Eukaryotes – An Overview

1. Eukaryotes – An Overview

2. Prokaryotes vs. Eukaryotes

3. Eukaryotes Animals, plants, fungi, and protists are eukaryotes, organisms whose cells are organized into complex structures by internal membranes. The most characteristic membrane-bound structure is the nucleus. The presence of a nucleus gives these organisms their name: which comes from the Greek ευ, meaning good/true, and κάρυον, meaning nut, referring to the nucleus. Many eukaryotic cells contain other membrane-bound organelles such as mitochondria, chloroplasts and Golgi bodies. Eukaryotes often have unique flagella made of microtubules in a 9+2 arrangement. Cell division in eukaryotes is also different from organisms without a nucleus. This process involves separating the duplicated chromosomes, through movements directed by microtubules. There are two types of these division processes. In mitosis, one cell divides to produce two genetically-identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two copies of each chromosome, one from each parent) undergoes a process of recombination between each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes), each of which has only a single complement of chromosomes, each one being a unique mix and match of the corresponding pair of parental chromosomes. Eukaryotes appear to be monophyletic, and thus make up one of the three domains of life. The two other domains, bacteria and archaea (prokaryotes (without a nucleus)), share none of the previously-described features, though the eukaryotes do share some aspects of their biochemistry with the archaea, and, as such, are grouped with the archaea in the clade Neomura.

4. Taxonomy Carl Linnaeus, also known as Carl Linné, Latinized as Carolus Linnaeus, also known after his ennoblement as Carl von Linné (May 13, 1707 – January 10, 1778), was a Swedish botanist, physician and zoologist who laid the foundations for the modern scheme of nomenclature. He is known as the "father of modern taxonomy." He is also considered one of the fathers of modern ecology.

5. Kingdoms of biology Note that the equivalences in this table are not perfect. e.g. Haeckell placed the red algae (Haeckell's Florideae; modern Florideophyceae) and blue-green algae (Haeckell's Archephyta; modern Cyanobacteria) in his Plantae, but in modern classifications they are considered protists and bacteria respectively. However, despite this and other failures of equivalence, the table gives a useful simplification; empires are erroneously attributed to Chatton in the table who did not rank the 2 groups nor formally name them).

6. Taxonony A Bikont is a eukaryotic cell with two flagella. Another shared trait of bikonts is the fusion of two genes into a single unit: the genes for thymidylate synthase (TS) and dihydrofolate reductase (DHFR) encode a single protein with two functions (Cavalier-Smith, 2006). The genes are separately translated in unikonts. Some research suggests that a unikont (a eukaryotic cell with a single flagellum) was the ancestor of opisthokonts (Animals, Fungi and related forms) and Amoebozoa, and a bikont was the ancestor of Archaeplastida (Plants and relatives), Excavata, Rhizaria, and Chromalveolata. Cavalier-Smith has suggested that Apusozoa, which are typically considered incertae sedis, are in fact bikonts.

7. Taxonony • The opisthokonts (Greek: οπίσθω- (opisthō-) = "rear, posterior" + κοντός (kontos) = "pole" i.e. flagellum) are a broad group of eukaryotes, including both the animal and fungus kingdoms, together with the phylum Choanozoa of the protist kingdom. Both genetic and ultrastructural studies strongly support that opisthokonts form a monophyletic group. One common characteristic is that flagellate cells, such as most animal sperm and chytrid spores, propel themselves with a single posterior flagellum. This gives the groups its name. In contrast, flagellate cells in other eukaryote groups propel themselves with one or more anterior flagella. • The Archaeplastida or Primoplantae are a major line of eukaryotes, comprising the land plants, green and red algae, and a small group called the glaucophytes. All of these organisms have plastids surrounded by two membranes, suggesting they developed directly from endosymbiotic cyanobacteria. In all other groups, plastids are surrounded by three or four membranes, and were acquired secondarily from green or red algae. • The Rhizaria are a major line of protists. They vary considerably in form, but for the most part they are amoeboids with filose, reticulose, or microtubule-supported pseudopods. Many produce shells or skeletons, which may be quite complex in structure, and these make up the vast majority of protozoan fossils. Nearly all have mitochondria with tubular cristae. There are three main groups of Rhizaria:Cercozoa - Various amoebae and flagellates, usually with filose pseudopods and common in soilForaminifera - Amoeboids with reticulose pseudopods, common as marine benthosRadiolaria - Amoeboids with axopods, common as marine plankton

8. Taxonony Ernst Haeckel's presentation of a three-kingdom system (Plantae, Protista, Animalia) in his 1866 Generelle Morphologie der Organismen). The hierarchy of biological classification's major eight taxonomic ranks. A domain contains one or more kingdoms. Intermediate minor rankings are not shown.

9. Animals Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan becomes fixed as they develop, usually early on in their development as embryos, although some undergo a process of metamorphosis later on in their life. Most animals are motile - they can move spontaneously and independently. Animals are heterotrophs - they are dependent on other organisms (e.g. plants) for sustenance. Most known animal phyla appeared in the fossil record as marine species during the Cambrian explosion, about 542 million years ago.

10. Animal cells An animal cell is a form of eukaryotic cell that makes up many tissues in animals. The animal cell is distinct from other eukaryotes, most notably plant cells, as they lack cell walls and chloroplasts, and they have smaller vacuoles (lysosomes). Due to the lack of a rigid cell wall, animal cells can adopt a variety of shapes, and a phagocytic cell can even engulf other structures. There are many different cell types. For instance, there are approximately 210 distinct cell types in the adult human body.

11. Animal cell culture Cell culture is the process by which prokaryotic, eukaryotic or plant cells are grown under controlled conditions. In practice the term "cell culture" has come to refer to the culturing of cells derived from multicellular eukaryotes, especially animal cells. The historical development and methods of cell culture are closely interrelated to those of tissue culture and organ culture. Animal cell culture became a routine laboratory technique in the 1950s, but the concept of maintaining live cell lines separated from their original tissue source was discovered in the 19th century. Established human cell lines One of the earliest human cell lines, descended from Henrietta Lacks, who died of the cancer that those cells originated from, the cultured HeLa cells shown here have been stained with Hoechst turning their nuclei blue. Cell lines that originate with humans have been somewhat controversial in bioethics, as they may outlive their parent organism and later be used in the discovery of lucrative medical treatments. It is estimated that about 20% of human cell lines are not the kind of cells they were generally assumed to be. The reason for this is that some cell lines exhibit vigorous growth and thus can cross-contaminate cultures of other cell lines, in time overgrowing and displacing the original cells. The most common contaminant is the HeLa cell line. While this may not be of significance when general properties such as cell metabolism are researched, it is highly relevant e.g. in medical research focusing on a specific type of cell.

12. Animal cell culture Applications • Mass culture of animal cell lines is fundamental to the manufacture of viral vaccines and many products of biotechnology. Biological products produced by recombinant DNA (rDNA) technology in animal cell cultures include enzymes, hormones, immunobiologicals (monoclonal antibodies, interleukins, lymphokines), and anticancer agents. Although many simpler proteins can be produced using rDNA in bacterial cultures, more complex proteins that are glycosylated (carbohydrate-modified), currently must be made in animal cells. The cost of growing mammalian cell cultures is high, so research is underway to produce such complex proteins in insect cells or in higher plants. • Cell culture is a fundamental component of tissue culture and tissue engineering, as it establishes the basics of growing and maintaining cells ex vivo. • Vaccines for polio, measles, mumps, rubella, and chickenpox are currently made in cell cultures. Novel ideas in the field include recombinant DNA-based vaccines, such as one made using human adenovirus (a common cold virus) as a vector, or the use of adjuvants.

14. Plants Plants are a major group of life forms and include familiar organisms such as trees, herbs, bushes, grasses, vines, ferns, mosses, and green algae. About 350,000 species of plants, defined as seed plants, bryophytes, ferns and fern allies, are estimated to exist currently. As of 2004, some 287,655 species had been identified, of which 258,650 are flowering and 15,000 bryophytes (see table below). Green plants, sometimes called metaphytes, obtain most of their energy from sunlight via a process called photosynthesis.

15. Plant cells • Plant cells are different from the cells of other eukaryotic organisms. Their distinctive features are: • A large central vacuole (enclosed by a membrane, the tonoplast), which maintains the cell's turgor and controls movement of molecules between the cytosol and sap • A cell wall made up of cellulose and protein, and in many cases lignin, and deposited by the protoplast on the outside of the cell membrane; this contrasts with the cell walls of fungi, which are made of chitin, and prokaryotes, which are made of peptidoglycan • The plasmodesmata, linking pores in the cell wall that allow each plant cell to communicate with other adjacent cells; this is different from the network of hyphae used by fungi • Plastids, especially chloroplasts that contain chlorophyll, the pigment that gives plants their green color and allows them to perform photosynthesis • Plant groups without flagella (including conifers and flowering plants) also lack centrioles that are present in animal cells.

16. Transgenic plants Transgenic plants possess a gene or genes that have been transferred from a different species. Although DNA of another species can be integrated in a plant genome by natural processes, the term "transgenic plants" refers to plants created in a laboratory using recombinant DNA technology. The aim is to design plants with specific characteristics by artificial insertion of genes from other species or sometimes entirely different kingdoms. Varieties containing genes of two distinct plant species are frequently created by classical breeders who deliberately force hybridization between distinct plant species when carrying out interspecific or intergeneric wide crosses with the intention of developing disease resistant crop varieties. Classical plant breeders use a number of in vitro techniques such as protoplast fusion, embryo rescue or mutagenesis to generate diversity and produce plants that would not exist in nature. Such traditional techniques (used since about 1930 on) have never been controversial, or been given wide publicity except among professional biologists, and have allowed crop breeders to develop varieties of basic food crop, wheat in particular, which resist devastating plant diseases such as rusts. Methods used in traditional breeding that generate plants with DNA from two species by non-recombinant methods are widely familiar to professional plant scientists, and serve important roles in securing a sustainable future for agriculture by protecting crops from pests and helping land and water to be used more efficiently

17. Fungi A fungus is any eukaryotic organism that is a member of the kingdom Fungi. The fungi are heterotrophic organisms characterized by a chitinous cell wall, and in the majority of species, filamentous growth as multicellular hyphae forming a mycelium; some fungal species also grow as single cells. Sexual and asexual reproduction is commonly via spores, often produced on specialized structures or in fruiting bodies. Some fungal species have lost the ability to form specialized reproductive structures, and propagate solely by vegetative growth. Yeasts, molds, and mushrooms are examples of fungi. The fungi are a monophyletic group that is phylogenetically clearly distinct from the morphologically similar slime molds (myxomycetes) and water molds (oomycetes). The fungi are more closely related to animals than plants, yet the discipline of biology devoted to the study of fungi, known as mycology, often falls under a branch of botany.

18. Fungal cell • Fungal cells are most similar to animal cells, with the following exceptions: • A cell wall containing chitin • Fungi contain large vacuoles • Less definition between cells; the hyphae of higher fungi have porous partitions called septa, which allow the passage of cytoplasm, organelles, and, sometimes, nuclei. Primitive fungi have few or no septa, so each organism is essentially a giant multinucleate supercell; these fungi are described as coenocytic. • Only the most primitive fungi, chytrids, have flagella. Diagram showing a yeast cell

19. Yeast • Yeasts are a growth form of eukaryotic microorganisms classified in the kingdom Fungi, with about 1,500 species described; they dominate fungal diversity in the oceans. Most reproduce asexually by budding, although a few do by binary fission. Yeasts are unicellular, although some species with yeast forms may become multicellular through the formation of a string of connected budding cells known as pseudohyphae, or true hyphae as seen in most molds. Yeast size can vary greatly depending on the species, typically measuring 3–4 µm in diameter, although some yeasts can reach over 40 µm. • The yeast species Saccharomyces cerevisiae has been used in baking and fermenting alcoholic beverages for thousands of years. It is also extremely important as a model organism in modern cell biology research, and is the most thoroughly researched eukaryotic microorganism. Researchers have used it to gather information into the biology of the eukaryotic cell and ultimately human biology. Other species of yeast, such as Candida albicans, are opportunistic pathogens and can cause infection in humans. Yeasts have recently been used to generate electricity in microbial fuel cells, and produce ethanol for the biofuel industry. • Yeasts do not form a specific taxonomic or phylogenetic grouping. At present it is estimated that only 1% of all yeast species have been described. The term "yeast" is often taken as a synonym for S. cerevisiae, however the phylogenetic diversity of yeasts is shown by their placement in both divisions Ascomycota and Basidiomycota. The budding yeasts ("true yeasts") are classified in the order Saccharomycetales.

20. Yeast growth and nutrition • Yeasts are chemoorganotrophs as they use organic compounds as a source of energy and do not require sunlight to grow. The main source of carbon is obtained by hexose sugars such as glucose and fructose, or disaccharides such as sucrose and maltose. Some species can metabolize pentose sugars, alcohols, and organic acids. Yeast species either require oxygen for aerobic cellular respiration (obligate aerobes), or are anaerobic but also have aerobic methods of energy production (facultative anaerobes). Unlike bacteria, there are no known yeast species that grow only anaerobically (obligate anaerobes). Also, because they are adapted to them, yeasts grow best in a neutral pH environment. • Yeasts will grow over a temperature range of 10°-37°C, with an optimal temperature range of 30°-37°C, depending on the type of species. S. cerevisiae works best at about 30°C. There is little activity in the range of 0°-10°C. Above 37°C yeast cells become stressed and will not divide properly. Most yeast cells die above 50°C. The cells can survive freezing under certain conditions, with viability decreasing over time. • Yeasts are ubiquitous in the environment, but are most frequently isolated from sugar-rich samples. Some good examples include fruits and berries (such as grapes, apples or peaches), and exudates from plants (such as plant saps or cacti). Some yeasts are found in association with soil and insects. Yeast are generally grown in the laboratory on solid growth media or liquid broths. Common media used for the cultivation of yeasts include; potato dextrose agar (PDA) or potato dextrose broth, Wallerstien Laboratories Nutrient agar (WLN), Yeast Peptone Dextrose agar (YPD), and Yeast Mould agar or broth (YM).

21. Yeast reproduction: a genetic model • Yeasts have asexual and sexual reproductive cycles; however the most common mode of vegetative growth in yeast is asexual reproduction by budding or fission. Here a small bud, or daughter cell, is formed on the parent cell. The nucleus of the parent cell splits into a daughter nucleus and migrates into the daughter cell. The bud continues to grow until it separates from the parent cell, forming a new cell. The bud can develop on different parts of the parent cell depending on the genus of the yeast. • Under high stress conditions haploid cells will generally die, however under the same conditions diploid cells can undergo sporulation, entering sexual reproduction (meiosis) and producing a variety of haploid spores, which can go on to mate (conjugate), reforming the diploid. The yeast cell's life cycle.1. Budding2. Conjugation3. Spore

22. Other eukaryotic cells Eukaryotes are a very diverse group, and their cell structures are equally diverse. Many have cell walls; many do not. Many have chloroplasts, derived from primary, secondary, or even tertiary endosymbiosis; and many do not. Some groups have unique structures, such as the cyanelles of the glaucophytes, the haptonema of the haptophytes, or the ejectisomes of the cryptomonads. Other structures, such as pseudopods, are found in various eukaryote groups in different forms, such as the lobose amoebozoans or the reticulose foraminiferans. The glaucophytes, also known as glaucocystophytes or glaucocystids, are a small group of freshwater microscopic algae. The haptophytes, classed either as the Prymnesiophyta or Haptophyta, are a family of algae.

23. Amoebozoa The Amoebozoa are a major group of amoeboid protozoa, including the majority that move by means of internal cytoplasmic flow. Their pseudopodia are characteristically blunt and finger-like, called lobopodia. Most are unicellular, and are common in soils and aquatic habitats, with some found as symbiotes of other organisms, including several pathogens. The Amoebozoa also include the slime moulds, multinucleate or multicellular forms that produce spores and are usually visible to the unaided eye. Amoebozoa vary greatly in size. Many are only 10-20 μm in size, but they also include many of the larger protozoa. The famous species Amoeba proteus may reach 800 μm in length, and partly on account of its size is often studied as a representative cell. Multinucleate amoebae like Chaos and Pelomyxa may be several millimetres in length, and some slime moulds cover several square feet.

24. Radiolaria Radiolarians (also radiolaria) are amoeboid protozoa that produce intricate mineral skeletons, typically with a central capsule dividing the cell into inner and outer portions, called endoplasm and ectoplasm. They are found as zooplankton throughout the ocean, and because of their rapid turn-over of species, their tests are important diagnostic fossils found from the Cambrian onwards. Some common radiolarian fossils include Actinomma, Heliosphaera and Hexadoridium.

25. Endosymbiont Theory An endosymbiont is any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis (Greek: endo = inner, sym = together and biosis = living).

26. Endosymbiont Theory • The endosymbiotic theory concerns the origins of mitochondria and plastids (e.g. chloroplasts), which are organelles of eukaryotic cells. According to this theory, these organelles originated as separate prokaryotic organisms which were taken inside the cell as endosymbionts. Mitochondria developed from proteobacteria (in particular, Rickettsiales or close relatives) and chloroplasts from cyanobacteria. • According to the endosymbiont theory, an anaerobic cell probably ingested an aerobic bacterium but failed to digest it. The aerobic bacterium flourished within the cell because the cell’s cytoplasm was abundant in half-digested food molecules. The bacterium digested these molecules with oxygen and gained great amounts of energy. Because the bacterium had so much energy, it probably leaked some of it as ATP into the cell’s cytoplasm. This benefited the anaerobic cell because it enabled it to digest food aerobically. Eventually, the aerobic bacterium could no longer live independently from the cell, and it therefore became a mitochondrion. The origin of the chloroplast is very similar to that of the mitochondrion. A cell must have captured a photosynthetic cyanobacterium and failed to digest it. The cyanobacterium thrived in the cell and eventually evolved into the first chloroplast. Other eukaryotic organelles may have also evolved through endosymbiosis. Scientists believe that cilia, flagella, centrioles, and microtubules may have come from a symbiosis between a spirilla-like bacterium and an early eukaryotic cell.

27. Endosymbiont Theory: Evidence • Evidence that mitochondria and plastids arose from ancient endosymbiosis of bacteria is as follows: • Both mitochondria and plastids contain DNA that is different from that of the cell nucleus and that is similar to that of bacteria (in being circular and in its size). • They are surrounded by two or more membranes, and the innermost of these shows differences in composition from the other membranes of the cell. The composition is like that of a prokaryotic cell membrane. • New mitochondria and plastids are formed only through a process similar to binary fission. In some algae, such as Euglena, the plastids can be destroyed by certain chemicals or prolonged absence of light without otherwise affecting the cell. In such a case, the plastids will not regenerate. • Much of the internal structure and biochemistry of plastids, for instance the presence of thylakoids and particular chlorophylls, is very similar to that of cyanobacteria. Phylogenetic estimates constructed with bacteria, plastids, and eukaryotic genomes also suggest that plastids are most closely related to cyanobacteria. • Some proteins encoded in the nucleus are transported to the organelle, and both mitochondria and plastids have small genomes compared to bacteria. This is consistent with an increased dependence on the eukaryotic host after forming an endosymbiosis. Most genes on the organellar genomes have been lost or moved to the nucleus. Most genes needed for mitochondrial and plastid function are located in the nucleus. Many originate from the bacterial endosymbiont. • Plastids are present in very different groups of protists, some of which are closely related to forms lacking plastids. This suggests that if chloroplasts originated de novo, they did so multiple times, in which case their close similarity to each other is difficult to explain. Many of these protists contain "secondary" plastids that have been acquired from other plastid-containing eukaryotes, not from cyanobacteria directly. • Among the eukaryotes that acquired their plastids directly from bacteria (known as Primoplantae), the glaucophyte algae have chloroplasts that strongly resemble cyanobacteria. In particular, they have a peptidoglycan cell wall between their two membranes. • These organelles' ribosomes are like those found in bacteria (70s). • Proteins of organelle origin, like those of bacteria, use N-formylmethionine as the initiating amino acid.