Eukaryotic Biology and Protists

• Eukaryotes are defined as a domain containing single and multi-celled organisms.
• Eukaryotes have cells containing membrane-bound organelles
• Eukaryotic cells have cytoskeletons
• Eukaryotes get energy and nutrients in various ways
• Eukaryotes have a complex phylogeny.

Protists

• The informal name of the "kingdom" of mostly unicellular eukaryotes is Protista

• Advances in eukaryotic systematics have caused significant changes to protist classification

• Protists are a paraphyletic group, and Protista is no longer a valid kingdom.

• Protists are eukaryotes, so they have organelles and are more complex than bacteria and archaea

• All eukaryotes that are not animals, plants, or fungi are protists

• Most protists are unicellular, but some colonial and multicellular species exist

• There are multiple versions of eukayotic trees

• Plenty of disputes remain and the topic is complicated.

Basic Eukaryotic Biology

• Eukaryotes exhibit more structural and functional diversity than any other domain
• Single-celled eukaryotes can be very complex, with all biological functions carried out by organelles in each individual cell
• Eukaryotes are nutritionally diverse
• Some are Photoautotrophs: contain chloroplasts
• Some are Heterotrophs: which absorb organic molecules or ingest larger food particles
• Some are Mixotrophs: combine photosynthesis and heterotrophic nutrition
• Eukaryotes can reproduce asexually or sexually
• Various processes happen in each form of reproduction
• Mitosis in single-celled eukaryotes differs from the process in multicellular eukaryotes
• Meiosis is unique to eukaryotes.
• Much Eukaryote diversity is believed to have come from endosymbiosis
• Mitochondria evolved by endosymbiosis of an aerobic bacterium
• Plastids evolved by endosymbiosis of a photosynthetic cyanobacterium
• The plastid-bearing lineage of eukaryotes evolved into red and green algae
• On several occasions during eukaryotic evolution, red and green algae underwent secondary endosymbiosis and were ingested by a heterotrophic eukaryote
• It is not thought that amitochondriates (lacking mitochondria) are the oldest lineage of eukaryotes
• The understanding of the relationships among eukaryotic groups continues to change rapidly
• One division divides all eukaryotes into six supergroups.

Six Supergroups of Eukarya

• There are six supergroups: Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, Opisthokonta

Excavata

• The clade Excavata is characterized by its cytoskeleton
• The controversial group includes the diplomonads, parabasalids, and euglenozoans
• Diplomonads have modified mitochondria called mitosomes
• They are often parasites such as Giardia intestinalis
• Parabasalids have reduced mitochondria called hydrogenosomes
• It includes Trichomonas vaginalis, the pathogen causing yeast infections in human females
• Euglenozoa is a diverse clade that all have a spiral or crystalline rod of unknown function inside their flagella
• Some are obligate photoautotrophs but the majority are heterotrophs
• Kinetoplastids have a single mitochondrion with an organized mass of DNA called a kinetoplast
• Many are parasitic such as Trypanosomes that causes African sleeping sickness, Chagas disease, and Leishmaniasis
• Euglenids have one or two flagella that emerge from a pocket at one end of the cell.

Chromalveolata

• This clade is monophyletic and originated by a secondary endosymbiosis event, including red algae.
• This clade is controversial and includes the alveolates and the stramenopiles
• Superphylum Alveolata protists have membrane-bounded sacs (alveoli) just under the plasma membrane
• Alveolata includes the dinoflagellates, apicomplexans, and ciliates
• Phylum Dinoflagellates are a diverse group of aquatic mixotrophs and heterotrophs
• These dinoflagellates are abundant components of both marine and freshwater phytoplankton
• Each dinoflagellate has a characteristic shape reinforced by internal plates of cellulose in many species
• Dinoflagellate blooms are the cause of toxic "red tides'
• Not all red tides are red
• Not all red tides are harmful
• Phylum Apicomplexa are parasites of animals that cause serious human diseases
• One end, the apex, contains a complex of organelles specialized for penetrating a host
• Most have sexual and asexual stages that require two or more different host species for completion
• The apicomplexan Plasmodium is the parasite that causes malaria
• Plasmodium requires both mosquitoes and humans to complete its life cycle
• Approximately 2 million people die from malaria each year
• Sickle-cell anemia confers some protection

Phylum Stramenopila

• Diatoms are unicellular algae with a unique two-part, glass-like wall of hydrated silica
• Golden algae are unicellular (some colonial) and are named for their color, which results from their yellow and brown carotenoids
• Brown algae are the largest and most complex algae
• All are multicellular, with most being marine
• Brown algae include species commonly called "seaweeds"
• The algal body is plantlike but lacks true roots, stems, and leaves, and is called a thallus
• The rootlike holdfast anchors the stemlike stipe which in turn supports the leaflike blades
• A variety of life cycles has evolved among multicellular algae
• The most complex life cycles include an alternation of generations or the alternation of multicellular haploid and diploid forms
• Heteromorphic generations are structurally different, while isomorphic generations look similar.

Rhizaria

• DNA evidence supports Rhizaria as a monophyletic clade
• Amoebas move and feed by pseudopodia; some, but not all, belong to the clade Rhizaria
• Rhizarians include forams and radiolarians
• Both have hard shells called tests
• Pseudopodia extends through holes in the test.

Archaeplastids

• Archaeplastida is used by some scientists, and it includes red algae, green algae, and land plants
• Over a billion years ago, a heterotrophic eukaryote acquired a cyanobacterial endosymbiont
• The photosynthetic descendants of this ancient eukaryote evolved into red and green algae
• Land plants descended from green algae
• Red algae are reddish in color due to an accessory pigment phycobilin, which masks the green of chlorophyll
• Red algae are usually multicellular; the largest are seaweeds
• Green algae are named for their grass-green chloroplasts
• Plants descended from green algae
• The two main groups of green algae are chlorophytes and charophyceans
• Most chlorophytes live in fresh water, although many are marine
• Other chlorophytes live in damp soil as symbionts in lichens or in snow.

Unikonts

• Proposed supergroup of eukaryotes that includes animals, fungi, and closely related eukaryotes
• Amoebozoans are a supported clade that include ameobas and slime molds
• Unikonts contain amoebozoa and opisthokonta groups
• Opisthokonts are fungi and animals, discussed in detail later.

This section defines eukaryotes and describes their key characteristics, including membrane-bound organelles and cytoskeletons. It discusses protists, the informal group of mostly unicellular eukaryotes, and their complex classification. It also covers the structural and functional diversity of eukaryotes.