Bio Inorganic chemistry

Study of Inorganic elements in the living systems

11 20
Na Ca
22.98 40.08

19 12
K Mg
39.09 24.31
Sodium potassium pump
(1/5th of all the ATP used)

26 27 29 30

Fe Co Cu Zn
55.85 58.94 63.55 65.38

Hemoglobin Vit B12 Hemocyanin Carbonic anhydrase

Myoglobin Carboxypeptidase
Cytochromes
Ferredoxin
 Important roles metals play in biochemistry
1. Regulatory Action Sodium potassium channels and pump
Na, K Nerve signals and impulses, action potential
muscle contraction
2. Structural Role Calcium in bones, teeth
Ca, Mg provide strength and rigidity
3. Electron transfer agents Cytochromes: redox intermediates
Fe2+/Fe3+ membrane-bound proteins that contain heme groups
and carry out electron transport in Oxidative phosphorylation
4. Metalloenzymes Carbonic anhydrase, Carboxypeptidase
Zn biocatalysts, CO2 to HCO3, protein digestion

5. Oxygen carriers and storage Hemoglobin, Myoglobin, Hemocyanin

Fe, Cu 18 times more energy from glucose in
presence of O2

6. Metallo coenzymes Vitamin B 12

Co biomethylation
 Structure of a metallo-protein : A metal complex perspective

Spiral -  helix form of protein Tape -  Pleated sheet form of protein

Prosthetic groups – A metal complex positioned in a crevice. Some of the ligands for this
complex or some times all of the ligands are provided by the side groups of the amino acid
units.
The geometry around the metal and bond distances and angles are decided by the protein unit

Myoglobin Carbonic anhydrase

 Metalloenzymes and Oxygen carriers =
Protein + Cofactor
A cofactor is a non-protein chemical compound that is bound to a protein and is required for the
protein's biological activity. These proteins are commonly enzymes. Cofactors are either organic
or inorganic. They can also be classified depending on how tightly they bind to an enzyme, with
loosely-bound or protein-free cofactors termed coenzymes and tightly-bound cofactors termed
prosthetic groups.

Porphyrins with different

metals at its centre are a
common prosthetic group
in bioinorganic chemistry

Cytochrome C Coenzyme B12

Hemocyanin Myoglobin Chlorophyll

 Protoporphyrin IX and Heme

15 different ways to arrange the substituents around the porphyrin. Only one
isomer protopophyrin IX is found in the living system. Porphyrins are planar
and aromatic
Proteins –consists of different amino acids in a specific sequence connected by the peptide
bond –
 A few important amino acids relevant to the present course

HISTDINE This amino acid VALINE is a branched-chain GLUTAMIC ACID has carboxylic acid
has a pKa of 6.5. This amino acid having a functional group which is hydrophilic, has
means that, at hydrophobic isopropyl R pKa of 4.1 and exists in its negatively
physiologically relevant pH group. In sickle-cell charged deprotonated carboxylate form at
values, relatively small disease, valine substitutes physiological pH ranging from 7.35 to 7.45.
shifts in pH will change its for the hydrophilic amino
average charge. Below a pH acid glutamic acid in
of 6, the imidazole ring is hemoglobin.Valine is
mostly protonated. hydrophobic

SERINE Serine is an amino acid having

a CH2OH side group. By virtue of the
hydroxyl group, serine is classified as a
polar amino acid. Serine was first
obtained from silk protein, a
particularly rich source, in 1865.
The primary structure of a protein
The four levels of protein structure

H bond between side chains,

hydrophobic interactions,
disulfur linkages, electrostatic
interactions

See youtube video “protein structure” Univ of Surrey ’

Hemoglobin- a quaternary structure of a protein

4 units

Each unit has a

prosthetic group
(heme) embedded
in a crevice and
partly coordinated
by histidine units
 Inorganic Active site / Prosthetic group

In molecular biology the

active site (prosthetic group)
is part of an enzyme where
substrates bind and undergo
a chemical reaction. It can
perform its function only
when it is associated with
the protein unit

Ferredoxin (e transfer)
Heme in Myoglobin (O2
storage)

Carbonic anhydrase Nitrogen Fixation

Enzyme)
Inorganic Prosthetic group of three well known oxygen carriers

Present in
Vertebrates

Present in
molluscs

Present in some sea

worms
 Can the prosthetic unit part of a metalloprotein perform its normal function
without the protein unit around it ?

Fe2+ + O2 Fe2+ O
O
Free Heme

4+
Fe2+ O + Fe2+ 2 Fe O
O

Fe4+ O + Fe2+ Fe3+ O

Fe3+

Reversible binding of O2 is possible on when protein

unit is present around the heme unit
 Oxygen : A few Questions

Why do we need oxygen or why do we breathe?

What happens to oxygen in our body and where does it

happen?

What does this reaction produce and how?

How exactly is oxygen carried around and stored in the body?

How exactly is CO2 removed from the body?

Electron transfer agents Cytochromes: redox intermediates
Fe2+/Fe3+ membrane-bound proteins that contain
heme groups and carry out electron transport in Oxidative
phosphorylation

Cytochromes are, in general, membrane-bound (i.e. inner mitochondrial

membrane) heme proteins containing heme groups and are primarily
responsible for the generation of ATP via electron transport.

They are found bound on the inner mitochondrial membrane either

as monomeric proteins (e.g., cytochrome c) or as subunits of bigger
enzymatic complexes that catalyze redox reactions. These heme proteins
are classified on the basis of the position of their lowest energy
absorption band in the reduced state, as
cytochromes a (605 nm), b (~565 nm), and c (550 nm).
Electron transfer agents; e.g. Cytochrome C

S(Cys) Protein

protein S(Cys) Protein

N N
N N CH3
H Fe S
methionine
N N residue of
protein

OH
HO O
O
 Glycolysis + Oxidative phosphorylation: How food is converted into energy

Glucose + 36 ADP + 36 Pi + 36 H+ + 6 O2 6 CO2 + 36 ATP + 42 H2O

Glucose gives 18 times more energy when oxidized

ATP + H2O ADP + Pi + H+ + energy  G0 = - 7.3 kCal/mole

ATP : Universal currency for energy

Different forms of Cytochromes (except
Cytochrome P-450) are involved in the in living systems
electron transfer process leading to ATP
synthesis and conversion of O2 to H2O
See youtube video ‘cellular respiration ( electron transfer chain)’
 Actual structure of ATP synthase
unit (a molecular machine!)

Cytochromes a and a3 Cytochrome c oxidase with electrons delivered to

complex by soluble cytochrome c (hence the name)
Cytochromes b and c1 Cytochrome c reductase
Why do we need oxygen or why do we breathe?
Oxygen is required for efficiently converting glucose to energy and
generate ATP (Oxidative phosphorylation). In the presence of oxygen 18
times more energy is released from the oxidation of glucose
What happens to oxygen in our body and where does it
happen?
Oxygen gets converted to water. It happens on the inner membrane of
the mitochondrion exactly at the last stage of electron transport chain
(on cytochorme c oxidase)
How exactly does oxygen change to water ?
Protons present inside the mitochondrion along with the electrons of
the correct potential ( generated during oxidation of food and supplied
through the electron transport chain) react with O2 and convert it to
water generating a proton gradient
What does this reaction result in?
The proton gradient generated during the electron transport chain and
conversion of O2 to water drives the molecular machine called ATP
synthase which makes ATP from ADP and Pi (Inorganic phosphate). ATP
is the universal currency of energy in living systems Su…gar goes to
How exactly is oxygen carried around and stored in the body? ATP…. !

Youtube: ATP synthase molecular machines

 Cytochromes in the electron transport chain

Cytochrome reductase (or b): Complex

unit having 2 different hexacoordinated hemes and
an Fe-S cluster
Function :electron transfer and proton gradient
generation

Cytochrome c: Unit
having one
hexacoordinated heme
Function: electron transfer

Cytochrome c oxidase: Unit has

pentacoordinated heme and tricoordinated Cu
Ageing is related to
generation of oxygen based Function: electron transfer to O2 converting it to water
free radicals which degrade + proton gradient generation
mitochondrial membranes
 Redox intermediates in electron transfer
Cytochrome C

S(Cys) Protein

protein S(Cys) Protein

N N
N N CH3
H Fe S
methionine
N N residue of
protein

Protein chain has 103 amino acid OH

units in some fish, 104 units in HO O
O
terrestrial vertebrates and 112 in
plants

The most structurally well understood cytochrome. The heme active site is hexa
coordinated with N from a histidine residue and S from a methionine residue. Present
in photosynthesis and respiration chains- one of the oldest chemicals present in
biological processes
 Active site of Cytochrome c oxidase

The last enzyme in the respiratory electron

transport chain and is located in the
mitochondrial membrane. It receives an
electron from each of four cytochrome c
molecules, and transfers them to one
oxygen molecule, converting molecular
oxygen to two molecules of water.

The Fe is pentacoordinated and binds O2

(along with the Cu) before reducing it.
This is also the site which CN- binds
during cyanide poisoning [stabilizing the
Fe3+ state and preventing its redox (Fe2+/
Fe3+) activity] (Cyanide is a very strong
ligand) Youtube video: A metabolic poison How
cyanide disrupts ATP synthesis Cyanide
Summary reaction:
4 Fe 2+cytochrome + 8 H+in + O2 → 4 Fe 3+cytochrome + 2 H2O + 4 H+out
 Metalloenzymes: Carbonic Anhydrase
A single polypeptide chain ( M = 29,000) complexed to one
Zn2+ ion. The zinc prosthetic group in the enzyme is
coordinated in three positions by histidine side-chains. The
fourth coordination position is occupied by water. This causes
polarisation of the hydrogen-oxygen bond, making the oxygen
slightly more negative, thereby weakening the bond. A fourth
histidine is placed close to the substrate of water and accepts
a proton. This leaves a hydroxide attached to the zinc. The
reaction catalyzed by carbonic anhydrase is given below which
occurs 5000 times faster in presence of the enzyme:

in tissues- high CO2 concentration)

Carbonic anhydrase has one of the highest overall rates of reactions of any enzymes. This is
expressed in terms of turnover number of a catalyst (number of substrate molecules
converted per molecule of the enzyme per second; same as TOF in organometallic
catalysis). For human carbonic anhydrase it is 400,000 to 600,000 per second.

Most efficient catalytic reaction known so far !!

Reaction increases acidity in the tissues

 Metalloenzymes: Carbonic Anhydrase

Why Zinc?
A good Lewis Acid
Only one stable oxidation state
Complexes are labile than other
divalent metals
Favors tetrahedral geometry
The active site also contains specificity pocket for carbon dioxide, bringing it
close to the hydroxide group. This allows the electron rich hydroxide to attack
the carbon dioxide, forming bicarbonate

Carbonic anhydrase increases acidity in the vicinity..With enough carbonic

anhydrase enzymes present, therefore, carbon dioxide can cause a decrease in
the pH of the solution due to all the protons produced from its reaction with
water.
Watch Youtube video carboanhydrase
 DEOXYMYOGLOBIN OXYMYOGLOBIN
Distal
N histidine
N
N Protein
H N H H N Protein
N H
N N
N Fe
N Fe O
N N O
Protein Protein
Proximal
histidine

Fe2+ t2g4eg2, HIgh spin, radius 92 pm Fe3+ t2g5eg0, Low spin, radius 75 pm

Paramagnetic Diamagnetic

Fe 42 pm outside porphyrin plane Fe fits inside the porphyrin plane

Basics of oxygenation remains same for Hb and Mb. But there

are some differences in the way the four units get oxygenated.
This begins with pulling of the proximal histidine when Fe gets
inside the plane of the porphyrin ring upon oxygen binding
 The Bohr Effect

Christian Bohr, father of Niels Bohr discovered this effect. An increase in

concentration of protons and/or carbon dioxide will reduce the oxygen affinity
of hemoglobin

The chemical basis for the Bohr effect is due to the

formation of two salt bridges of the quaternary
structure. One of the salt bridges is formed by the
interaction between Histidine 146 and Lysine 40.
This connection will help to orient the histidine
residue to also interact in another salt bridge
formation with the negatively charged aspartate
94. The second bridge is formed with the aid of an
additional proton on the histidine residue.

Below a pH of 6, the imidazole ring of

histidine is mostly protonated thus
favoring salt bridge formation
A salt bridge ( weak
electrostatic interaction)