Eukaryotic cells are distinguished from viruses and from prokaryotes (bacteria and archea) by their intracellular organization and genetic complexity. Eukaryotic cells exist as protists or multicellular organisms. The principal characteristics of a eukaryotic cell can be summarized as follows (Fig. 1.1).
The cell membrane. The existence of cells relies on the separation between the external environment and an internal cytoplasm which carries out the chemistry of life. This boundary is maintained by a membrane which provides a barrier to the solution outside the cell, and holds the cytoplasm molecules and organelles inside. The cell membrane provides a hydrophobic boundary, which consists of phospholipids and sterols, embedded with proteins. The details of the composition of cell membrane lipids and sterols vary with nutritional state and temperature, and the specific molecules vary between taxa. For example, a characteristic sterol in plant cell membranes is stigmasterol, it is cholesterol in animals, tetrahymenol in ciliates and ergosterol in fungi. The cell membrane allows free passage of gases such as oxygen and carbon dioxide, and of small polar but uncharged molecules such as water through the proteins. It is relatively basal bodies contractile vacu mitochondrion < chromosome cytoskeleton basal bodies contractile vacu mitochondrion < chromosome cytoskeleton
Fig. 1.1. Generalized eukaryotic cell organelles.
nucleus with chromosomes
Golgi-dictyosome food vacuole
impermeable to all ions and most nutrients. The cell membrane proteins regulate the interaction between the external and internal environment. These proteins are responsible for binding molecules outside the cell, modifying the physiological state of the cytoplasm and responding to the external molecules. Some membrane proteins are actively regulating ion transport into and out of the cell. This exchange creates a potential difference across the cell membrane, with the cytoplasm often being at about -30 mV relative to the outside solution in a resting cell. Several responses can be stimulated through changes in the cell membrane. This can be a directional locomotion response (chemotaxis) towards or away from the stimulus. The response can be ingestion of the molecules by initiating phagocytosis of particles which are digested as food. Pinocytosis involves the ingestion of tiny vesicles of external solution. Specific large molecules can be internalized by binding receptor proteins in the membrane by endocytosis. Some membrane proteins act as hydrophilic channels that selectively permit entry of molecules, especially certain nutrients and ions. Other membrane proteins are enzymes that digest complex molecules in the external solution or inactivate toxins. The optimal functioning of the cell membrane proteins depends on the external solution composition, including pH, ion concentrations and osmotic pressure, because they affect the potential difference across the membrane. There are also a variety of external peripheral proteins attached to membrane proteins, and outward-facing oligosaccharides attached to the proteins and lipids. These oligosaccharides vary between individuals, between species and between higher taxonomic hierarchies. They can provide a signature for each mating type, population allele and species.
One molecule that crosses the cell membrane relatively freely is water. The passage of water through the membrane proteins but the selective exclusion of solutes is called osmosis. This is important for understanding periods of organism activity and inactivity. When the soil solution contains few solutes relative to the cytoplasm of cells, water will flow into the cell. This tends to happen after rain, when there is more water and the soil solution is diluted. In contrast, during soil desiccation, the soil solutes become concentrated in increasingly less water. At some point, the soil solution will be more concentrated with solutes than the cytoplasm. This will draw water out of the cytoplasm. Different species have different tolerances of and preferences for external solution composition. For the cytoplasm to function optimally, it requires a constant concentration. Therefore, species have developed various means of osmoregulation that permit adjustments and buffering of cell water content, against changes in the external solution. Terrestrial protozoa and chromista have a contractile vacuole which removes excess water from the cytoplasm and excretes it together with soluble nitrogenous wastes and other solutes (Patterson, 1980). The role of contractile vacuoles in osmoregulation is similar to that of nephridia and renal cells in multicellular species. However, the cell's ability to buffer these changes is limited. If the external solution becomes too concentrated or too dilute, the cell becomes inactive and shuts itself off from the environment. If the soil is dried or diluted too rapidly, or too much, cell lysis or death is caused as the cell membrane ruptures. Fungi do not have contractile vacuoles and desiccate when soil is too dry. They are protected from lysis by the cell wall. The filaments become active again when the cytoplasm absorbs soil water. Invertebrates regulate their water content through renal cells and nephridia, which couple osmoreg-ulation with nitrogenous waste excretion.
Food that will be used in the cell must enter through the cell membrane. Food is obtained by phagocytosis and osmotrophy (pinocytosis, receptor-mediated endocytosis and active transport through the membrane). Food particles that enter by phagocytosis need to be digested in food vacuoles with digestive enzymes from lysosomes. The enzymes available vary between species, so that different proportions of the food vacuole organic matter will be digested. The remaining undigested portion must be excreted from the cell by exocytosis, i.e. the transport of the vesicle to the membrane and evacuation of its contents out of the cell. The digestion of food material releases usable nutrient molecules and indigestible molecules. Nutrient molecules that have entered the cytoplasm become the source of energy for metabolism, cell growth and replication of the cell. For these processes to occur, a sufficient supply of balanced nutrients is required.
Cellular metabolism. For a cell to grow and divide, the nutrients it acquires must be used to provide both a source of chemical energy for reactions and substrate molecules for these reactions. Catabolism refers to the chemical breakdown of nutrients to provide a source of chemical energy for cellular reactions. Anabolism refers to the cellular reactions that use the chemical energy and the nutrients as substrate molecules to build the more complex biological molecules and organelles. The details of metabolism of nutrients vary between species. The amino acids, carbohydrates, lipids, nucleic acids and mineral ions, which are obtained from digestion and from the external solution, are the building blocks for the rest of the cell. The energy for carrying out these synthetic (or anabolic) reactions is obtained from the respiration pathway. The respiration pathway varies between species depending on the presence of mitochondria, hydrogenosomes, intracellular symbiotic bacteria or protists, and the panoply of enzymes available to the species. Therefore, species that have lost a mitochondrion during evolution are anaerobic, but those with mitochondria are aerobic or facultative anaerobes. Anaerobic species are common symbionts in the digestive tract of multicellular species, but free-living species also occur. The mitochondrion-independent pathway (glycolysis and fermentation) uses glucose molecules which are oxidized to two molecules of pyruvate, with a net yield of two adenosine triphosphate (ATP) molecules. Pyruvate can be oxidized further to smaller molecules (such as acetate, lactate or ethanol) to yield further energy. Glycolysis does not require oxygen and does not yield CO2. The glucose and other substrates for this set of reactions is obtained from digestion of food, from de novo synthesis from other molecules, or transport into the cell in species where that is possible. Normally, it is assumed that most free-living protozoa do not transport glucose through the membrane, but acetate and other soluble 2-3 carbon molecules often are. In species with mitochondria, a further sequence of reactions is possible which produce >30 ATP molecules from each glucose equivalent. The mitochondrion provides the cell with enzymes for the Krebs cycle, the electron transport chain and oxidative phosphorylation. These respiration reactions require oxygen as a final electron acceptor, pyruvate and acetyl-CoA as substrates from the cytoplasm, and release CO2 and H2O as end-products. The rate of these reactions varies with the supply of oxygen. For this reason, eukaryotic cells have a variety of oxygen-scavenging molecules such as haemoglobin and other haem-containing molecules. For example, plant roots produce leg-haemoglobin when the soil is water saturated and short of oxygen, and many protozoa have haemoglobin-like proteins. The efficiency of these oxygen scavengers at low partial pressure of oxygen in the solution (pO2) determines tolerance to near-anaerobic conditions (anaero-tolerance). Intermediate molecules produced during glycolysis and mitochondrial respiration reactions are used as substrates for the de novo synthesis of amino acids, nucleic acids, lipids, carbohydrates and complex macromolecules, which together form the cytoplasm and organelles. The release of chemical energy from the y-phosphate bond in ATP, to adenosine diphosphate (ADP) or adenosine monophosphate (AMP), is used to drive the metabolic pathways to synthesize, modify or degrade molecules in the cell. ATP is the main energy currency of the cell. The total amount of cellular ATP can be an assay of metabolic activity because it is short lived and unstable outside cells, in the soil solution.
Secretion and exocytosis. One important difference from prokaryotes (later in this chapter) is that eukaryotes are able to target large amounts of diverse enzymes and other molecules for secretion. The endomembrane network links the ribosomes, endoplasmic reticulum, Golgi and dictyosome to vesicles where the molecules and enzymes targeted for secretion accumulate. The vesicles are varied and named according to their function. Some contain digestive enzymes (lysosomes) that will fuse with ingested food vacuoles (or phagosomes). Others are destined to be secreted out of the cell (secretory vesicles) for external digestion of food resources. These secretory vesicles often accumulate near the cell membrane until a stimulus triggers their release en masse. For example, in fungal cells, when a suitable substrate is detected, large numbers of secretory vesicles with digestive enzymes fuse with the cell membrane and release the enzymes externally (exocytosis). Secretion of individual proteins out of the cell also occurs, but it is not as significant as exocytosis in releasing large amounts of material from the cell. (In prokaryotes (this chapter), secretion of small single proteins is the only means of secretion. A single eukaryotic secretory vesicle is many times larger than a whole prokaryotic cell.) Excretion of undigested remains of the food vacuoles occurs by targeting the food vacuole for fusion with the cell membrane and release of the contents outside. Often the remains of several food vacuoles will fuse before being excreted. Exocytosis is not restricted to vesicles with enzymes or old food vacuoles. Many species of protists and cells of multicellular species can secrete mucopolysaccharides, or release defensive organelles or chemicals, and pheromones (mating hormones). The release of mucus (from mucocysts) and defensive organelles (trichocysts) is triggered in defence against predation, and chemical or mechanical stimuli. Gland cells in invertebrate epithelium secrete mucus for sliding, absorbing water or providing a protective barrier.
Cytoskeleton. The shape of eukaryotic cells is determined by their external cell wall or internal cytoskeleton. In animal cells and protists which lack a cell wall, the shape is determined by stable microtubule networks and associated fine filaments which support the cell membrane and hold the nucleus and basal bodies in position. The basal bodies have an important role in orienting and organizing the cytoskeleton. The exact arrangement of these stable cytoskeletal networks varies between phyla and classes. The stable microtubular networks in the cell provide a frame with distinct anterior-posterior and left-right axes. The remaining cytoskeletal elements are organized from this. The cilium (or 'eukaryotic flagellum') is an extension of the cell membrane, supported by microtubular and associated elements (the axoneme) that extend from basal bodies. The cilium is responsible for pulling or pushing the cell through liquid films and free water. Hair-like protein extensions from the cilium are called mastigonemes and occur in certain taxa, especially in many chromista. The cilium is anchored at its base by a basal body which is composed of stable cytoskeletal proteins. The basal body (or kinetosome) consists of a core of circular microtubules and several anchoring elements extending into the cytoplasm. The basal body and its associated anchoring cytoskeleton are called a kinetid. Basal bodies occur in pairs in most taxa, and not all basal bodies are ciliated. In some taxa (such as Ciliophora, Hypermastigea and Opalinea), the entire cell is covered with cilia. The details of the kinetid structure are key to the correct identification of families and genera of protists. The transient cytoskeleton is more dynamic, continually changing in distribution. It is composed of transient microtubules, actin filaments and associated fine filaments. It is implicated in the amoeboid locomotion and shape changes of cells, as well as in directional transport of vesicles and organelles in the cytoplasm. Most protists without an external cell wall are capable of at least some amoeboid locomotion. Some taxa also have supporting elements under the cell membrane. For example, the euglenid species have a proteinaceous thickening (pellicle strips) that reinforces the membrane. Some classes of Ciliophora have additional membranes (the alveolae) and cytoskeleton which support the cell membrane. Lastly, many soil species also have a cell wall outside the cell membrane. In Testacealobosea, the cell wall consist of chitinous and proteinaceous secretions. In the Difflugida (Testacealobosea), the test is reinforced further with mineral soil particles cemented or embedded in the wall material. In several families (such as the Paramaoebida, Paraquadrulidae and Nebellidae) and in the Euglyphid (Filosea), the wall is composed of mineralized secreted plates of various shapes. In the Oomycetes and Hyphochytrea, the cell wall consists of tight fibrils of 0-glucans and cellulose deposited outside the cell membrane. In the fungi, it is composed of chitin, glucans and a variety of polysaccharides that vary between taxa. Species with an external cell wall are less able to change shape and squeeze through spaces. However, they are more resistant to abrupt changes in osmotic pressure and desiccation, which are more frequent in surface soil and litter.
Differentiation. In response to an environmental stimulus, protists can differentiate to an alternative morphology or functional role. The stimulus usually involves dilution or decrease of food resources, desiccation of soil, and changes in pH, temperature or salt composition. The differentiation response involves a dramatic replacement of the mRNA by a new population of mRNA molecules from activated genes, over a few minutes to hours. The result is a new set of proteins and enzymes that are synthesized to carry out a new set of reactions. The cell switches its function from growing and dividing into a non-feeding sexual pathway or into a dormant cyst stage. In some taxa, there is no known sexual pathway. For example, it is uncommon or at least unreported in the Amoebaea but observed in many Testacealobosea and Ciliophora. Some taxa respond to poor conditions by differentiating to a dispersal stage. For example, the Percolozoa are normally amoeboid cells that become ciliated dispersal cells when resources are reduced. However, probably all soil species are capable of encystment to resist desiccation or an unsuitable environment. Encystment involves a partial or complete resorption of the stable cytoskeletal network and loss of cell shape. The cell secretes a protective cell wall that is usually proteinaceous and/or chitinous. Encystment in soil species usually involves a gradual excretion of water through the contractile vacuoles that is important to confer chemical resistance by dehydration of the cell. Desiccation of the cyst in certain species can proceed to a near crystalline state which makes molecular manipulation and extractions difficult. The excystment stimulus varies between species, and involves the synthesis of new mRNA populations required for morphogenesis, metabolic and cell growth regulation proteins.
In multicellular species, differentiation is a continuous process that begins with egg fertilization or parthenogenesis, and through successive cell divisions during development into the mature adult. It results in differentiation of tissues and of cells within tissues, each with a distinct function. In these species, cells do not separate after cell division and remain attached, forming a multicellular organism with several tissues. Each tissue has cells with specific functions, such as osmoregulation in renal cells, contraction in muscles, nutrient endocytosis in the gut, enzyme secretion in digestive glands, and so on.
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