometry Acts as a Lewis acid
101
How can Zn catalyse amide/ester hydrolysis?
Aided by coordinating ligand in proteins (His) Large effective [OH-] in active site
102
What is the mono Zn-carbonyl mechanism for amide/ester hydrolysis?
103
What is the Zn-carbonyl mechanism for amide/ester hydrolysis with 2xZn?
104
What is the alcohol dehydrogenase mechanism using Zn-carbonyl?
105
What is the mechanism of carbonic anhydrase?
Hydrolysis of CO2 Produces carbonic acid
106
How are FeS centres used in lewis acid-base catalysis?
In aconitase which is included in the Krebs cycle
107
What does aconitase catalyse?
108
What is the cycle in aconitase catalysis of citrate?

Year 3 - Chemistry (12 decks)

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