biological inorganic chemistry

Question 1

bulk essential metals

Answer 1

high quantity found in body, have a structural role

na+ k+, charger carries that control ionic strength

mg2+ complexes with nucleotides, and other enzymes

ca2+ signalling, receptor ion channeles, kinases, myosin actin action

Question 2

trace essential metals

Answer 2

found in small concentrations but very important

Mo - n2 fixation, O atom transfer

Mn-water splitting enzyme

Ni - hydrogenase
Co - vitamin b12
zn - numerous enzyme, zinc fingers
FE - electron transport proteins, haemoglobin , n2 fixation, ferritin

Cu - electron transfer, 02 transport and activation

Question 3

ligands

Answer 3

electron donors - lone pair e- donate to form bond with ion

coordination complexes - bond to metals

coordination number - the number of ligands atoms directly bonded to central ion

types of ligand - monodenate (one e- pair donated) and bidentate (2 e-pairs donated)

Question 4

amino acids and ligands

Answer 4

amino acids can act as ligands, interacting with metal ion - display of this on sheet

Question 5

cofactors

Answer 5

ligands are cofactors

interact with the enzyme to facilitate the binding of substrates, stabilize reaction intermediates, or participate in the chemical transformations during catalysis.

Question 6

lewis acids

Answer 6

accept lone pair of electrons
- they polarise bonds and stabilise transition states

Question 7

examples of lewis acids

Answer 7

any positive ions

Zn2+ and Mg2+ are the favourites because they are just right

if the bonds created are too strong, can get stuck in transition state so need a good balance

Question 8

carbonic anhydrase

Answer 8

allows transport of co2 by this reaction

h20 + co2 –><– h2co3

when ph is low, co2 is carried around body as h2co3, due to the enzyme catalysing the reversible hydration of CO₂, to transport

contains a zinc ion (Zn²⁺) at its active site, which is crucial for its catalytic activity, making it a type of metalloenzyme.

Question 9

zinc in carbonic anhydrase

Answer 9

acts as a ligand

Protonation States: its function depends on the ability to interact with water molecules to facilitate the conversion of CO₂ to bicarbonate.
At very low pH (acidic conditions), the protonation of amino acid residues in the active site may interfere with the enzyme’s ability to bind water and perform the reaction. - when in blood

In very high pH (alkaline conditions), the enzyme’s structure may become destabilized, reducing activity. - when in lungs

Question 10

peptidases

Answer 10

uses zinc and amino acid residues to form ligand

peptides are very stable so zinc increases this reaction in order to cleave peptide bonds

Question 11

how peptidases works

Answer 11

the peptidase with zinc - zinc polarises the carbonyl bond of peptide to facilitated attack by water in order to cleave bond

zinc stabilise the new carboxylate group

Question 12

atp hydrolysis and magnesium

Answer 12

Magnesium ions help stabilize these charges by coordinating with the phosphate groups, allowing ATP to remain in a more stable, reactive form.

Mg²⁺ is essential for the activation of ATP

§

Question 13

homeostasis

Answer 13

maintaining metal ion concentrations at appropriate levels is essential for health

too high metal ions conc = toxic

too little conc = deficient

Question 14

chelation therapy

Answer 14

used to remove heavy metals or toxins

The process typically involves:

Chelating Agents: These are compounds (e.g., EDTA, DMSA, or DMPS) that have specific sites capable of binding to metal ions.

Binding and Removal: The chelating agent binds to toxic metals in the bloodstream, and the resulting complex is eliminated from the body through the kidneys.

Question 15

Cu issues

Answer 15

cu definicient = menkes diases

cu excess = wilsons disease

Question 16

iron in homeostasis

Answer 16

very important and if not enough, limits growth

store iron as a ball called ferritin

fe2+ is delivered by transferrin
- passes into cavity via pores
- oxidised to fe3+

in cavity forms fe2o3 crystals

Question 17

respiration + photosynthesis

Answer 17

c6h12o6 + 6o2 –><– 6co2 + 6h20 + energy

photosynthesis is the opposite

Question 18

dioxygen

Answer 18

reaction between triple o2 and organic molecules is spin forbidden (high activation energy) but it is thermodynamically favourable - so a slow reaction

because of this, won’t react with organic matter until reached kinetic barrier

Question 19

oxygen activation

Answer 19

metal sites like Fe and Cu bind to oxygen and reduce it via stepwise electron transfer - oxygen activation

making it ready for reaction

Question 20

triplet oxygen

Answer 20

Triplet oxygen refers to the ground-state molecular oxygen (O₂), where the two electrons in the outermost orbitals have parallel spins

It’s relatively stable but reactive. It’s the form of oxygen found in the atmosphere and is used by most organisms in aerobic respiration.

Triplet oxygen is not highly reactive on its own, but it can react under certain conditions or with certain catalysts.

Question 21

super oxide

Answer 21

Superoxide is a reactive radical ion that forms when molecular oxygen gains one electron.

Its chemical formula is O₂⁻.

Superoxide is highly reactive and can cause oxidative damage in cells, but it’s also an important intermediate in many biochemical processes, including respiratory chains in mitochondria and immune responses.

It is often produced as a by-product in cells when triplet oxygen is reduced,

Question 22

peroxide

Answer 22

Hydrogen peroxide (H₂O₂) is a stable compound formed when two superoxide molecules combine, or when oxygen is reduced by two electrons in biological systems.

It is less reactive than superoxide but still can be damaging to cells if not regulated.
It is used by immune cells to kill bacteria, and it can be converted into more reactive hydroxyl radicals (*OH) in the presence of metal ions.

Peroxide can be dangerous because it can cause oxidative damage to lipids, proteins, and DNA. However, it is also used in various disinfection and bleaching processes in industry.

Question 23

summary of reactive oxygen species

Answer 23

Triplet oxygen (O₂) is the stable, normal form of oxygen.

Superoxide (O₂⁻) is a reactive oxygen species formed when oxygen gains an electron.

Peroxide (H₂O₂) is a compound formed by two superoxide molecules or through oxygen reduction and is also reactive but less so than superoxide

Question 24

Fenton chemistry

Answer 24

involves the generation of highly reactive hydroxyl radicals (*OH) from hydrogen peroxide (H₂O₂) in the presence of iron(II) ions (Fe²⁺).

Fe
2+
+H
2
​
O
2
​
→Fe
3+
+OH
−
+*OH

Question 25

free radical production

Answer 25

fe2+ + h2o2 –> fe3+ + oh- + oh radical

fe3+ + h2o2 –> fe2+ + h+ + ooh radical

Question 26

superoxide dismutase

Answer 26

is an important antioxidant enzyme that helps protect cells from damage caused by superoxide radicals (O₂⁻), a type of reactive oxygen species (ROS)

SOD catalyzes the conversion of superoxide radicals (O₂⁻) into hydrogen peroxide (H₂O₂) and oxygen (O₂), thereby reducing the harmful effects of superoxide. The reaction is:

2
O
2
−
+
2
H
+
→
H
2
O
2
+
O
2
2O
2
−
​
+2H
+
→H
2
​
O
2
​
+O
2
​

Question 27

superoxide dismutase reaction

Answer 27

cu2+ + o2 radical - –> cu+ + o2

cu+ + o2radical - –> c2+ h2o2

Question 28

catalase

Answer 28

gets ride of hydrogen peroxide
4 subunits binding to a heme fe3+ ligand

2h2o2 –> 2h2o + o2

Question 29

catalase reaction explained

Answer 29

peroxide reduction

peroxide oxidation

Question 30

respiration

Answer 30

proton translocation drives ATP synthesis

electrons passed through the elector transport chain

Question 31

respirasome

Answer 31

The respirasome is a complex assembly of enzymes involved in the electron transport chain (ETC) and oxidative phosphorylation in mitochondria. It facilitates the transfer of electrons from NADH and FADH₂ to oxygen, generating ATP. The main complexes involved in the respirasome are Complex I, Complex II, and Complex IV.

Question 32

complex I NADH: Ubiquinone Oxidoreductase

Answer 32

Function: Complex I is the first enzyme in the ETC and catalyzes the transfer of electrons from NADH (produced in the citric acid cycle) to ubiquinone (CoQ), reducing it to ubiquinol (CoQH₂).

Mechanism: As electrons are transferred, protons (H⁺) are pumped across the inner mitochondrial membrane into the intermembrane space, creating a proton gradient.

Energy Production: The electron transfer is coupled to the pumping of protons, contributing to the electrochemical proton gradient used by ATP synthase to produce ATP.

Question 33

complex II Succinate Dehydrogenase

Answer 33

Function: Complex II links the citric acid cycle to the electron transport chain. It transfers electrons from succinate (via FADH₂, formed in the citric acid cycle) to ubiquinone.

Mechanism: Unlike Complex I, Complex II does not pump protons across the membrane. It only transfers electrons and reduces ubiquinone to ubiquinol (CoQH₂), which feeds into Complex III.

Energy Production: Although it does contribute electrons to the ETC, Complex II does not directly contribute to the proton gradient, so it generates less energy compared to Complex I.

Question 34

Complex IV: Cytochrome c Oxidase

Answer 34

Function: Complex IV is the final enzyme complex in the electron transport chain. It catalyzes the transfer of electrons from cytochrome c (which has carried electrons from Complex III) to oxygen (O₂), reducing it to water (H₂O).

Mechanism: Electrons are passed through metal centers in the complex (copper and iron centers), and protons are pumped across the membrane into the intermembrane space. The reduction of oxygen to water is essential for keeping the electron flow moving through the chain.

Energy Production: Like Complex I, Complex IV contributes to the proton gradient by pumping protons, which is crucial for ATP synthesis.

Question 35

electron transfer

Answer 35

very important in respiration and photosynthesis

controls reduction during these processes

Question 36

complex 1

Answer 36

NADH –> NAD+

e- from NADH input into complex

this oxidises to NAD +

transfer e- to coenzyme Q so complex 1 can pump 4 H+ into IMS

start of proton gradient

Question 37

complex 2

Answer 37

FADH2 –> FAD

e- from FADH2 inputted
this oxidised FADH2 and transfers e- to COQ
reducing COQ to COQH2

no proton pumping in this one

Question 38

complex 3

Answer 38

COQH2 –> B –> C

e- form reduced COQ are transferred to cytochrome B then to cytochrome C

this pumps 4 H+ into IMS

city C is a mobile carrier to transfer e- to complex 4c

Question 39

complex 4

Answer 39

e- from reduced cytochrome transfer e- to cytoA then to oxygen which acts as a final e- acceptor to reduce and form water

complex 4 pumps 2H+ into IMS

completes ETC as OXYGEN –> WATER

Question 40

ATP synthase

Answer 40

proton gradient allows h+ to move down gradient from IMS back into mitochondria through ATP synthase which catalyses ADP + P –> ATP

Question 41

factors that influence rate of proton/electron transfer

Answer 41

distance - most important

intervening medium

driving force

reorganisation of cofactors - most important

Question 42

distance factor

Answer 42

the closer the two are, the faster

the rate of electron transfer decays exponentially with distance

closer the cofactors = higher the rate

Question 43

intervening medium factor

Answer 43

This medium can be a vacuum, a solvent, or a biological structure (e.g., proteins or membranes)

when the two are fully conjugated, B = 0

compared to a vacuum Beta = 2.8

Question 44

driving force factor

Answer 44

the difference in the reduction potentials of the donor and acceptor influence electron transfer in 2 ways

equilibrium position - The difference in reduction potentials determines the thermodynamic favorability of the electron transfer reaction:

Higher Driving Force (larger reduction potential difference):
The reaction becomes more exergonic (negative ΔG), favoring electron transfer and stabilizing the acceptor as the reduced species.
This sets the equilibrium position, where the ratio of reduced acceptor to oxidized donor increases with larger driving forces.
Lower Driving Force (smaller reduction potential difference):
The reaction is less thermodynamically favorable or even endergonic, reducing the extent of ET at equilibrium.

rate - Marcus theory
- Small driving force (low -ΔG):
ET is slower because the energy barrier is large, leading to lower rates.
Moderate driving force (optimal -ΔG):
ET rate peaks when the driving force approximately equals the reorganization energy (
Δ
G
∘
≈
−
λ
ΔG
∘
≈−λ), minimizing the activation energy for ET.
Excessive driving force (very high -ΔG):
The rate decreases due to the inverted region of Marcus Theory. This occurs because overly exergonic reactions push the system into a state where nuclear rearrangements hinder efficient transfer.

Question 45

reorganisation of cofactors factor

Answer 45

the electron must tunnel between donor and acceptor
k0 is heavily dependent on reorganisation energy

this takes into account bond length, coordination, geometry, spin state changes

if donor or acceptor change their them, affect he e- transfer rate

Question 46

plastocyanin

Answer 46

electron carrier during photosynthesis

cu2+ + e- –> <– cu 1+
blue copper centre surrounded by amino acid residues

when in oxidised state ( CU2+) favours a square planar form but when in reduced state cu1+, favours a tetrahedral form

sooooooo, it is a pseudo tetrahedral form known as its enteric state - optimised for both oxidation and reduction - this makes the e- transfer much quicker

Question 47

cytochrome C

Answer 47

heme plane large conjugated sysmte which gives cofactor a larger molecular orbital - a large D

no spin state change when transferring e-, so low reorganisation energy = good

Question 48

myoglobin

Answer 48

oxygen storage protein in muscles - gives muscles its pink colour

has a heme group that hydrogen bonds to oxygen to keep in place

myoglobin is highly abundant and combats Fe ion atoms

Question 49

myoglobin binding

Answer 49

colour changes
when o2 bound = deep red
n=o - pink colour
c=o irreversible binding

binds to o2 reversibly and holds and then releases when oxygen conc is low. like in exercise

Question 50

haemoglobin

Answer 50

active site very similar to myoglobin
Fe2 heme

has 2 alpha and 2 beta subunits, tetrameric - allows for cooperative binding
4 oxygen s can bind

Question 51

cooperative binding

Answer 51

enables efficient uptake and release of oxygen

Question 52

haemoglobin changing states

Answer 52

His residue displaces the alpha helix causing T state to R state protein change allowing oxygen to bind

r- state has a higher affinity for oxygen than

the tetramer is more stable in all the same states so it one changes, they all change to r- state