Pigment molecules absorb light of different wavelengths so that our eyes see the colours of the spectrum that they reflect or transmit.

chlorophyll b
chlorophyll a
anthocyanin
carotenoid

The bright pigments of autumnal leaves, mature fruits and other colourful plant parts generally result from the unmasking or accumulation of cell constituents belonging to two different families of biochemicals - carotenoids and phenolics.

The chemical structures of carotenoids are based on a long zigzag chain of carbon and hydrogen atoms, frequently with a six-membered ring at one or both ends.  Here are the structures of three abundant leaf carotenoids and an unusual one that appears during winter senescence of box leaves.

The presence, structure and chemical modification of these rings determine the colour of the carotenoid, which could be anything from yellow through orange to bright red.

Lycopene

The colour of ripe tomatoes or bell peppers is due to the carotenoid lycopene.  As the green chlorophylls disappear from senescing foliage, carotenoids are revealed and often further accumulated to give leaves their characteristic golden colour.

Carotenoids are hydrophobic - they will not dissolve in water and will bury themselves in cell membranes or lipid droplets rather than brave an aqueous environment.  It is not surprising, therefore, that they are located more or less exclusively in the plastids of senescing leaves or ripening fruits.

This also explains why the red-orange colour of tomato puree preferentially associates with oil globules on the surface of your ragu sauce when it cools - and why it concentrates in the detergent foam when the pan is washed.

The second family of senescence pigments consists of the phenolics.  This family is extensive and comprises a diverse range of chemical structures.  The anthocyanins are responsible for some of the most beautiful of the autumnal colours - reds, purples and even blues.

The anthocyanin cyanidin

Other phenolics contributing to senescence colours include the yellow flavonoids. 

Basic chemical structure of a flavonoid

There are also examples of phenolics that are not themselves coloured but which act like "optical brighteners" to enhance the colours of other pigments - as happens, for example, in the glowing golden autumn foliage of the Ginkgo tree. 

Another phenolic active in senescence is salicylic acid.  It seems to have many jobs in plant development and stress response; so many in fact that its pain-relieving properties (in the form of aspirin) are frequently needed by researchers for whom sorting out its functions is a real headache.

 Unlike the carotenoids, anthocyanins, flavonoids and other phenolics are generally quite water-soluble and this is reflected in where they live in the plant cell - not in the plastid, which is too hydrophobic, but in the wet environment of the vacuole.

That glass of red wine is an aqueous solution of anthocyanin (plus, of course, some other fun stuff like alcohol, fragrances, flavours and so on)

Thus the family histories of carotenoids and phenolics present a window on the state and interaction of the major organelles of plant cells as they develop, senesce, ripen and die.

The story of carotenoids and phenolics in senescing leaves is told in more detail in HJ Ougham, P Morris, H Thomas (2005) The colors of autumn leaves as symptoms of cellular recycling and defenses against environmental stresses. Current Topics in Developmental Biology 66: 135-160