Eukaryote

A eukaryote is a life form whose cells' DNA is contained in nuclei. Eukaryotes are that small proportion of life on Earth that aren't bacteria or archaea.

The most characteristic feature of a eukaryotic cell, the nucleus, consists of a nucleoplasm surrounded by a double nuclear membrane pierced by nuclear pores. The nucleoplasm contains the (linear) chromosomes of the cell, which are organised into heterochromatin, which stains only a little, and euchromatin, which stains more densely. The most important euchromatic area is the nucleolus, in which ribosomes are formed. The name derives from εύ-καρυον (eu-karyon)—true kernel, or the nucleus.

Eukaryotic characteristics

 * 1) Double-membrane bound nucleus containing linear chromosomes.
 * 2) Complex 9+2-type undulipodium, cytoskeleton, cytosis and mitosis.
 * 3) Many membrane-bound organelles and double membrane-bound endosymbionts.
 * 4) They can grow 'large' because cytoplasmic streaming allows rapid transport across the cell - 100 μm.



The nucleus
The role of the nucleus is three-fold:


 * 1) Storage and protection of the genome.
 * 2) Regulation of gene expression.
 * 3) Creation of ribosomes.

DNA storage takes up about 10% of the cell of both prokaryotes (nucleoid area) and eukaryotes (nucleus). However, don't forget that some of the genome lives elsewhere: plasmids, endosymbionts (mitochondria), etc. The nucleus of eukaryotes also protects the genome from the cytoskeleton. Condensation of genome during mitosis is required to withstand these stresses. This is not relevant in prokaryotes, as they lack a cytoskeleton. The existence of the nucleus permits processing of mRNA, and therefore defers translation. Alternative splicing can be performed to generate different proteins from the same RNA primary transcript. mRNA is capped and tailed to permit it to exit the nucleus. rRNA and tRNA are also heavily processed by RNA editing, i.e. base modification (this also occurs to some mRNA in trypanosomes). rRNA modification occurs in the nucleolus, where ribosomes are constructed.

The nucleus is bound by a double-membrane, which is contiguous through the nuclear pores, known as the nuclear envelope. The pores are required to allow RNA out and membrane lipids in (which is needed for growth during S phase).

The inner face of the inner nuclear envelope (INE) is coated by the nuclear lamina, which contains intermediate fibres called lamins A, B and C (at least in mammals). Phosphorylation of lamins by kinases cause nuclear envelope breakdown during prometaphase. Chromosomes occupy definite positions within the nucleus because of the interaction between lamins and telomeres, for example the Rabl conformation in yeast.

In the Rabl conformation, the centromeres are at the pole closest to MTOC; and the telomeres at other, bound to the nuclear lamina. This orientation probably reduces tangling, and is inherited from mitosis. Later in interphase, the chromosomes may lose the Rabl conformation, but chromosomes still occupy discrete territories in the nucleus.

The outer nuclear envelope (ONE) is surrounded by other intermediate fibres, and is essentially just the RER surrounding the nucleus, and continuous with it. The space between the INE and ONE is termed the perinuclear space, and is continuous with the RER cisternae.

Cell wall
The cell wall of eukaryotes (when present) is usually composed of a β-(1→4)-glucan of some sort. In fungi, it is mostly chitin (N-acetylaminoglucan), in plants cellulose, but more exotic ingredients are common. Animal cells lack a wall, but may have a glycocalyx, which is a layer of thickened glycoproteins surrounding them and connecting them to the extracellular matrix.

Mitochondria
Almost all eukaryotes have mitochondria, which are the remains of bacteria that became endosymbionts of the eukaryotic cell about a billion years ago. They perform oxidative phosphorylation and generate energy in the form of ATP for the cell. They have their own 70S ribosomes and some of their own DNA. Mitochondria have a double membrane surrounding them, the inner one is highly folded into cristae, surrounding a matrix space.

Chloroplasts
Photosynthetic eukaryotes also have chloroplasts, which are the remains of cyanobacteria that also became endosymbiotic. They have a triple membrane system. The outer membrane surrounds the inner membrane, which itself surrounds the stroma, in which are embedded a number of thylakoid membranes, some of which occur in stacks called grana. Those that are unstacked are termed intergrana. The thylakoids surround another compartment, termed the lumen. Chloroplasts are one of several different sorts of plastid. Others include proplasts (immature plastids), chromoplasts (full of pigments), etioplasts (formed in the dark) and amyloplasts (full of starch). Plastids carry out photosynthesis, converting light energy into ATP and NADH.



Cytoskeleton
Eukaryotes have a cytoskeleton, which is composed of a number of interacting fibre types. The first are the actin microfilaments, which, with the motor protein myosin, form the muscles of the cytoskeleton (and in sarcosomes, form actual muscles too). The actin cytoskeleton forms a cortex beneath the plasmalemma of most eukaryotic cells, which is involved in changes to the external shape of the cell (such as the formation of pseudopodia in amoebae).The second fibre type are intermediate filaments, composed of spectrin, keratin, vimentin, nuclear lamins and other proteins. The intermediate filaments help maintain the relative positions of organelles and give the cell mechanical strength. The third type of cytoskeletal filament are the microtubules, which form the spindle during cell divisions (meiosis and mitosis), and give structure to the cell membrane, forming microvilli. They also form undulipodia, which are waving structures with a typical 9+2 structure, found in cilia (short undulipodia) and flagella (longer ones). The microtubules are composed of tubulin, and are organised by a microtubule organising centre (the centrosome and centrioles in animals), in which the − ends of the microtubules (which grow more slowly than the + ends) are embedded. Vesicles traffic along the microtubules under the influence of motor proteins such as kinesin (which transports items from the −→+ ends, i.e. away from the MTOC) and dynein (which traffics items from +→−). Tubulin is homologous to the FtsZ protein that is involved in bacterial fission.

The body of the cell is composed of a heterogeneous mixture of proteins and solutes called the cytosol. The cytosol contains many 80S ribosomes, on which protein synthesis takes place.

Membranes
The endomembranes and plasmalemma form a continuous membrane system in the eukaryote cell. The cell contains a rich diversity of membranes, in addition to those found in the endosymbiotic organelles. The outer cell membrane or plasmalemma, controls what gets in and out of the cell by the use of pores, symports, antiports and pumps. It is composed of a fluid mosaic of proteins embedded in a phospholipid bilayer, as are all membranes. The plasmalemma also interacts with the extracellular space through receptors, gap junctions, plasmodesmata, and synapses.



Endoplasmic reticulum
The endomembranes include the nuclear membrane, already mentioned, and the rough and smooth endoplasmic reticula (RER and SER). The lamellae of the rough endoplasmic reticulum are continuous throughout the cell, and also contiguous with the nuclear membrane. They are the site of synthesis for proteins destined for the endomembrane system and the extracellular space, with which its lumen (the cisternal space) is topologically identical. The tubules of the SER are responsible for steroid and lipid synthesis. After translation on ribosomes attached to the RER, proteins are carried in small transport vesicles to the Golgi bodies (dictyosomes), where they go undergo modification to the glycosylation they received as they were imported into the RER. After modification, some proteins are exported from the trans-Golgi network in export vesicles to the extracellular space. The ER is continuous with the nuclear envelope, and probably evolved at the same time, possibly by invaginations of the sort seen in the mesosomes of bacteria.

The rough ER differs from the smooth ER morphologically. The RER's cytoplasmic surface is studded with ribosomes, and it has flattened cisternae (rather than tubular ones). The RER is denser than SER due to presence of ribosomes. Consequently, disrupted ER 'microsomes' can be separated using density gradient centrifugation.



Other structures
Other proteins are destined for the endolysosome system. Material engulfed from outside by phagocytosis (solids) and pinocytosis (liquids) are packaged into phagosomes, and internal organelles destined for destruction are packed into autophagosomes. Endolysosomes containing digestive enzymes fuse with the phagosomes and digest their contents. The fused organelles produced are the cells disposal system, and are called lysosomes. Very large lysosomes are found in plants where they help to bulk the cell with water. Here they are called vacuoles, and are surrounded by a membrane called to tonoplast. Other vacuoles are involved in osmoregulation: for example contractile vacuoles in Amoeba.

Finally, a number of smaller vesicles are found in the cytosol. They are called microsomes, and most seem to be peroxisomes, containing the enzyme catalase, which degrades hydrogen peroxide produced by respiration. In germinating plant seed, many glyoxysomes are present, which perform fat oxidation for growth. Some vesicles also contain food reserves, such as fat droplets.

Eukaryotic DNA is bound by histones, and requires some degree of unpacking for expression. Much of their genome is composed of parasitic DNA and introns. Three RNA polymerases exists, (approximately) one for each sort of major RNA product:

RNApol-I - rRNA. RNApol-II - mRNA and snRNA. RNApol-III - tRNA and 5S rRNA. RNA is heavily processed in the nucleus, which allows deferred translation. They possess large 80S ribosomes.