Lecture 10: Eukaryotes and Protists

Lecture 10: Eukaryotes and Protists
Last lecture we discussed the diversity of prokaryotes. Now we’re going to move along
the tree of life to the eukaryotes, which is mostly covered in Chapter 27.
The term Protist refers to most of the eukaryotes, with the exception of plants, animals
and fungi. Historically, all eukaryotes that are not animals, plant or fungi have been
called ‘protists’. As a result, Protists are NOT a monophyletic or “natural” group (Figure
27.1), it is a paraphyletic group. (A paraphyletic group is a group that contains some but
not all of the descendants from their common ancestor.)
Today we’ll focus on the origin of eukaryotic cells and then talk a bit about protists.
The origin of eukaryotic cells
Even though the group Prokaryotes is also paraphyletic (convince yourself by look at the
tree of life – Figure 1.7!), the domains Archaea and Bacteria share some things in
common that include the way they divide to make new cells (a process called binary
fission), the organization of their DNA (circular rather than chromosomes), the fact that
they have only copy of their DNA (they are haploid and not diploid), and that they are all
unicellular (except, to my knowledge, a few very rudimentary multicellular organisms,
like the cyanobacteria I told you about last lecture).
In contrast, eukaryotic cells have LOTS of differences. Somewhere along the lineage that
led to eukaryotes, these things evolved: a nucleus, the process of mitosis (cell division),
the process of meiosis (cell division for sexual reproduction), organelles like
mitochondria and chloroplasts, linear (not circular) chromosomes, diploidy (two copies of
genes, one from mom and one from dad) and even complex multicellularity. Wow.
So, how did the prokaryotic cell evolve into a eukaryotic cell? It is thought that the
eukaryotic cell was derived by a couple of processes:
1. The origin of the nucleus. Figure 27.11 in your book shows a hypothesis as to
how the nuclear envelope may have formed thought the process of
invagination. However, it is important to realize that many more things had to
occur to form a nucleus. For example:
a. Eukaryotes package their DNA into chromosomes.
b. Eukaryotes undergo mitosis
c. Most eukaryotes have a diploid phase of their life cycle.
One primitive eukaryote, Giardia lamblia, may give some insight into the
origin of the nucleus. Giardia is a protist that appears to represent a sort of
“missing link” between prokaryotes and eukaryotes. One of the neat things

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about Giardia is that it has not one but two nuclei. However, the two nuclei
are haploid. This existence of two haploid nuclei in Giardia suggests that
nuclei could have evolved in the following manner:
Haploid prokaryote  primitive eukaryote with single haploid nucleus 
primitive eukaryote with two haploid nuclei  eukaryote with single diploid
nucleus
[Remember: haploid = one copy of genes; diploid = two copies of genes]
While we can hypothesize about the origin of the nuclear envelope, we know
relatively little about the rest of the steps that led to the eukaryotic nucleus.
For example, Giardia has DNA arranged in chromosomes packaged with
histones. We don’t know how DNA evolved from being in a circular
arrangement in prokaryotes to a chromosomal arrangement in eukaryotes.
[A strange feature of Giardia is that it was thought to lack mitochondria, and
so it was thought to represent a really primitive eukaryotic cell before
mitochondria were formed. In fact, though, the evidence suggest that it has (or
had) a mitochondria. Scientists now think that mitochondria were formed
somewhere early in the branch that leads to eukaryotes.]
[As a side note, just for fun and not to be tested, it is cool to realize that
Giardia is not alone in having a “weird” nucleus. One exciting example is
Oxytricha trifallax. Like Giardia, Oxytricha has two nuclei call the micro- and
macro-nucleus. The micronucleus is passed on to the next generation, but the
macronucleus is where proteins are made. The weird thing about the
micronucleus is that the genetic code is completely scrambled, because in this
nucleus genes are fragmented in >200,000 different sequences. Somehow
when the macronucleus is made from the micronucleus, all of the pieces of the
genome become unscrambled. It is super bizarre, and no one knows why it
happens. They are also kind of pretty, in their own weird way:
https://www.youtube.com/watch?v=nFC5MUc2lNs]
2. The endosymbiotic incorporation of prokaryotic cells to form mitochondria and
chloroplasts. The endosymbiotic theory hypothesizes that some early eukaryotic
cells engulfed prokaryotic cells and kept them instead of digesting them.
A symbiosis is a close and prolonged physical relationship between individuals of
two different species. “Endo” means “within”, so an endosymbiosis refers to a
symbiosis between two organisms where one organism is within the other.
The endosymbiotic theory hypothesizes the following: 1) a prokaryote was
engulfed by phagocytosis (phagocytosis is a term that refers to the engulfment and
eating of one cell by another) by a primitive eukaryotic cell, 2) the prokaryote was
not digested immediately but acted as an endosymbiont (endosymbiont = internal
symbiont) that helped cellular metabolism, 3) eventually both the host and

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endosymbiont lost the ability to exist on their own because of their mutualistic
symbiosis.
For example, mitochondria are thought to have arisen by an endosymbiosis of an
aerobic heterotrophic prokaryote. Mitochondria are organelles that are responsible
for cellular respiration. They are involved in the breakdown of pyruvate with
oxygen to release carbon dioxide, water and lots of energy (in the form of ATP)
that can be used for the cell to synthesize compounds. See figure 27.8.
Mitochondria are universally found in eukaryotes, and it is hypothesized that the
mitochondrial endosymbiotic event occurred just once.
Chloroplasts are thought to have originated when a eukaryote engulfed a
photosynthetic cyanobacterium. Chloroplasts are the sight of photosynthesis in
eukaryotes. Unlike mitochondria, chloroplasts are not universal to eukaryotes;
they are not found in animals, fungi and some other groups.
It appears that chloroplasts have originated on multiple occasions. For example, it
appears the first (primary) chloroplast endosymbiotic event occurred in the
evolutionary branch that leads (eventually) to Plants. The primitive eukaryotes
with a chloroplast were also engulfed by some ancestral Protist on more than one
occasion. The engulfment of a eukaryote with a chloroplast by another eukaryote
is called a secondary endosymbiotic event. See Figure 27.9 and 27.10.
The endosymbiotic theory was first hypothesized in the late 1800s and re-
championed in the 1970’s by Lynn Margulis. The theory was criticized widely for
many years, but it is now generally accepted. What is the evidence in favor of this
theory?
1. chloroplast and mitochondria are the right size to have come from
prokaryotic cells.
2. The membranes of chloroplast and mitochondrion have enzyme and
transport systems resembling those of prokaryotes.
3. organelles divide by a splitting process that is similar to prokaryotes - i.e.,
fission not mitosis.
4. Both mitochondrion and chloroplasts have circular DNA, like prokaryotes,
5. Both mitochondrion and chloroplasts contain machinery for DNA
replication and translation, suggesting they were once free-living. Their
translation machine (i.e., ribosomes) are small and prokaryote-like.
6. Molecular systematics has shown that mitochondrial and chloroplast genes
are “prokaryotic like”, in being more similar to prokaryotic genes than
eukaryotic genes. (see Figure 28.10)
*** We finished here in the lecture, and we’ll pick up this lecture again next Monday
(2/3)***

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Diversity among Protists
The group Protist contains both multi-cellular and unicellular eukaryotes. It is an
incredibly diverse Kingdom that contains some of the earliest-branching eukaryotes.
However, it is not a ‘natural’ or monophyletic group; it is paraphyletic.
The Protists contains far too many organisms to cover in comprehensively, so I’ll
mention only a few prominent taxa (taxa is the plural of taxon; it refers to a group of
species) before I turn in more detail to one particular taxon.
The Foraminifera: are single-celled, heterotrophic organisms with calcium
carbonate shells. Most of the estimated 4,000 living species of foraminiferans in
the world's oceans. Of these, only about 40 species are planktonic, that is they
float in the water. The remaining species live on the bottom of the ocean, on
shells, rock and seaweeds or in the sand and mud of the bottom. In places,
foraminifera are so abundant that the sediment on the bottom is mostly made up
of their shells.
They are particularly interesting because of their extensive fossil record.
Paleontologists are able to use foraminiferans fossils to decipher changes in the
earth’s climate.
Euglenids: I’ll only mention one, a neat little protist call Trichonyma that lives in
termite guts and helps termites digest wood.
Apicomplexans: Apicomplexans are parasitic protozoa. From a human standpoint,
the most important apicomplexan is Plasmodium falcipurum. Plasmodium is a
parasite that causes malaria, which, after years on the decline, is once again one of
the major causes of disease, particularly in the third world.
The current global picture: from World Health Organization:
• Malaria is a public health problem today in more than 90 countries,
inhabited by a total of some 2 400 million people -- 40% of the world's
population.
• Worldwide prevalence of the disease is estimated to around 300-500
million clinical cases each year.
• More than 90% of all malaria cases are in sub-Saharan Africa. Mortality
due to malaria is estimated to be over 1 million deaths each year. The vast
majority of deaths occur among young children in Africa, especially in
remote rural areas with poor access to health services.
In addition to thinking in terms of phylogenies, I also want you to start thinking
about life cycles. For example, the life-cycle of the malaria parasite is complex. It
lives in at least two different hosts (humans and mosquitoes). Once it is in
humans, Plasmodium proliferates in specialized regions of the human body (the

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liver and red blood cells), and part of the life cycle features separate male and
female parasites. Remember, it needs all of this to reproduce. Crazy, right?
Dinoflagellates: Dinoflagellates are mostly unicellular algae, with roughly half of
the dinoflagellates being autotrophs. (Some of the other dinoflagellates are
parasites.) There are about 4000 living species of dinoflagellates known.
Dinoflagellates are often covered by hard shells made of cellulose and silicate,
and they often have two flagella to propel them through the water.
Dinoflagellates are a very important of the food chain, because they serve as a
food source for a broad array of fish and other animals in marine and fresh-water
environments. Occasionally a particular species of dinoflagellate will encounter
conditions that allow it to proliferate like crazy. When this happens, a “red tide”
can ensue. Usually these “red tides” are harmless, but occasionally the
dinoflagellate in the red tide produces a toxic substance. When that happens, the
death toll on other species in the environment – like fish, whales and birds – can
be very high.
Algae: Algae are the ‘plant-like’ protists; they are mostly autotrophic, mostly
aquatic organisms and mostly multicellular. Algae play an important role in the
ecology of the planet because they are responsible for fixing half of the world’s
carbon and thereby liberating oxygen. I want to draw your attention to three types
of algae: red, green and brown. Based on Figure 27.7, do these three types of
algae make a monophyletic group?
Kelp is a brown algae, and it has many uses, ranging from potash (which was
used in the production of gunpowder during World War I), to emulsifiers that are
used in many products we encounter every day (ice cream, gelatins, lotions, etc.)
Green Algae: Green algae have many similarities to plants, including the
molecules used to trap light energy during photosynthesis (i.e., chlorophyll), their
cell walls, and other similarities.
Green algae can be multicellular or unicellular. The multicellular forms are
relatively simple; that is, there are not as many distinct tissue types as we find in
plants.
Aquatic green algae is primarily found in fresh-water environments, although
there are marine forms. Some green algae even inhabit very moist terrestrial
environments.
Some final points about Protists (and particularly algae):
1) Multi-cellularity - Unlike Bacteria or Archaea, some protists are fairly complex
multi-cellular organisms, such as brown algae.

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I don’t want to say too much more about multi-cellularity, except to point out that
multi-cellularity likely evolved on more than one occasion. We can see that fact by
looking at the Tree of Life (Figure 30.2) and recognizing that multi-cellularity
evolved in the animals and for some algae; so it has evolved on at least two separate
occasions.
2) Chlorophyll – All eukaryotic autotrophic algae contain chlorophyll ‘a’, which is a
chemical that captures light energy for the photosynthetic reaction. Chlorophyll ‘a’ is
the same chlorophyll used by plants for photosynthesis and is responsible for the
green pigment in plants. In addition to this green pigment, algae also have other
pigments that form the basis for algal taxonomy (i.e., the pigments cause the brown,
red and green tints that guide classification of algae). Green algae, like plants,
contain chlorophyll ‘b’ in addition to chlorophyll ‘a’. Unlike plants, brown algae
contain ‘c’ in addition to chlorophyll ‘a’, and red algae contain only chlorophyll ‘a’.
3) Even though plants evolved from a green algal ancestor, it is not always clear if
green algae should be considered within plants or not. Your book takes the view that
green algae are plants and not protists. The important thing to remember is not
whether green algae is a plant or not, but rather that green algae shares many
similarities with Land Plants, again suggesting that plants evolved from an ancestor
similar to green algae.
4) Alternation of generations: Both green and brown algae experience alternation of
generations. Alternation of generations is a life-cycle that consists of a multicellular
diploid phase AND a multicellular haploid phase. You need to know alternation of
generations.
Figure 27.17a
• The life cycle consists of haploid (one set of chromosomes) and diploid
(two sets of chromosomes) phases. The alternation between multicellular
haploid and diploid stages is known as alternation of generations.
• The dominant diploid form is the sporophyte, so called because it
produces spores. The sporophyte is a diploid multicellular individual that
produces spores by meiosis.
• Spores are haploid. Spores divide mitotically to generate a multicellular
haploid individual called the gametophyte. Some organisms have spores
that differentiate into separate male and female gametophytes, or the
gametophyte can be bisexual (both sexes).
• The spores develop into the gametophyte, the haploid phase of the life-
cycle. In some algae, the gametophyte looks exactly like the sporophyte,
but usually the gametophyte and the sporophyte look different.
• The gametophyte produces sperm and egg, which eventually fuse during
the process of fertilization (or syngamy)
• The zygote, which is the immediate result of syngamy, now has two
copies of genes and is therefore diploid, and it develops into the

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sporophyte. After some growth and cell divison, the zygote becomes an
embryo
• With the development of a sporophyte, the life cycle begins all over again!
Some additional important points about Figure 27.17a:
• the spores are motile – i.e., they swim!
• the gametes also swim
• therefore, WATER is very important for reproduction of Algae!
• water is also important for other reasons... i.e., support system, nutrients,
etc.
5) Sex. Bacteria and the Archaea reproduce by fission – that is, the cells simply divide.
They do not have sex or separate sexes. In contrast, most eukaryotes undergo meiosis
to form gametes of two different sexes. These gametes then combine in the zygote.
It’s likely that the common ancestor to the Eukarya also had sex, since sex is nearly
universal among eukaryotes.
As an aside, there is some mystery as to why sex evolved, because it includes a “two-
fold” cost. This cost comes from a simple fact: to make one offspring requires two
parents when there is sex, but only parent when there is no sex. For this reason, it is
not clear why sex is maintained, but it is thought that it is because sex allows for
more genetic combinations in offspring (combinations of mom and dad’s alleles),which leads to more chances to produce offspring with high fitness.