B.9 Biological pigments

Understanding 1:Biological pigments are coloured compounds produced by metabolism

Chromophores• In order to absorb electromagnetic

radiation in the UV-Vis region of the spectrum, molecules must generally contain a double bond in the form of CC, CO or a benzene ring.

• These groups, which give rise to absorptions in the UV-Vis region, are called chromophores.

• Electromagnetic radiation in ultraviolet-visible region of the spectrum is absorbed to promote electrons from a low energy (molecular orbital) in molecules to a higher energy level(molecular orbital)

Understanding 2:The colour of pigments is due to highly conjugated systems with delocalized electrons, which have intense absorption bands in the visible region

Conjugated systems• A conjugated system is a

sequence of alternating single and double bonds in a molecule

• The bonds highlighted in figure below form a conjugated system

• Not part of this system• They are separated from the other double bonds

by more than one single bonds

BUT!!

TO BE CONJUGATED…

• The double bonds must alternate with single bonds

If 2 single bonds between the double bonds then the system is not conjugated

• Another example of conjugated system…

• We can see from this figure that electrons are delocalise in a conjugated system because p orbitals can overlap along the whole chain

Absorption of electromagnetic radiation and colour

• For a compound to be coloured, its molecules must absorb visible light (electromagnetic radiation, wavelength about 400-750 nm)

• Therefore, if a molecule absorb absorbs radiation between these wavelengths, it will be coloured.

• The longer the conjugated system, the longer the wavelengths of the radiation absorbed.

• If a conjugated system involves 8 doubles bond, the molecules should absorb in the visible region of the spectrum

• Hence, be coloured.

The longer a conjugated chain (delocalised system), the longer the wavelength of radiation absorbed by a

molecule.

• A system of 11 conjugated double bonds• Absorbs light in the blue-green part of the visible

spectrum• Appears red

• Only have a system with 5 conjugated double bonds• Does not absorb visible light• It only absorbs ultraviolet radiation• Therefore, it is colourless

Retinol

• Chlorophyll a and b have long conjugated systems

• They absorb light in the 400-500 nm and 600-700 nm region

• The green light in the middle of the spectrum is not absorbed, and so these molecules look green in natural light.

Application & skills:Explanation of the sigmoidal shape of haemoglobin's oxygen dissociation curve in terms of the cooperative binding of haemoglobin to oxygen

The binding of oxygen to haemoglobin

• Hemoglobin consist of 4 polypeptides sub-units

• Each of which contains a heme prosthetic group

• With the iron at the centre of the heme• Having oxidation number of +2

The binding of oxygen to haemoglobin

• Each heme can carry one molecules of oxygen.

• So, each hemoglobin unit can transport four molecules of oxygen.

The binding of oxygen to haemoglobin

• The iron in the heme can bond to 6 ligands• In the unbound state, the Fe2+ is bonded to

5 ligands: 4 : nitrogen atoms (of porphyrin)1 : amino acid (that attached it to protein)

• When molecular oxygen binds, this becomes the 6th ligands.

• Called Oxygenated hemoglobin

The binding of oxygen to haemoglobin

• Binding of the oxygen molecules result in Fe2+ being oxidised to Fe3+

• In hemoglobin, the oxygen binds reversibly, allowing its release to tissue cells

Affinity of hemoglobin for oxygen changes as the partial pressure of

oxygen changes

The scale on the y axis represents the fraction of iron ions bound to oxygen molecules. This is called oxygen binding curve/oxygen dissociation curve

Partial pressure of oxygen low, hemoglobin has a low affinity for oxygen

Oxygen affinity increases as the partial pressure of oxygen increases

• This suggest that its becomes easier for oxygen to bind to hemoglobin when some oxygen molecules have already bound to the iron – cooperative binding

• Hemoglobin have tetrameric structure with 4 iron-heme complex.

• The binding of oxygen to one of the iron ions in the tetramer changes the shape (conformation) of the protein

• Its becomes easier for oxygen molecules to bind to the other sites

• This is an allosteric effect – the binding of a molecule at one site has an effect on another site.