Eukaryote

Eukaryote

Overview
A eukaryote is an organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...

 whose cells
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....

 contain complex structures enclosed within membranes
Biological membrane
A biological membrane or biomembrane is an enclosing or separatingmembrane that acts as a selective barrier, within or around a cell. It consists of a lipid bilayer with embedded proteins that may constitute close to 50% of membrane content...

. Eukaryotes may more formally be referred to as the taxon
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...

 Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic
Prokaryote
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

 cells is the nucleus
Cell nucleus
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...

, or nuclear envelope
Nuclear envelope
A nuclear envelope is a double lipid bilayer that encloses the genetic material in eukaryotic cells. The nuclear envelope also serves as the physical barrier, separating the contents of the nucleus from the cytosol...

, within which the genetic material is carried. The presence of a nucleus gives eukaryotes their name, which comes from the Greek
Greek language
Greek is an independent branch of the Indo-European family of languages. Native to the southern Balkans, it has the longest documented history of any Indo-European language, spanning 34 centuries of written records. Its writing system has been the Greek alphabet for the majority of its history;...

 ευ (eu, "good") and κάρυον (karyon, "nut" or "kernel").
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Encyclopedia
A eukaryote is an organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...

 whose cells
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....

 contain complex structures enclosed within membranes
Biological membrane
A biological membrane or biomembrane is an enclosing or separatingmembrane that acts as a selective barrier, within or around a cell. It consists of a lipid bilayer with embedded proteins that may constitute close to 50% of membrane content...

. Eukaryotes may more formally be referred to as the taxon
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...

 Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic
Prokaryote
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

 cells is the nucleus
Cell nucleus
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...

, or nuclear envelope
Nuclear envelope
A nuclear envelope is a double lipid bilayer that encloses the genetic material in eukaryotic cells. The nuclear envelope also serves as the physical barrier, separating the contents of the nucleus from the cytosol...

, within which the genetic material is carried. The presence of a nucleus gives eukaryotes their name, which comes from the Greek
Greek language
Greek is an independent branch of the Indo-European family of languages. Native to the southern Balkans, it has the longest documented history of any Indo-European language, spanning 34 centuries of written records. Its writing system has been the Greek alphabet for the majority of its history;...

 ευ (eu, "good") and κάρυον (karyon, "nut" or "kernel"). Most eukaryotic cells also contain other membrane-bound organelle
Organelle
In cell biology, an organelle is a specialized subunit within a cell that has a specific function, and is usually separately enclosed within its own lipid bilayer....

s such as mitochondria
Mitochondrion
In cell biology, a mitochondrion is a membrane-enclosed organelle found in most eukaryotic cells. These organelles range from 0.5 to 1.0 micrometers in diameter...

, chloroplast
Chloroplast
Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.Chloroplasts are green...

s and the Golgi apparatus
Golgi apparatus
The Golgi apparatus is an organelle found in most eukaryotic cells. It was identified in 1898 by the Italian physician Camillo Golgi, after whom the Golgi apparatus is named....

. All species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...

 of large complex organisms are eukaryotes, including animal
Animal
Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and...

s, plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...

s and fungi
Fungus
A fungus is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds , as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from plants, animals, and bacteria...

, although most species of eukaryote are protist
Protist
Protists are a diverse group of eukaryotic microorganisms. Historically, protists were treated as the kingdom Protista, which includes mostly unicellular organisms that do not fit into the other kingdoms, but this group is contested in modern taxonomy...

 microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...

s.

Cell division
Cell division
Cell division is the process by which a parent cell divides into two or more daughter cells . Cell division is usually a small segment of a larger cell cycle. This type of cell division in eukaryotes is known as mitosis, and leaves the daughter cell capable of dividing again. The corresponding sort...

 in eukaryotes is different from that in organisms without a nucleus (prokaryotes). It involves separating the duplicated chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...

s, through movements directed by microtubules. There are two types of division processes. In mitosis
Mitosis
Mitosis is the process by which a eukaryotic cell separates the chromosomes in its cell nucleus into two identical sets, in two separate nuclei. It is generally followed immediately by cytokinesis, which divides the nuclei, cytoplasm, organelles and cell membrane into two cells containing roughly...

, one cell divides to produce two genetically identical cells. In meiosis
Meiosis
Meiosis is a special type of cell division necessary for sexual reproduction. The cells produced by meiosis are gametes or spores. The animals' gametes are called sperm and egg cells....

, which is required in sexual reproduction
Sexual reproduction
Sexual reproduction is the creation of a new organism by combining the genetic material of two organisms. There are two main processes during sexual reproduction; they are: meiosis, involving the halving of the number of chromosomes; and fertilization, involving the fusion of two gametes and the...

, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination
Genetic recombination
Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...

 of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.

Eukaryotes appear to be monophyletic, and so make up one of the three domains
Domain (biology)
In biological taxonomy, a domain is the highest taxonomic rank of organisms, higher than a kingdom. According to the three-domain system of Carl Woese, introduced in 1990, the Tree of Life consists of three domains: Archaea, Bacteria and Eukarya...

 of life. The two other domains, Bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

 and Archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...

, are prokaryotes and have none of the above features. Eukaryotes represent a tiny minority of all living things; even in a human body there are 10 times more microbes than human cells. However, due to their much larger size their collective worldwide biomass is estimated at about equal to that of prokaryotes.

Cell features


Eukaryotic cells are typically much larger than those of prokaryote
Prokaryote
The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

s. They have a variety of internal membranes and structures, called organelle
Organelle
In cell biology, an organelle is a specialized subunit within a cell that has a specific function, and is usually separately enclosed within its own lipid bilayer....

s, and a cytoskeleton
Cytoskeleton
The cytoskeleton is a cellular "scaffolding" or "skeleton" contained within a cell's cytoplasm and is made out of protein. The cytoskeleton is present in all cells; it was once thought to be unique to eukaryotes, but recent research has identified the prokaryotic cytoskeleton...

 composed of microtubule
Microtubule
Microtubules are a component of the cytoskeleton. These rope-like polymers of tubulin can grow as long as 25 micrometers and are highly dynamic. The outer diameter of microtubule is about 25 nm. Microtubules are important for maintaining cell structure, providing platforms for intracellular...

s, microfilament
Microfilament
Microfilaments are the thinnest filaments of the cytoskeleton, a structure found in the cytoplasm of all eukaryotic cells. These linear polymers of actin subunits are flexible and relatively strong, resisting buckling by multi-piconewton compressive forces and filament fracture by nanonewton...

s, and intermediate filament
Intermediate filament
Intermediate filaments are a family of related proteins that share common structural and sequence features. Intermediate filaments have an average diameter of 10 nanometers, which is between that of 7 nm actin , and that of 25 nm microtubules, although they were initially designated...

s, which play an important role in defining the cell's organization and shape. Eukaryotic DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 is divided into several linear bundles called chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...

s, which are separated by a microtubular spindle during nuclear division.

Internal membrane


Eukaryote cells include a variety of membrane-bound structures, collectively referred to as the endomembrane system
Endomembrane system
The endomembrane system is composed of the different membranes that are suspended in the cytoplasm within a eukaryotic cell. These membranes divide the cell into functional and structural compartments, or organelles...

. Simple compartments, called vesicles
Vesicle (biology)
A vesicle is a bubble of liquid within another liquid, a supramolecular assembly made up of many different molecules. More technically, a vesicle is a small membrane-enclosed sack that can store or transport substances. Vesicles can form naturally because of the properties of lipid membranes , or...

 or vacuole
Vacuole
A vacuole is a membrane-bound organelle which is present in all plant and fungal cells and some protist, animal and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic molecules including enzymes in solution, though in certain...

s, can form by budding off other membranes. Many cells ingest food and other materials through a process of endocytosis
Endocytosis
Endocytosis is a process by which cells absorb molecules by engulfing them. It is used by all cells of the body because most substances important to them are large polar molecules that cannot pass through the hydrophobic plasma or cell membrane...

, where the outer membrane invaginates
Invagination
Invagination means to fold inward or to sheath. In biology, this can refer to a number of processes.* Invagination is the morphogenetic processes by which an embryo takes form, and is the initial step of gastrulation, the massive reorganization of the embryo from a simple spherical ball of cells,...

 and then pinches off to form a vesicle. It is probable that most other membrane-bound organelles are ultimately derived from such vesicles.

The nucleus is surrounded by a double membrane (commonly referred to as a nuclear envelope
Nuclear envelope
A nuclear envelope is a double lipid bilayer that encloses the genetic material in eukaryotic cells. The nuclear envelope also serves as the physical barrier, separating the contents of the nucleus from the cytosol...

), with pores that allow material to move in and out. Various tube- and sheet-like extensions of the nuclear membrane form what is called the endoplasmic reticulum
Endoplasmic reticulum
The endoplasmic reticulum is an organelle of cells in eukaryotic organisms that forms an interconnected network of tubules, vesicles, and cisternae...

 or ER, which is involved in protein transport and maturation. It includes the rough ER where ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....

s are attached to synthesize proteins, which enter the interior space or lumen. Subsequently, they generally enter vesicles, which bud off from the smooth ER. In most eukaryotes, these protein-carrying vesicles are released and further modified in stacks of flattened vesicles, called Golgi bodies
Golgi apparatus
The Golgi apparatus is an organelle found in most eukaryotic cells. It was identified in 1898 by the Italian physician Camillo Golgi, after whom the Golgi apparatus is named....

 or dictyosomes.

Vesicles may be specialized for various purposes. For instance, lysosome
Lysosome
thumb|350px|Schematic of typical animal cell, showing subcellular components. [[Organelle]]s: [[nucleoli]] [[cell nucleus|nucleus]] [[ribosomes]] [[vesicle |vesicle]] rough [[endoplasmic reticulum]]...

s contain enzymes that break down the contents of food vacuoles, and peroxisome
Peroxisome
Peroxisomes are organelles found in virtually all eukaryotic cells. They are involved in the catabolism of very long chain fatty acids, branched chain fatty acids, D-amino acids, polyamines, and biosynthesis of plasmalogens, etherphospholipids critical for the normal function of mammalian brains...

s are used to break down peroxide
Peroxide
A peroxide is a compound containing an oxygen–oxygen single bond or the peroxide anion .The O−O group is called the peroxide group or peroxo group. In contrast to oxide ions, the oxygen atoms in the peroxide ion have an oxidation state of −1.The simplest stable peroxide is hydrogen peroxide...

, which is toxic otherwise. Many protozoa
Protozoa
Protozoa are a diverse group of single-cells eukaryotic organisms, many of which are motile. Throughout history, protozoa have been defined as single-cell protists with animal-like behavior, e.g., movement...

 have contractile vacuoles, which collect and expel excess water, and extrusome
Extrusome
Extrusomes are membrane-bound structures in some eukaryotes which, under certain conditions, discharge their contents outside the cell. There are a variety of different types, probably not homologous, and serving various functions....

s, which expel material used to deflect predators or capture prey. In multicellular organisms, hormone
Hormone
A hormone is a chemical released by a cell or a gland in one part of the body that sends out messages that affect cells in other parts of the organism. Only a small amount of hormone is required to alter cell metabolism. In essence, it is a chemical messenger that transports a signal from one...

s are often produced in vesicles. In higher plants, most of a cell's volume is taken up by a central vacuole, which primarily maintains its osmotic pressure.

Mitochondria and plastids


Mitochondria
Mitochondrion
In cell biology, a mitochondrion is a membrane-enclosed organelle found in most eukaryotic cells. These organelles range from 0.5 to 1.0 micrometers in diameter...

 are organelles found in nearly all eukaryotes. They are surrounded by two membranes (each a phospholipid bi-layer
Lipid bilayer
The lipid bilayer is a thin membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around cells. The cell membrane of almost all living organisms and many viruses are made of a lipid bilayer, as are the membranes surrounding the cell nucleus...

), the inner of which is folded into invaginations called cristae, where aerobic respiration takes place. Mitochondria contain their own DNA. They are now generally held to have developed from endosymbiotic prokaryotes, probably proteobacteria
Proteobacteria
The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....

. The few protozoa that lack mitochondria have been found to contain mitochondrion-derived organelles, such as hydrogenosome
Hydrogenosome
A hydrogenosome is a membrane-enclosed organelle of some anaerobic ciliates, trichomonads and fungi. The hydrogenosomes of trichomonads produce molecular hydrogen, acetate, carbon dioxide and ATP by the combined actions of pyruvate:ferredoxin oxido-reductase, hydrogenase, acetate:succinate CoA...

s and mitosome
Mitosome
A mitosome is an organelle found in some unicellular eukaryotic organisms. The mitosome has only recently been found and named, and its function has not yet been well characterized. It was termed a 'crypton' by one group, but that name is no longer in use....

s; and thus probably lost the mitochondria secondarily.

Plants and various groups of algae
Algae
Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...

 also have plastid
Plastid
Plastids are major organelles found in the cells of plants and algae. Plastids are the site of manufacture and storage of important chemical compounds used by the cell...

s. Again, these have their own DNA and developed from endosymbiotes, in this case cyanobacteria. They usually take the form of chloroplast
Chloroplast
Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.Chloroplasts are green...

s, which like cyanobacteria contain chlorophyll
Chlorophyll
Chlorophyll is a green pigment found in almost all plants, algae, and cyanobacteria. Its name is derived from the Greek words χλωρος, chloros and φύλλον, phyllon . Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to obtain energy from light...

 and produce organic compounds (such as glucose
Glucose
Glucose is a simple sugar and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate...

) through photosynthesis
Photosynthesis
Photosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...

. Others are involved in storing food. Although plastids likely had a single origin, not all plastid-containing groups are closely related. Instead, some eukaryotes have obtained them from others through secondary endosymbiosis or ingestion.

Endosymbiotic origins have also been proposed for the nucleus, for which see below, and for eukaryotic flagella
Flagellum
A flagellum is a tail-like projection that protrudes from the cell body of certain prokaryotic and eukaryotic cells, and plays the dual role of locomotion and sense organ, being sensitive to chemicals and temperatures outside the cell. There are some notable differences between prokaryotic and...

, supposed to have developed from spirochaete
Spirochaete
Spirochaetes belong to a phylum of distinctive Gram-negative bacteria, which have long, helically coiled cells...

s. This is not generally accepted, both from a lack of cytological
Cell biology
Cell biology is a scientific discipline that studies cells – their physiological properties, their structure, the organelles they contain, interactions with their environment, their life cycle, division and death. This is done both on a microscopic and molecular level...

 evidence and difficulty in reconciling this with cellular reproduction.

Cytoskeletal structures




Many eukaryotes have long slender motile cytoplasmic projections, called flagella
Flagellum
A flagellum is a tail-like projection that protrudes from the cell body of certain prokaryotic and eukaryotic cells, and plays the dual role of locomotion and sense organ, being sensitive to chemicals and temperatures outside the cell. There are some notable differences between prokaryotic and...

, or similar structures called cilia
Cilium
A cilium is an organelle found in eukaryotic cells. Cilia are slender protuberances that project from the much larger cell body....

. Flagella and cilia are sometimes referred to as undulipodia, and are variously involved in movement, feeding, and sensation. They are composed mainly of tubulin
Tubulin
Tubulin is one of several members of a small family of globular proteins. The most common members of the tubulin family are α-tubulin and β-tubulin, the proteins that make up microtubules. Each has a molecular weight of approximately 55 kiloDaltons. Microtubules are assembled from dimers of α- and...

. These are entirely distinct from prokaryotic flagella. They are supported by a bundle of microtubules arising from a basal body
Basal body
A basal body is an organelle formed from a centriole, and a short cylindrical array of microtubules. It is found at the base of a eukaryotic undulipodium and serves as a nucleation site for the growth of the axoneme microtubules...

, also called a kinetosome or centriole
Centriole
A Centriole is a barrel-shaped cell structure found in most animal eukaryotic cells, though it is absent in higher plants and most fungi. The walls of each centriole are usually composed of nine triplets of microtubules...

, characteristically arranged as nine doublets surrounding two singlets. Flagella also may have hairs, or mastigonemes
Mastigonemes
Mastigonemes are lateral "hairs" found covering the flagella of heterokont and cryptophyte algae. They are approximately 15 nm in diameter, and usually consist of a tubular shaft that itself terminates in smaller "hairs". It is believed that they assist in locomotion by increasing the surface...

, and scales connecting membranes and internal rods. Their interior is continuous with the cell's cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...

.

Microfilamental structures composed by actin
Actin
Actin is a globular, roughly 42-kDa moonlighting protein found in all eukaryotic cells where it may be present at concentrations of over 100 μM. It is also one of the most highly-conserved proteins, differing by no more than 20% in species as diverse as algae and humans...

 and actin binding proteins, e.g., α-actinin
Actinin
Actinin is a microfilament protein. α-Actinin is necessary for the attachment of actin filaments to the Z-lines in skeletal muscle cells, and to the dense bodies in smooth muscle cells...

, fimbrin
Fimbrin
-Structure:Fimbrin belongs to the calponin homology domain superfamily of actin cross-linking proteins. Like other members of this superfamily, which include α-actinin, β-spectrin, dystrophin, ABP-120 and filamin, it has a conserved 27 kDa actin-binding domain that contains a tandem duplication of...

, filamin
Filamin
Filamins are a class of proteins that hold two actin filaments at large angles.Types include:* FLNA* FLNB* FLNC...

 are present in submembraneous cortical layers and bundles, as well. Motor proteins of microtubules, e.g., dynein
Dynein
Dynein is a motor protein in cells which converts the chemical energy contained in ATP into the mechanical energy of movement. Dynein transports various cellular cargo by "walking" along cytoskeletal microtubules towards the minus-end of the microtubule, which is usually oriented towards the cell...

 or kinesin
Kinesin
A kinesin is a protein belonging to a class of motor proteins found in eukaryotic cells. Kinesins move along microtubule filaments, and are powered by the hydrolysis of ATP . The active movement of kinesins supports several cellular functions including mitosis, meiosis and transport of cellular...

 and actin, e.g., myosins provide dynamic character of the network.

Centrioles are often present even in cells and groups that do not have flagella. They generally occur in groups of one or two, called kinetids, that give rise to various microtubular roots. These form a primary component of the cytoskeletal structure, and are often assembled over the course of several cell divisions, with one flagellum retained from the parent and the other derived from it. Centrioles may also be associated in the formation of a spindle during nuclear division.

Significance of cytoskeletal structures is underlined in determination of shape of the cells, as well as their being essential components of migratory responses like chemotaxis
Chemotaxis
Chemotaxis is the phenomenon in which somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food by swimming towards the highest concentration of food molecules,...

 and chemokinesis
Chemokinesis
Motile response of unicellular prokaryotic or eukaryotic organisms to chemicals that cause the cell to make some kind of change in their migratory/swimming behaviour. Changes involve an increase or decrease of speed, alterations of amplitude or frequency of motile character, or direction of migration...

. Some protists have various other microtubule-supported organelles. These include the radiolaria and heliozoa
Heliozoa
Heliozoa are phagotrophs. They are roughly spherical amoeboids with many stiff, microtubule-supported projections called axopods radiating outward from the cell surface. These give them the characteristic sun-like appearance for which they are named, and are variously used for capturing food,...

, which produce axopodia used in flotation or to capture prey, and the haptophyte
Haptophyte
The haptophytes, classified either as the Prymnesiophyta or Haptophyta, are a division of algae.The term "Haptophyceae" is sometimes used. This ending implies classification at a lower level...

s, which have a peculiar flagellum-like organelle called the haptonema. An animal cell is a form of eukaryotic cell that makes up many tissues in animals.

Plant cell wall


Plant cells have a cell wall, a fairly rigid layer outside the cell membrane
Cell membrane
The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...

, providing the cell with structural support, protection, and a filtering mechanism. The cell wall also prevents over-expansion when water enters the cell. The major polysaccharides making up the primary cell wall of land plants are cellulose
Cellulose
Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to over ten thousand β linked D-glucose units....

, hemicellulose
Hemicellulose
A hemicellulose is any of several heteropolymers , such as arabinoxylans, present along with cellulose in almost all plant cell walls. While cellulose is crystalline, strong, and resistant to hydrolysis, hemicellulose has a random, amorphous structure with little strength...

, and pectin
Pectin
Pectin is a structural heteropolysaccharide contained in the primary cell walls of terrestrial plants. It was first isolated and described in 1825 by Henri Braconnot...

. The cellulose microfibril
Microfibril
The microfibril is a very fine fibril, or fiber-like strand, consisting of glycoproteins and cellulose. It is usually, but not always, used as a general term in describing the structure of protein fiber, examples are hair and sperm tail. Its most frequently observed structural pattern is 9+2...

s are linked via hemicellulosic tethers to form the cellulose-hemicellulose network, which is embedded in the pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan
Xyloglucan
Xyloglucan is a hemicellulose that occurs in the primary cell wall of all vascular plants, however essential enzymes for xyloglucan metabolism, like XTH and β1→4-Glucan Synthase are found in Charophyceae algae. In many dicotyledonous plants, it is the most abundant hemicellulose in the primary cell...

.

Differences among eukaryotic cells


There are many different types of eukaryotic cells, though animals and plants are the most familiar eukaryotes, and thus provide an excellent starting point for understanding eukaryotic structure. Fungi and many protists have some substantial differences, however.

Animal cell




An animal cell is a form of eukaryotic cell that makes up many tissues
Biological tissue
Tissue is a cellular organizational level intermediate between cells and a complete organism. A tissue is an ensemble of cells, not necessarily identical, but from the same origin, that together carry out a specific function. These are called tissues because of their identical functioning...

 in animal
Animal
Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and...

s. The animal cell is distinct from other eukaryotes, most notably plant cells, as they lack cell wall
Cell wall
The cell wall is the tough, usually flexible but sometimes fairly rigid layer that surrounds some types of cells. It is located outside the cell membrane and provides these cells with structural support and protection, and also acts as a filtering mechanism. A major function of the cell wall is to...

s and chloroplast
Chloroplast
Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.Chloroplasts are green...

s, and they have smaller vacuole
Vacuole
A vacuole is a membrane-bound organelle which is present in all plant and fungal cells and some protist, animal and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic molecules including enzymes in solution, though in certain...

s. Due to the lack of a rigid cell wall
Cell wall
The cell wall is the tough, usually flexible but sometimes fairly rigid layer that surrounds some types of cells. It is located outside the cell membrane and provides these cells with structural support and protection, and also acts as a filtering mechanism. A major function of the cell wall is to...

, animal cells can adopt a variety of shapes, and a phagocytic
Phagocyte
Phagocytes are the white blood cells that protect the body by ingesting harmful foreign particles, bacteria, and dead or dying cells. Their name comes from the Greek phagein, "to eat" or "devour", and "-cyte", the suffix in biology denoting "cell", from the Greek kutos, "hollow vessel". They are...

 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.

Plant cell


Plant cells
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....

 are quite different from the cells of the other eukaryotic organisms. Their distinctive features are:
  • A large central vacuole
    Vacuole
    A vacuole is a membrane-bound organelle which is present in all plant and fungal cells and some protist, animal and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic molecules including enzymes in solution, though in certain...

     (enclosed by a membrane, the tonoplast), which maintains the cell's turgor and controls movement of molecule
    Molecule
    A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...

    s between the cytosol
    Cytosol
    The cytosol or intracellular fluid is the liquid found inside cells, that is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondrion into compartments....

     and sap
    Plant sap
    Sap is a fluid transported in xylem cells or phloem sieve tube elements of a plant. It transports water and nutrients throughout the plant....

  • A primary cell wall
    Cell wall
    The cell wall is the tough, usually flexible but sometimes fairly rigid layer that surrounds some types of cells. It is located outside the cell membrane and provides these cells with structural support and protection, and also acts as a filtering mechanism. A major function of the cell wall is to...

     containing cellulose
    Cellulose
    Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to over ten thousand β linked D-glucose units....

    , hemicellulose
    Hemicellulose
    A hemicellulose is any of several heteropolymers , such as arabinoxylans, present along with cellulose in almost all plant cell walls. While cellulose is crystalline, strong, and resistant to hydrolysis, hemicellulose has a random, amorphous structure with little strength...

     and pectin
    Pectin
    Pectin is a structural heteropolysaccharide contained in the primary cell walls of terrestrial plants. It was first isolated and described in 1825 by Henri Braconnot...

    , deposited by the protoplast
    Protoplast
    Protoplast, from the ancient Greek πρῶτον + verb πλάθω or πλάττω , initially referred to the first organized body of a species.Protoplast has several biological definitions:...

     on the outside of the cell membrane
    Cell membrane
    The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...

    ; this contrasts with the cell walls of fungi
    Fungus
    A fungus is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds , as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from plants, animals, and bacteria...

    , which contain chitin
    Chitin
    Chitin n is a long-chain polymer of a N-acetylglucosamine, a derivative of glucose, and is found in many places throughout the natural world...

    , and the cell envelope
    Cell envelope
    The cell envelope is the cell membrane and cell wall plus an outer membrane, if one is present.Most bacterial cell envelopes fall into two major categories: Gram positive and Gram negative. These are differentiated by their Gram staining characteristics....

    s of prokaryote
    Prokaryote
    The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

    s, in which peptidoglycan
    Peptidoglycan
    Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of bacteria , forming the cell wall. The sugar component consists of alternating residues of β- linked N-acetylglucosamine and N-acetylmuramic acid...

    s are the main structural molecules
  • The plasmodesmata
    Plasmodesmata
    Plasmodesmata are microscopic channels which traverse the cell walls of plant cells and some algal cells, enabling transport and communication between them. Species that have plasmodesmata include members of the Charophyceae, Charales and Coleochaetales , as well as all embryophytes, better known...

    , linking pores in the cell wall that allow each plant cell to communicate with other adjacent cells; this is different from the functionally analogous system of gap junction
    Gap junction
    A gap junction or nexus is a specialized intercellular connection between a multitude of animal cell-types. It directly connects the cytoplasm of two cells, which allows various molecules and ions to pass freely between cells....

    s between animal cells.
  • Plastid
    Plastid
    Plastids are major organelles found in the cells of plants and algae. Plastids are the site of manufacture and storage of important chemical compounds used by the cell...

    s, especially chloroplast
    Chloroplast
    Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.Chloroplasts are green...

    s that contain chlorophyll
    Chlorophyll
    Chlorophyll is a green pigment found in almost all plants, algae, and cyanobacteria. Its name is derived from the Greek words χλωρος, chloros and φύλλον, phyllon . Chlorophyll is an extremely important biomolecule, critical in photosynthesis, which allows plants to obtain energy from light...

    , the pigment that gives plant
    Plant
    Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...

    s their green color and allows them to perform photosynthesis
    Photosynthesis
    Photosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...

  • Higher plants, including conifers
    Pinophyta
    The conifers, division Pinophyta, also known as division Coniferophyta or Coniferae, are one of 13 or 14 division level taxa within the Kingdom Plantae. Pinophytes are gymnosperms. They are cone-bearing seed plants with vascular tissue; all extant conifers are woody plants, the great majority being...

     and flowering plant
    Flowering plant
    The flowering plants , also known as Angiospermae or Magnoliophyta, are the most diverse group of land plants. Angiosperms are seed-producing plants like the gymnosperms and can be distinguished from the gymnosperms by a series of synapomorphies...

    s (Angiospermae) lack the flagellae
    Flagellum
    A flagellum is a tail-like projection that protrudes from the cell body of certain prokaryotic and eukaryotic cells, and plays the dual role of locomotion and sense organ, being sensitive to chemicals and temperatures outside the cell. There are some notable differences between prokaryotic and...

     and centriole
    Centriole
    A Centriole is a barrel-shaped cell structure found in most animal eukaryotic cells, though it is absent in higher plants and most fungi. The walls of each centriole are usually composed of nine triplets of microtubules...

    s that are present in animal cells.

Fungal cell


Fungal cells are most similar to animal cells, with the following exceptions:
  • A cell wall that contains chitin
    Chitin
    Chitin n is a long-chain polymer of a N-acetylglucosamine, a derivative of glucose, and is found in many places throughout the natural world...

  • Less definition between cells; the hypha
    Hypha
    A hypha is a long, branching filamentous structure of a fungus, and also of unrelated Actinobacteria. In most fungi, hyphae are the main mode of vegetative growth, and are collectively called a mycelium; yeasts are unicellular fungi that do not grow as hyphae.-Structure:A hypha consists of one or...

    e of higher fungi have porous partitions called septa
    Septum
    In anatomy, a septum is a wall, dividing a cavity or structure into smaller ones.-In human anatomy:...

    , 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.

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 glaucophyte
Glaucophyte
The glaucophytes, also known as glaucocystophytes or glaucocystids, are a small group of freshwater microscopic algae. Together with the red algae and green algae plus land plants , they form the Archaeplastida...

s, the haptonema of the haptophyte
Haptophyte
The haptophytes, classified either as the Prymnesiophyta or Haptophyta, are a division of algae.The term "Haptophyceae" is sometimes used. This ending implies classification at a lower level...

s, or the ejectisomes of the cryptomonad
Cryptomonad
The cryptomonads are a group of algae, most of which have plastids. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10-50 μm in size and flattened in shape, with an anterior groove or pocket...

s. Other structures, such as pseudopod
Pseudopod
Pseudopods or pseudopodia are temporary projections of eukaryotic cells. Cells that possess this faculty are generally referred to as amoeboids. Pseudopodia extend and contract by the reversible assembly of actin subunits into microfilaments...

s, are found in various eukaryote groups in different forms, such as the lobose amoebozoa
Amoebozoa
The Amoebozoa are a major group of amoeboid protozoa, including the majority that move by means ofinternal cytoplasmic flow. Their pseudopodia are characteristically blunt and finger-like,...

ns or the reticulose foraminiferans.

Reproduction


Nuclear division is often coordinated with cell division
Cell division
Cell division is the process by which a parent cell divides into two or more daughter cells . Cell division is usually a small segment of a larger cell cycle. This type of cell division in eukaryotes is known as mitosis, and leaves the daughter cell capable of dividing again. The corresponding sort...

. This generally takes place by mitosis
Mitosis
Mitosis is the process by which a eukaryotic cell separates the chromosomes in its cell nucleus into two identical sets, in two separate nuclei. It is generally followed immediately by cytokinesis, which divides the nuclei, cytoplasm, organelles and cell membrane into two cells containing roughly...

, a process that allows each daughter nucleus to receive one copy of each chromosome. In most eukaryotes, there is also a process of sexual reproduction, typically involving an alternation between haploid generations, wherein only one copy of each chromosome is present, and diploid generations, wherein two are present, occurring through nuclear fusion (syngamy) and meiosis
Meiosis
Meiosis is a special type of cell division necessary for sexual reproduction. The cells produced by meiosis are gametes or spores. The animals' gametes are called sperm and egg cells....

. There is considerable variation in this pattern, however.

Eukaryotes have a smaller surface area to volume ratio than prokaryotes, and thus have lower metabolic rates and longer generation times. In some multicellular organisms, cells specialized for metabolism will have enlarged surface areas, such as intestinal vili.

Origin and evolution


The origin of the eukaryotic cell was a milestone in the evolution of life, since they include all complex cells and almost all multi-cellular organisms. The timing of this series of events is hard to determine; Knoll
Andrew H. Knoll
Andrew H. Knoll is the Fisher Professor of Natural History and a Professor of Earth and Planetary Sciences at Harvard University. He is best known for his work on Precambrian microfossils and using stable isotopes for stratigraphic correlation, but has longstanding interests in geobiology,...

 (2006) suggests they developed approximately 1.6–2.1 billion years ago. Some acritarch
Acritarch
Acritarchs are small organic fossils, present from approximately to the present. Their diversity reflects major ecological events such as the appearance of predation and the Cambrian explosion.-Definition:In general, any small, non-acid soluble Acritarchs are small organic fossils, present from...

s are known from at least 1650 million years ago, and the possible alga Grypania
Grypania
Grypania is an early, tube-shaped fossil from the Proterozoic Eon. The organism could have been a giant bacterium or bacterial colony, but because of its size and consistent form, is more likely to have been a eukaryotic alga. The oldest probable Grypania fossils date to about 2.1 billion years...

has been found as far back as 2100 million years ago.

Organised living structures have been found in 2.1 billion year old black shales of the Palaeoproterozoic Francevillian B Formation in Gabon. They suggest eukaryotic life could have evolved at that time. Fossils that are clearly related to modern groups start appearing around 1.2 billion years ago, in the form of a red alga, though recent work suggests the existence of fossilized filamentous algae in the Vindhya basin dating back to 1.6 to 1.7 billion years ago.

Biomarkers suggest that at least stem eukaryotes arose even earlier. The presence of sterane
Sterane
Steranes are a class of 4-cyclic compounds derived from steroids or sterols via diagenetic and catagenetic degradation and saturation. Steranes have an androstane skeleton with a side chain at carbon C-17. The sterane structure constitutes the core of all sterols. Steranes are sometimes used as...

s in Australia
Australia
Australia , officially the Commonwealth of Australia, is a country in the Southern Hemisphere comprising the mainland of the Australian continent, the island of Tasmania, and numerous smaller islands in the Indian and Pacific Oceans. It is the world's sixth-largest country by total area...

n shale
Shale
Shale is a fine-grained, clastic sedimentary rock composed of mud that is a mix of flakes of clay minerals and tiny fragments of other minerals, especially quartz and calcite. The ratio of clay to other minerals is variable. Shale is characterized by breaks along thin laminae or parallel layering...

s indicates that eukaryotes were present 2.7 billion years ago.

Classification


Even back to Antiquity
Ancient history
Ancient history is the study of the written past from the beginning of recorded human history to the Early Middle Ages. The span of recorded history is roughly 5,000 years, with Cuneiform script, the oldest discovered form of coherent writing, from the protoliterate period around the 30th century BC...

 the two clade
Clade
A clade is a group consisting of a species and all its descendants. In the terms of biological systematics, a clade is a single "branch" on the "tree of life". The idea that such a "natural group" of organisms should be grouped together and given a taxonomic name is central to biological...

s of animal
Animal
Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and...

s and plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...

s were recognized. They were given the taxonomic rank
Taxonomic rank
In biological classification, rank is the level in a taxonomic hierarchy. Examples of taxonomic ranks are species, genus, family, and class. Each rank subsumes under it a number of less general categories...

 of Kingdom (biology)
Kingdom (biology)
In biology, kingdom is a taxonomic rank, which is either the highest rank or in the more recent three-domain system, the rank below domain. Kingdoms are divided into smaller groups called phyla or divisions in botany...

 by Linnaeus. Though he included the fungi with plants with some reservations, it was later realized that they are quite distinct and warrant a separate kingdom, the composition of which was not entirely clear until the 1980s. The various single cell eukaryotes were originally placed with plants or animals when they became known. The German biologist Georg A. Goldfuss coined the word protozoa
Protozoa
Protozoa are a diverse group of single-cells eukaryotic organisms, many of which are motile. Throughout history, protozoa have been defined as single-cell protists with animal-like behavior, e.g., movement...

in 1830 to refer to organisms such as ciliate
Ciliate
The ciliates are a group of protozoans characterized by the presence of hair-like organelles called cilia, which are identical in structure to flagella but typically shorter and present in much larger numbers with a different undulating pattern than flagella...

s and coral
Coral
Corals are marine animals in class Anthozoa of phylum Cnidaria typically living in compact colonies of many identical individual "polyps". The group includes the important reef builders that inhabit tropical oceans and secrete calcium carbonate to form a hard skeleton.A coral "head" is a colony of...

s, and this group was expanded until it encompassed all single cell eukaryotes, and given their own kingdom, the Protista by Ernst Haeckel
Ernst Haeckel
The "European War" became known as "The Great War", and it was not until 1920, in the book "The First World War 1914-1918" by Charles à Court Repington, that the term "First World War" was used as the official name for the conflict.-Research:...

 in 1866. The eukaryotes thus came to be composed of four kingdoms:
  • Kingdom Protista
  • Kingdom Plantae
  • Kingdom Fungi
  • Kingdom Animalia


The protists were understood to be "primitive forms", and thus an evolutionary grade
Evolutionary grade
In alpha taxonomy, a grade refers to a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.-Definition:...

, united by their primitive unicellular nature. The disentanglement of the deep splits in the tree of life only really got going with DNA sequencing, leading to a system of domain
Domain (biology)
In biological taxonomy, a domain is the highest taxonomic rank of organisms, higher than a kingdom. According to the three-domain system of Carl Woese, introduced in 1990, the Tree of Life consists of three domains: Archaea, Bacteria and Eukarya...

s rather than kingdoms as top level rank being put forward by Carl Woese
Carl Woese
Carl Richard Woese is an American microbiologist and physicist. Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese and which is now standard practice. He was also the originator of the RNA world hypothesis in 1977,...

, uniting all the eukaryote kingdoms under the eukaryote domain. At the same time, work on the protist tree intensified, and is still actively going on today. Several alternative classifications have been forwarded, though there is no consensus in the field.

A classification produced in 2005 for the International Society of Protistologists, which reflected the consensus of the time, divided the eukaryotes into six supposedly monophyletic 'supergroups'. Although the published classification deliberately did not use formal taxonomic ranks, other sources have treated each of the six as a separate Kingdom.
Excavata
Excavate
The excavates are a major kingdom of unicellular eukaryotes, often known as Excavata. The phylogenetic category Excavata, proposed by Cavalier-Smith in 2002, contains a variety of free-living and symbiotic forms, and also includes some important parasites of humans.-Characteristics:Many excavates...

 
Various flagellate
Flagellate
Flagellates are organisms with one or more whip-like organelles called flagella. Some cells in animals may be flagellate, for instance the spermatozoa of most phyla. Flowering plants do not produce flagellate cells, but ferns, mosses, green algae, some gymnosperms and other closely related plants...

 protozoa
Amoebozoa
Amoebozoa
The Amoebozoa are a major group of amoeboid protozoa, including the majority that move by means ofinternal cytoplasmic flow. Their pseudopodia are characteristically blunt and finger-like,...

 
Most lobose amoeboid
Amoeboid
Amoeboids are single-celled life-forms characterized by an irregular shape."Amoeboid" and "amœba" are often used interchangeably even by biologists, and especially refer to a creature moving by using pseudopodia. Most references to "amoebas" or "amoebae" are to amoeboids in general rather than to...

s and slime mould
Slime mould
Slime mold or mould is a broad term describing protists that use spores to reproduce. Slime molds were formerly classified as fungi, but are no longer considered part of this kingdom....

s
Opisthokonta  Animal
Animal
Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and...

s, fungi
Fungus
A fungus is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds , as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from plants, animals, and bacteria...

, choanoflagellate
Choanoflagellate
The choanoflagellates are a group of free-living unicellular and colonial flagellate eukaryotes considered to be the closest living relatives of the animals...

s, etc.
Rhizaria
Rhizaria
The Rhizaria are a species-rich supergroup of unicellular eukaryotes. This supergroup was proposed by Cavalier-Smith in 2002. They vary considerably in form, but for the most part they are amoeboids with filose, reticulose, or microtubule-supported pseudopods...

 
Foraminifera
Foraminifera
The Foraminifera , or forams for short, are a large group of amoeboid protists which are among the commonest plankton species. They have reticulating pseudopods, fine strands of cytoplasm that branch and merge to form a dynamic net...

, Radiolaria, and various other amoeboid
Amoeboid
Amoeboids are single-celled life-forms characterized by an irregular shape."Amoeboid" and "amœba" are often used interchangeably even by biologists, and especially refer to a creature moving by using pseudopodia. Most references to "amoebas" or "amoebae" are to amoeboids in general rather than to...

 protozoa
Chromalveolata
Chromalveolate
Chromalveolata is a eukaryote supergroup first proposed by Thomas Cavalier-Smith as a refinement of his kingdom Chromista, which was first put forward in 1981. Chromalveolata was proposed to represent the result of a single secondary endosymbiosis between a line descending from a bikont and a red...

 
Stramenopiles
Heterokont
The heterokonts or stramenopiles are a major line of eukaryotes currently containing more than 100,000 known species. Most are algae, ranging from the giant multicellular kelp to the unicellular diatoms, which are a primary component of plankton...

 (or Heterokonta), Haptophyta
Haptophyte
The haptophytes, classified either as the Prymnesiophyta or Haptophyta, are a division of algae.The term "Haptophyceae" is sometimes used. This ending implies classification at a lower level...

, Cryptophyta
Cryptomonad
The cryptomonads are a group of algae, most of which have plastids. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10-50 μm in size and flattened in shape, with an anterior groove or pocket...

 (or cryptomonads), and Alveolata
Alveolate
The alveolates are a major line of protists.-Phyla:There are four phyla, which are very divergent in form, but are now known to be close relatives based on various ultrastructural and genetic similarities:...

Archaeplastida
Archaeplastida
The Archaeplastida are a major group of eukaryotes, comprising the red and green algae and the land plants, together with a small group called the glaucophytes. The plastids of all of these organisms are surrounded by two membranes, suggesting they developed directly from endosymbiotic...

 (or Primoplantae)
Land plants
Embryophyte
The land plants or embryophytes, more formally Embryophyta or Metaphyta, are the most familiar group of plants. They are called 'land plants' because they live primarily in terrestrial habitats, in contrast with the related green algae that are primarily aquatic. The embryophytes include trees,...

, green algae, red algae, and glaucophyte
Glaucophyte
The glaucophytes, also known as glaucocystophytes or glaucocystids, are a small group of freshwater microscopic algae. Together with the red algae and green algae plus land plants , they form the Archaeplastida...

s


However, in the same year (2005), doubts were expressed as to whether some of these supergroups were monophyletic, particularly the Chromalveolata, and a review in 2006 noted the lack of evidence for several of the supposed six supergroups.

Phylogeny


rRNA trees constructed during the 1980s and 1990s left most eukaryotes in an unresolved "crown" group (not technically a true crown
Crown group
A crown group is a group consisting of living representatives, their ancestors back to the most recent common ancestor of that group, and all of that ancestor's descendants. The name was given by Willi Hennig, the formulator of phylogenetic systematics, as a way of classifying living organisms...

), which was usually divided by the form of the mitochondrial cristae; see crown eukaryotes
Crown eukaryotes
Crown eukaryotes are an artificial group of eukaryotic organisms found at the top of molecular phylogenetic trees including both eukaryotes and prokaryotes...

. The few groups that lack mitochondria branched separately, and so the absence was believed to be primitive; but this is now considered an artifact of long-branch attraction, and they are known to have lost them secondarily.

, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup
SAR supergroup
The SAR supergroup is a clade that includes Stramenopiles , Alveolates, and Rhizaria.The first letter of each group provides the "SAR" in the name.It includes most of the organisms in the Chromalveolata grouping, but not Hacrobia....

, so that Rhizara is not one of the main eukaryote groups; also that the Amoeboza and Opisthokonta are each monophyletic and form a clade, often called the unikont
Unikont
Unikonts are members of the Unikonta, a taxonomic group proposed by Thomas Cavalier-Smith.It includes amoebozoa, opisthokonts, and Apusozoa.-Clade:...

s. Beyond this, there does not appear to be a consensus.

Chromalveolata+Rhizaria


Some analyses disassemble the Chromalveolata+Rhizaria, showing close relationships with the Archaeplastida. For example, in 2007, Burki et al. produced a tree of the form shown below.

Bikonts and unikonts


In another analysis, the Hacrobia are shown nested inside the Archaeplastida, which together form a clade with most of the Excavata, before joining the SAR clade of Stramenopiles, Alveolata and Rhizaria. Together all of these groups make up the bikonts, the Amoebozoa and Opisthokonta forming the unikonts.
The division of the eukaryotes into two primary clades, unikonts and bikonts, derived from an ancestral uniflagellar organism and an ancestral biflagellar organism, respectively, had been suggested earlier.

Expanded Chromalveolata


Other analyses place the SAR supergroup within an expanded Chromalveolata, although they differ on the placement of the resulting five groups. Rogozin et al. in 2009 produced the tree shown below, where the primary division is between the Archaeplastida and all other eukaryotes.
More commonly the expanded Chromalveolata is shown as more closely related to the Archaeplastida, producing a tree of the form shown below.

Alternative views


A paper published in 2009 which re-examined the data used in some of the analyses presented above as well as performing new ones, strongly suggested that the Archaeplastida are polyphyletic. The phylogeny finally proposed in the paper is shown below.
Overall it seems that although progress has been made, there are still very significant uncertainties in the evolutionary history and classification of eukaryotes. As Roger & Simpson say "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution."

Relationship to Archaea


Eukaryotes are more closely related to Archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...

 than Bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

, at least in terms of nuclear DNA and genetic machinery, and one controversial idea is to place them with Archaea in the clade Neomura
Neomura
Neomura is a clade composed of the two domains of life of Archaea and Eukaryota. The group was first proposed by Thomas Cavalier-Smith and its name means "new walls"; so called because it is thought to have evolved from Bacteria, and one of the major changes was the replacement of peptidoglycan...

. However, in other respects, such as membrane composition, eukaryotes are similar to Bacteria. Three main explanations for this have been proposed:
  • Eukaryotes resulted from the complete fusion of two or more cells, wherein the cytoplasm formed from a eubacterium, and the nucleus from an archaeon, from a virus
    Viral eukaryogenesis
    Viral eukaryogenesis is the hypothesis that the cell nucleus of eukaryotic life forms evolved from a large DNA virus in a form of endosymbiosis within an archaea cell, being a form of symbiogenesis...

    , or from a pre-cell.
  • Eukaryotes developed from Archaea, and acquired their eubacterial characteristics from the proto-mitochondrion.
  • Eukaryotes and Archaea developed separately from a modified eubacterium.


There is also the Kronocyte theory for the origin of the Eukaryotic cell. This postulates that a primitive Eukaryotic cell emerged from the pre-DNA world but retained the earlier RNA based chemistry from which all modern life emerged. This primitive cell is called the Kronocyte. According to this hypothesis an RNA based Kronocyte coexisted with the DNA based Archaea (and probably eubacteria) and became the modern eukaryotic cell after a number of major endosymbioses—the first was the incorporation of an Archaea that introduced DNA metabolism and the nucleus, then the incorporation of an alphaproteobacter that became the mitochondria (and photosynthetic bacteria found in today's plants as chloroplasts). The Kronocyte hypothesis explains the large number of genes that are today only found in Eukaryotes but not in Archaea or Bacteria.

Endomembrane system and mitochondria


The origins of the endomembrane system and mitochondria are also unclear. The phagotrophic hypothesis proposes that eukaryotic-type membranes lacking a cell wall originated first, with the development of endocytosis, whereas mitochondria were acquired by ingestion as endosymbionts. The syntrophic hypothesis proposes that the proto-eukaryote relied on the proto-mitochondrion for food, and so ultimately grew to surround it. Here the membranes originated after the engulfment of the mitochondrion, in part thanks to mitochondrial genes (the hydrogen hypothesis
Hydrogen hypothesis
The hydrogen hypothesis is a model proposed by William F. Martin and Miklós Müller in 1998 that describes a possible way in which the mitochondrion arose as an endosymbiont within a prokaryote , giving rise to a symbiotic association of two cells from which the first eukaryotic cell could have...

 is one particular version).

In a study using genomes to construct supertree
Supertree
A supertree is a single phylogenetic tree assembled from a combination of smaller phylogenetic trees, which may have been assembled using different datasets or a different selection of taxa. Supertree algorithms can highlight areas where additional data would most usefully resolve any ambiguities...

s, Pisani et al. (2007) suggest that, along with evidence that there was never a mitochondrion-less eukaryote, eukaryotes evolved from a syntrophy
Syntrophy
Syntrophy, Cross-feeding, or Cross feeding is the phenomenon that one species lives off the products of another species.For example house dust mites live off human skin flakes, of which a healthy human being produces about 1 gram per day...

 between an archaea closely related to Thermoplasmatales
Thermoplasmatales
In taxonomy, the Thermoplasmatales are an order of the Thermoplasmata. All are acidophiles, growing optimally at pH below 2. Picrophilus is currently the most acidophilic of all known organisms growing at a minimum pH of 0.06. Many of these organisms do not contain a cell wall, although this is...

 and an α-proteobacterium
Proteobacteria
The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....

, likely a symbiosis
Symbiosis
Symbiosis is close and often long-term interaction between different biological species. In 1877 Bennett used the word symbiosis to describe the mutualistic relationship in lichens...

driven by sulfur or hydrogen. The mitochondrion and its genome is a remnant of the α-proteobacterial endosymbiont.

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