Biological pigments are colored compounds produced by metabolism. Their color is due to highly conjugated systems with delocalized electrons, which absorb visible light. The longer the conjugated system, the longer the wavelengths absorbed and the color observed. Chlorophylls are examples of pigments with long conjugated systems that absorb blue-green and orange-red light, appearing green. The color of a pigment depends on the length of its conjugated system and the wavelengths of light it absorbs.

1. B.9 Biological pigments

2. Understanding 1:
Biological pigments are coloured
compounds produced by
metabolism

3. 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 C=C,
C=O or a benzene ring.
• These groups, which give rise to
absorptions in the UV-Vis region, are
called chromophores.

4. • 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)

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

6. Conjugated systems
• A conjugated system is a
sequence of alternating single and double
bonds in a molecule

7. • The bonds highlighted in figure below form
a conjugated system

8. • Not part of this system
• They are separated from the other double bonds by more
than one single bonds
BUT!!

9. • The double bonds must alternate with single bonds

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

11. • Another example of conjugated system…

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

13. 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.

14. • 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.

15. 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

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

17. • Chlorophyll a and b
have long
conjugated
systems
• They absorb light
in the 400-500 nm
and 600-700 nm
region

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

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

20. 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

21. The binding of oxygen to
haemoglobin
• Each heme can carry one molecules of
oxygen.
• So, each hemoglobin unit can transport
four molecules of oxygen.

22. 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

23. 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

24. Affinity of hemoglobin for oxygen changes as
the partial pressure of oxygen changes

25. 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

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

27. Oxygen affinity increases as the partial pressure of oxygen increases

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

29. • 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

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