Option for IB Chemistry HL

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.