Above: a 3D computer model of Chlamydomonas, a single-celled green alga found in freshwater and soil. The study of
such organisms really should not need justification. They are, like all living things, highly sophisticated machines and to
ignore the inner workings of such natural machines would be truly ignorant of humanity. They deserve to be studied on
aesthetics alone, but as people increasingly need financial reasons to do anything at all on planet Earth (except,
paradoxically to waste vast amounts of money and resources on their own petty pleasures!), it can be pointed out that
these organisms make ideal 'model organisms'. Animal cells can be very difficult to work with and there is much that can
be learned about the fundamental process of life itself by studying such organisms. They do also have several potential
technological uses.  A schematic of the detailed internal structure (shown in section) is given below:
There are many different species of Chlamydomonas and the details differ. All possess the usual eukaryotic cell
organelles (nucleus (G), endoplasmic reticulum (not shown), Golgi apparatus (H) (usually x 1-4 arrayed around the
nucleus), vesicles (F), lipid droplets and mitochondria (A)). The mitochondria are often branched, and probably
divide and move around the cell. They can be found inside the cup of the chloroplast, at the front of the cell, and
squeezed between the chloroplast and the cell-surface membrane. A single cup-shaped chloroplast (I) fills about
the posterior two-thirds of the cell and this contains one or two pyrenoids. This fixed carbon is converted into
starch, which is stored as starch grains in the chloroplast. Starch grains are distributed throughout the chloroplast,
but are concentrated around the pyrenoid.

Pyrenoid(s): contain the enzyme RuBisCO (Ribulose bisphosphate carboxylase/oxygenase) which is responsible
for fixing carbon into carbohydrate during photosynthesis.

Contractile vacuoles: one pair of contractile vacuoles are situated near the front-end of the cell (topmost in the
diagram). These expel excess water which enters the cell by osmosis when the surrounding solution is more dilute
than the cell cytoplasm (that is when the surrounding water has a higher water potential).

Flagella (E): one pair of (smooth) flagella project from the anterior or apical end of the cell. These enable the cell
to swim by executing breast-stroke like movements. Each flagellum crosses the cell wall through a collar and is
rooted in the cytoplasm by a
basal body. Two long rootlets of microtubule-bundles extend from each basal body
into the cell (not shown), one bundle contains two microtubules, the other four. Thus there are four bundles
altogether, which meet in a cross beneath the basal bodies, with the microtubule doublets opposite one-another
(and the quadruple bundles also opposite one another) in a 4-2-4-2 cruciate (cross) arrangement. A pair of
contractile bundles (rhizoplasts) also connect the two basal bodies together, maintaining them at an angle of about
80 degrees. These contractile bundles contain the protein
centrin, which contracts by supercoiling. Contraction of
the rhizoplasts, moves the nucleus forward and detaches the antenna and is a shock response (and as one of its
functions may allow the cell to escape from predators which have grabbed hold of its flagella?). Another contractile
bundle also joins the basal bodies to the nucleus. If the cells are grown on solid surfaces like agar (in which the
cells cannot swim) flagella are not synthesised. During
mitosis (cell division occurring in asexual reproduction) the
basal bodies detach from the flagella (which are absorbed and so disappear) and resume their function as
centrioles, organising the microtubule spindle which separates the chromatid pairs to each daughter cell.

Eye-spot (stigma). The highly reflective red eyespot, found only on one side of the cell inside the chloroplast is
constructed of either a flat or parabolic plate of granules spaced at a quarter of the wavelength of the light they
reflect. They, therefore, appear to behave as a
quarter-wave plate which reflects light of a certain wavelength in
such a way that the
waves combine by constructive interference, intensifying the light. A parabolic plate (shaped
like a satellite-receiver dish antenna) makes an ideal reflector, since it has the property of focusing the reflected
light. Certain colours of light are thus reflected and focused onto the light sensor itself, which is situated in the cell
membrane above the stigma. This receptor is tuned to match the wavelength of light reflected by the
stigma. Occurring only one side of the cell enables the cell to detect the direction of a light source. This is assisted
by the fact that the cells rotate as they swim, tracing out helical paths. Thus, the light sensor will be periodically
exposed to a higher light intensity if the  cell is swimming at an angle to the light source, but will remain evenly
illuminated if the cell swims towards it. A powerful light microscope will reveal the eyespot very clearly glinting as the
cell rotates in the light.

Cell Wall. Chlamydomonas is surrounded by a rigid cell wall, but unlike plant cells in which the cell wall is made of
cellulose (a glucose polymer), the
Chlamydomonas wall is made of fibrous glycoproteins (in most algae it consists of
carbohydrate polymers) and is triple-layered. The apical papilla is a small hemispherical or flattened projection of
the cell wall between the two flagella.

Genetics. Microscopy usually reveals 8 chromosomes in the haploid nucleus, however, genetic studies suggest
that there are 16-17 genetic units or so, which suggests that each visible chromosome contains two molecules of
DNA, instead of the more usual one.
Chlamydomonas sexual cycle

Stage 1

The mature vegetative cells are haploid (n). When nutrients especially nitrogen (ammonia) are depleted and
present in low concentrations,
Chlamydomonas activates its sexual cycle and the cells differentiate into
gametes, each vegetative cell becoming a single gamete. Some species and strains also require blue light as
a stimulus for gamete development. The gametes are present in two genetic polarities, plus and minus, and
fertilisation can only occur between two gametes of opposite polarity. The gametes shed their cell walls,
which are dissolved by an
autolysin enzyme. The gametes have sticky glycoprotein projections on their
flagella (visible under the electron microscope as tiny stalked projections with globular heads). Plus cells
have a glycoprotein which will interact with and stick to the complementary glycoprotein on minus cells (rather
like velcro). The flagellae thus adhere along their length, expressing more of these glycoprotein
(which is more concentrated toward the flagella tips) to strengthen the bond. Some species are homothallic -
meaning that gametes descended from the same parent can fuse (self-fertilisation) whilst others are
heterothallic (meaning that at least two parental stocks are needed for cross-fertilisation). Compatible
gametes apparently bump into one another and adhere by chance, as apparently no sex pheromones are
produced to attract gametes of the opposite polarity.

Stage 2

At least in Chlamydomonas eugamatos, the plus gametes pushes back the flagella of the minus gamete. In
all forms a
cytoplasmic bridge (copulation tube) grows between the two gametes, joining their front (apical)
ends together.

Stage 3

The adherent flagella disengage from one another. Depending on species, these coupled cells may swim
around for several hours connected in this manner and in
Chlamydomonas eugamatos only the plus-cell
flagella remain active during this phase. Other gametes may join them, adhering to the complementary
adhesins on their flagella, and a clump of cells may form.

Stage 4

The two adherent gametes, one plus and one minus, will later undergo cell fusion or plasmogamy
(cytogamy) which takes a few minutes. Light is a necessary stimulus to initiate plasmogamy, and in the
darkness the joined gametes will keep swimming until they die. In
Chlamydomonas eugamatos this fusion
occurs between the two front ends, but in some forms it occurs side-on. This fused quadriflagellate cell,
called a
plasmozygote, continues swimming for some time.

Stage 5

The two nuclei fuse, first of all their outer membranes fuse together, and then the inner membranes break
and join together. The cell now has a diploid (2n) nucleus. The flagella disintegrate from their tips down. The,
now non-motile, zygote becomes invested in a thick warty wall and becomes filled with starch and lipid
reserves and enters a dormant stage. This kind of zygote is called a

Stage 6

After a few days the hypnozygote spore is able to germinate once suitable conditions of light and sufficient
nitrogen supply return. Germination begins with a meiotic reduction division, forming four haploid daughter
cells. The spore wall breaks down and the four daughter cells escape as mature vegetative cells and the
cycle is complete.

In the species usually considered, the plus and minus gametes look identical (isogamy) but in some species
the plus gametes (male gametes) are much smaller than the minus gametes (female gametes) and these are
said to be anisogamous. In the soil-dwelling
Chlamydomonas  zimbabwaensis a single vegetative cell will
divide to form many small plus gametes, contained within the parental cell wall. When these male gametes
escape they release a sex pheromone which induces vegetative cells to escape from their walls and form
(much larger) minus or female gametes. In some species, the minus gametes are immotile (eggs) and these
forms are said to be oogamous.

Chlamydomonas can also reproduce asexually as illustrated below:
Chlamydomonas asexual cycle
releasing 4, 8, 16 or more cells from a single parent. Mitosis is closed, meaning that the nuclear membrane
does not break down. Instead microtubules of the mitotic spindle cross the nuclear envelope through pores
in either end of the nucleus. Chlamydomonas is haploid and only the zygote is diploid. Such an organism is
described as
haplontic. (In contrast, human beings are diplontic - they are diploid and only the gametes are

Circadian cycles

Like many motile algae, Chlamydomonas will swim toward the surface to intercept the light during the day
and then swim deeper down at night (probably in order to disperse and escape predators). The proteins it
needs for photosynthesis, UV protection and nitrogen assimilation whilst nourishing itself in the day also
undergo a daily cycle as more of these proteins are synthesised during the daytime. These cycles are not
simply passive responses to light, rather the cells have internal biological clocks, enabling them to anticipate
the dawn and so prepare and make the most of the available light. This clock is constantly reset by brief
exposure to light, allowing the clock to remain correct throughout the year and at different latitudes.
Pov-Ray model of Chlamydomonas