Download Some application of d block metal in biology

Some application of d block metal
in biology
By Prof Yeap Guan Yeow
Important biological elements
At least 25 elements:C, H, N, O
Na, K, Mg, Ca, P, S, Cl, Si and Fe
V, Cr, Mn, Co, Ni, Cu, Zn, Mo, W, Se, F and I
Biomolecules
A molecule that naturally occurs in living organisms.
Different types:
Small molecules:
-
Lipid, Phospholipid, glycolipid, Sterol
Vitamin
Hormone, Neurotransmitter
Carbohydrate, Sugar
Disaccharide
Monomers:
-
Amino acid
Nucleotide
Phosphate
Monosaccharide
Polymers:
-
Peptide, Oligopeptide, Polypeptide, Protein
Nucleic acid, I.d. DNA, RNA
Oligosaccharide, Polysaccharide
Lignin
LIPIDS are broadly defined as any fat-soluble (lipophilic),
naturally-occurring molecule, such as fats, oils, waxes, cholesterol,
sterols, fat-soluble vitamins (such as vitamins A, D, E and K),
monoglycerides, diglycerides, phospholipids, and others.
The main biological functions of lipids include energy storage,
acting as structural components of cell membranes, and participating
as important signaling molecules.
Amino Acid
In chemistry, an amino acid is a molecule containing
both amine and carboxyl functional groups.
In biochemistry, this term refers to alpha-amino acids
with the general formula H2NCHRCOOH, where R is an
organic substituent.
Example: Phenylalanine
Peptides (from the Greek π_π_____, "small digestibles")
(i) Short polymers formed from the linking, in a defined
order, of _-amino acids.
(ii) The link between one amino acid residue and the next
is known as an amide bond or a peptide bond.
Less abundant species
Na, K and Cl for osmotic control and nerve action
Mg2+ in chlorophyll
Ca for bone formation
For transition metal complexes:
Fe
- Ferritin, Transferrin, Haemoglobin
Co
- Vitamin B12
Cu
- Haemocyanin
Zn
Ferritin
- A water-soluble metalloprotein in which the Fe is stored
in the liver, bone marrow and spleen.
- Contains up to 4500 high-spin Fe3+ in the form of
microcrystalline oxohydroxophosphate of composition
(FeO.OH)8(FeO.H2PO4)
- Can release iron if the blood has a low Fe concentration,
and it can help to store excess Fe if the
blood and tissues have a high Fe concentration.
- Functions as a "buffer" against Fe deficiency
and, to a lesser extent, against iron overload.
Protein shell in ferritin
Ferritin
(a) Ferritin has the shape of a hollow sphere.
Inside the sphere, Fe is stored in the Fe(III) oxidation
state. It is incorporated in the mineral ferrihydrite,
[FeO(OH)]8[FeO(H2PO4)], which is attached to the inner
wall of the sphere.
(b) To release Fe when the body needs it, the Fe must be
changed from the Fe(III) to the Fe(II) oxidation state.
(c) In the Fe(II) state, iron breaks away from the lattice as
the Fe2+ ion. The positive charge of the Fe2+ ion attracts
the electronegative O atoms of H2O, and a H2O "cage"
forms around the ion, with six H2O molecules surrounding
the ion .
(d) Fe becomes soluble as a hydrated Fe2+ ion , Fe(H2O)62+,
and it can be released from the ferritin protein via the
channels in the spherical shell.
Transferrin
 A glycoproteins (ie. Compounds of proteins and
carbohydrates) which binds Fe very tightly but
reversibly.
 The affinity of transferrin for Fe(III) is extremely
high (1023 M-1 at pH 7.4) but decreases progressively
with decreasing pH below neutrality.
 When not bound to iron, it is known as
"apo-transferrin"
 Include serum transferrin, lactoferrin (in milk) and
ovotransferrin (present in egg white)
Binding site in transferrin
Siderophores
(i)
Organisms with O-donor polydentate ligand
called siderophores scavenge for Fe.
(ii) Examples of siderophores are anions derived from:- enterobactin
- desferrichrome
- desferrioxamine
Enterobactin (also known as Enterochelin) is a high affinity
siderophore that acquires iron for microbial systems.
It is primarily found in gram-negative bacteria, such as
Escherichia coli and Salmonella typhimurium.
It is the strongest siderophore known, binding
to the ferric ion (Fe3+) with the affinity (K = 1052 M-1).
Haemoglobin & Myoglobin
- Both are haem-iron myoglobin
Haemoglobin
- Protein that transports oxygen (O2 ) in human blood
from the lungs to the tissues of the body
- Molecular weight of ~64500
- Is a globular protein (i.e., folded into a compact,
nearly spherical shape) and consists of four subunits
- A tetramer
Upon the reaction of O2 with haemoglobin:
- Coordination is accompained by electron transfer
- High-spin Fe(II) was oxidized to low-spin Fe(III) and
reducing O2 to [O2]-
The blue strands are a ribbon
representation to emphasize
the helical structure.
The green dotted lines show
the hydrogen bonding
between the -NH and -CO
functional groups.
Each heme group contains an
iron atom that is able to bind
to one oxygen (O2) molecule
Haemoglobin contains four
heme groups, each
haemoglobin protein can bind
four oxygen molecules.
Porphyrin
Heterocyclic macromolecules that can serve
as a tetradentate ligand.
a three-dimensional
molecular model of
heme coordinated to
the histidine residue
(a monodentate
ligand) of the
hemoglobin protein
A two-dimensional drawing
of heme coordinated to the
histidine residue, which is
part of the hemoglobin
protein. In this figure, the
protein is deoxygenated;
i.e., there is no oxygen
molecule bound to the
heme group.
Conformational Changes Upon Binding of Oxygen
In deoxygenated state:
The heme group is nonplanar when it is in its deoxygenated
state (not bound to an oxygen molecule); the iron atom is pulled
out of the plane of the porphyrin toward the histidine residue to
which it is attached. This nonplanar configuration is characteristic
of the deoxygenated heme group and is commonly referred to as
a "domed" shape.
The valence electrons in the atoms surrounding iron in the heme
group and the valence electrons in the histidine residue form
"clouds" of electron density. (Electron density refers to the probability
of finding an electron in a region of space.)
Because electrons repel one another, the regions occupied by the
valence electrons in the heme group and in the histidine residue are
pushed apart.
Hence, the porphyrin adopts the domed (nonplanar) configuration
in which the Fe is out of the plane of the porphyrin ring.
In oxygenated state
When in the heme group is in its oxygenated state
(i.e., the Fe atom is bound to an oxygen molecule),
the porphyrin ring adopts a planar configuration in which
the Fe lies in the plane of the porphyrin ring.
Representations of electron-density clouds
of the deoxygenated heme group (pink)
and the attached histidine residue
(light blue). These regions of electron
density push one another apart,
and the iron atom in the center is
drawn out of the plane. (The bent line
represents the nonplanar shape of the
heme group.)
Representations of electron-density clouds
of the oxygenated heme group (pink), the
attached histidine residue (light blue), and
the attached oxygen molecule (gray).
The oxygenated heme assumes a planar
configuration, and the central iron atom
occupies a space in the plane of the heme
group (depicted by a straight red line).
Myoglobin
- Molecular weight of ~17000
- A monomer with a protein chain consisting of 1
53 amino acid residues