What is cytoplasm made off?
Cytoplasm
In cell biology, the cytoplasm is all of the material within a cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The main components of the cytoplasm are cytosol – a gel-like substance, the organelles – the cell's internal sub-structures, and various cytoplasmic inclusions. The cytoplasm is about 80% water and usually colorless.
Cytoplast
Cytoplast = Cytoplasm + Plasma membrane
Red blood cell
The cytoplasm of erythrocytes is rich in hemoglobin, an iron-containing biomolecule that can bind oxygen and is responsible for the red color of the cells and the blood. The cell membrane is composed of proteins and lipids, and this structure provides properties essential for physiological cell function such as deformability and stability while traversing the circulatory system and specifically the capillary network.
Cytoplasm
The physical properties of the cytoplasm have been contested in recent years. It remains uncertain how the varied components of the cytoplasm interact to allow movement of particles and organelles while maintaining the cell’s structure. The flow of cytoplasmic components plays an important role in many cellular functions which are dependent on the permeability of the cytoplasm. An example of such function is cell signalling, a process which is dependent on the manner in which signaling molecules are allowed to diffuse across the cell. While small signaling molecules like calcium ions are able to diffuse with ease, larger molecules and subcellular structures often require aid in moving through the cytoplasm. The irregular dynamics of such particles have given rise to various theories on the nature of the cytoplasm.
Cytopathology
Cytopathology (from Greek , "kytos", "a hollow"; , "pathos", "fate, harm"; and , "-logia") is a branch of pathology that studies and diagnoses diseases on the cellular level. The discipline was founded by  George Nicolas Papanicolaou in 1928. Cytopathology is generally used on samples of free cells or tissue fragments, in contrast to histopathology, which studies whole tissues.
Viroplasm
A viroplasm is a perinuclear or a cytoplasmic large compartment where viral replication and assembly occurs. The viroplasm formation is caused by the interactions between the virus and the infected cell, where viral products and cell elements are confined. Virosomes are also called 'virus factories', and 'virus inclusions'.
Calcium signaling
The resting concentration of Ca in the cytoplasm is normally maintained around 100 nM, variously reported as 20,000- to 100,000-fold lower than typical extracellular concentration. To maintain this low concentration, Ca is actively pumped from the cytosol to the extracellular space, the endoplasmic reticulum (ER), and sometimes into the mitochondria. Certain proteins of the cytoplasm and organelles act as buffers by binding Ca. Signaling occurs when the cell is stimulated to release Ca ions from intracellular stores, and/or when Ca enters the cell through plasma membrane ion channels.
List of types of proteins
The cytoskeleton is composed of protein filaments in the cytoplasm.
Cytoplast
A cytoplast is a medical term which is defined as cell membrane plus cytoplasm. It is occasionally used to describe a cell in which the nucleus has been removed.
Syncytin-1
Syncytin-1 mediated trophoblast fusion is essential for normal placental development. The placenta is composed on two cell layers: cytotrophoblast and syncytiotrophoblast layer. Cytotrophoblasts are continually dividing, non-differentiated cells and syncytiotrophoblasts are fully differentiated, non dividing, fused cells. Syncytin-1 expression on the surface of cytotrophoblasts and syncytiotrophoblasts mediate fusion. The syncytiotrophoblast layer is the necessary interface between the developing embryo and the maternal blood supply, allowing nutrient and waste exchange and blocking maternal immune cell invasion, preventing immune rejection of the foetus. Syncytiotrophoblasts are forced into senescence by fusion. Therefore, cytotrophoblast proliferation is necessary for growth and maintenance of the syncytiotrophoblast layer. Syncytin-1 expression in cytotrophoblasts promotes G1/S transition and proliferation thereby ensuring continual replenishment of the cytotrophoblast pool. The name syncytin derives from its involvement in the formation of syncytium, the multinucleated syncytiotrophoblast protoplasm. There is another endogenous retroviral envelope protein expressed in the placenta from a different ERV family: syncytin-2 (of HERV-FRD).
Etioplast
They are converted to chloroplasts via the stimulation of chlorophyll synthesis by the plant hormone cytokinin soon after exposure to light. Thylakoids and grana arise from the prolamellar bodies during this process.
Endoplasm
Endoplasm generally refers to the inner (often granulated), dense part of a cell's cytoplasm. This is opposed to the ectoplasm which is the outer (non-granulated) layer of the cytoplasm, which is typically watery and immediately adjacent to the plasma membrane. These two terms are mainly used to describe the cytoplasm of the amoeba, a protozoan, eukaryotic cell. The nucleus is separated from the endoplasm by the nuclear envelope. The different makeups/viscosities of the endoplasm and ectoplasm contribute to the amoeba's locomotion through the formation of a pseudopod. However, other types of cells have cytoplasm divided into endo- and ectoplasm. The endoplasm, along with its granules, contains water, nucleic acids amino acids, carbohydrates, inorganic ions, lipids, enzymes, and other molecular compounds. It is the site of most cellular processes as it houses the organelles that make up the endomembrane system, as well as those that stand alone. The endoplasm is necessary for most metabolic activities, including cell division.
Endoplasmic reticulum
The sarcoplasmic reticulum (SR), from the Greek σάρξ "sarx" ("flesh"), is smooth ER found in myocytes. The only structural difference between this organelle and the smooth endoplasmic reticulum is the medley of proteins they have, both bound to their membranes and drifting within the confines of their lumens. This fundamental difference is indicative of their functions: The endoplasmic reticulum synthesizes molecules, while the sarcoplasmic reticulum stores calcium ions and pumps them out into the sarcoplasm when the muscle fiber is stimulated. After their release from the sarcoplasmic reticulum, calcium ions interact with contractile proteins that utilize ATP to shorten the muscle fiber. The sarcoplasmic reticulum plays a major role in excitation-contraction coupling.
Protoplasm
In some definitions, it is a general term for the cytoplasm (e.g., Mohl, 1846), but for others, it also includes the nucleoplasm (e.g., Strasburger, 1882). For Sharp (1921), "According to the older usage the extra-nuclear portion of the protoplast ["the entire cell, excluding the cell wall"] was called "protoplasm," but the nucleus also is composed of protoplasm, or living substance in its broader sense. The current consensus is to avoid this ambiguity by employing Strasburger's ["(1882)"] terms cytoplasm ["coined by Kölliker (1863), originally as synonym for protoplasm"] and nucleoplasm (["term coined by van Beneden (1875), or"] karyoplasm, ["used by"] Flemming ["(1878)"])". The cytoplasm definition of Strasburger excluded the plastids ("Chromatoplasm").
Egg cell
Ooplasm (also: oöplasm) is the yolk of the ovum, a cell substance at its center, which contains its nucleus, named the germinal vesicle, and the nucleolus, called the germinal spot.
Amoeboid movement
The protoplasm of an amoeba is made up of an outer layer termed the ectoplasm which surrounds an inner portion called the endoplasm. The ectoplasm consists of a gelatinous semisolid called plasma gel whereas the endoplasm is made up of a less viscous fluid called plasma sol. The ectoplasm owes its highly viscous state, in part, to the cross-linking actomyosin complex it contains. Locomotion of an amoeba is thought to occur due to the sol-gel conversion of the protoplasm within its cell. 'Sol-gel conversion describes the contraction and relaxation events which are enforced by osmotic pressure and other ionic charges.'
Extranuclear inheritance
Mitochondria are organelles which function to transform energy as a result of cellular respiration. Chloroplasts are organelles which function to produce sugars via photosynthesis in plants and algae. The genes located in mitochondria and chloroplasts are very important for proper cellular function, yet the genomes replicate independently of the DNA located in the nucleus, which is typically arranged in chromosomes that only replicate one time preceding cellular division. The extranuclear genomes of mitochondria and chloroplasts however replicate independently of cell division. They replicate in response to a cell's increasing energy needs which adjust during that cell's lifespan. Since they replicate independently, genomic recombination of these genomes is rarely found in offspring, contrary to nuclear genomes in which recombination is common.
Mitochondrial diseases are inherited from the mother, not from the father: mitochondria with their mitochondrial DNA from the mother's egg cell are incorporated into the zygote and passed to daughter cells, whereas those from the sperm are not.
Oocyte
Oocytes are rich in cytoplasm, which contains yolk granules to nourish the cell early in development.
Chloroplast
Chloroplasts are organelles that conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in plant and algal cells. They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like "Arabidopsis" and wheat.
Expression vector
Most heterologous proteins are expressed in the cytoplasm of "E. coli". However, not all proteins formed may be soluble in the cytoplasm, and incorrectly folded proteins formed in cytoplasm can form insoluble aggregates called inclusion bodies. Such insoluble proteins will require refolding, which can be an involved process and may not necessarily produce high yield. Proteins which have disulphide bonds are often not able to fold correctly due to the reducing environment in the cytoplasm which prevents such bond formation, and a possible solution is to target the protein to the periplasmic space by the use of an N-terminal signal sequence. Another possibility is to manipulate the redox environment of the cytoplasm. Other more sophisticated systems are also being developed; such systems may allow for the expression of proteins previously thought impossible in "E. coli", such as glycosylated proteins.
Endoplasm
The cytosol makes up the semifluid portion of the endoplasm, in which materials are suspended. It is a concentrated aqueous gel with molecules so crowded and packed together within the water base that its behavior is more gel-like than liquid. It is water based but contains both small and large molecules, giving it density. It has several functions, including physical support of the cell, preventing collapse, as well as degrading nutrients, transport of small molecules, and containing the ribosomes responsible for protein synthesis.
Endoplasm
Cytosol contains predominantly water, but also has a complex mixture of large hydrophilic molecules, smaller molecules and proteins, and dissolved ions. The contents of the cytosol change based on the needs of the cell. Not to be confused with the cytoplasm, the cytosol is only the gel matrix of the cell which does not include many of the macromolecules essential to cellular function.
Sarcoplasm
It contains mostly myofibrils (which are composed of sarcomeres), but its contents are otherwise comparable to those of the cytoplasm of other cells. It has a Golgi apparatus near the nucleus, mitochondria just inside the cell membrane (sarcolemma), and a smooth endoplasmic reticulum (specialized for muscle function and called the sarcoplasmic reticulum).
Cytoplasmic streaming
Photosynthesis converts light energy into chemical energy in the form of adenosine triphosphate (ATP). This occurs in the chloroplasts of plants cells. Light photons interact with various intermebrane proteins of the cholorplast to accomplish this. However, these proteins can become saturated with photons, making them unable to function until the saturation is alleviated. This is known as the Kautsky effect and is a cause of inefficiency on the ATP production mechanism. Cytoplasmic streaming in "Chara corallina", however, enables chloroplasts to move around the stem of the plant. Thus, the chloroplasts move into lighted regions and shaded regions. This intermittent exposure to photons due to cytoplasmic streaming actually increases the photosynthetic efficiency of chloroplasts. Photosynthetic activity is generally assessed using chlorophyll fluorescence analysis.
Necroplasm
Necroplasm was originally indistinct/synonymous with psychoplasm, the substance of which Hell itself is composed. It is similar in properties, but special in that it can exist on Earth without needing to remain in one of Hell's spheres of influence as well as being allowed to traverse the mortal world without violating the non-aggression pact between Heaven and Hell. Necroplasm was a creation of the Grand-Mal Demon known as Leviathan and is exclusive to the 8th Sphere of Hell. He used it to create a demon in his own image, known as The Malebolgia (Mal), who turned on his master and usurped the 8th Sphere for his own. This gave Malebolgia full control over the necroplasmic reserves and thus the ability to create a unique army of warriors known as Hellspawn which he uses to tip the balance of power in Hell toward the 8th Sphere.
Dormancy
Recent research has characterized the bacterial cytoplasm as a glass forming fluid approaching the liquid-glass transition, such that large cytoplasmic components require the aid of metabolic activity to fluidize the surrounding cytoplasm, allowing them to move through a viscous, glass-like cytoplasm. During dormancy, when such metabolic activities are put on hold, the cytoplasm behaves like a solid glass, freezing subcellular structures in place and perhaps protecting them, while allowing small molecules like metabolites to move freely through the cell, which may be helpful in cells transitioning out of dormancy.
Cytoplasmic polyadenylation element
Cytoplasmic polyadenylation should be distinguished from nuclear polyadenlyation; cytoplasmic polyadenylation occurs in the cytoplasm in specific mRNAs as opposed to occurring in the nucleus and affecting almost all eukaryotic mRNAs. Among other functions, a prominent role for the CPE has been identified in oogenesis, spermatogenesis, mitosis, and the growth of new synapses The role of the CPE was first characterized in Xenopus oocytes and embryos but recent research has identified roles for the CPE in somatic cells. Some proto-oncogene mRNAs have been shown to contain CPEs. One such gene is "Myc". The level of production of the different CPEB proteins determines whether the expression of Myc leads to tumor formation. The tumor suppressor gene "TP53" has also been shown to be regulated by a CPE. Cell lines that do not produce CPEB show lower levels of the protein p53 and become immortal instead of showing senescence.
Periplasm
The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the "periplasmic space" in gram-negative bacteria. Using cryo-electron microscopy it has been found that a much smaller periplasmic space is also present in gram-positive bacteria.
Cytokinesis
Cytokinesis () is the part of the cell division process during which the cytoplasm of a single eukaryotic cell divides into two daughter cells. Cytoplasmic division begins during or after the late stages of nuclear division in mitosis and meiosis. During cytokinesis the spindle apparatus partitions and transports duplicated chromatids into the cytoplasm of the separating daughter cells. It thereby ensures that chromosome number and complement are maintained from one generation to the next and that, except in special cases, the daughter cells will be functional copies of the parent cell. After the completion of the telophase and cytokinesis, each daughter cell enters the interphase of the cell cycle.
Plasmodium (life cycle)
A plasmodium is an amoeboid, multinucleate and naked mass of cytoplasm that contains many diploid nuclei. The resulting structure, a coenocyte, is created by many nuclear divisions without the process of cytokinesis, which in other organisms pulls newlydivided cells apart. In some cases, the resulting structure is a syncytium, created by the fusion of cells after division.
Calcium release activated channel
A common mechanism by which such cytoplasmic calcium signals are generated involves receptors that are coupled to the activation of phospholipase C. Phospholipase C generates inositol 1,4,5-trisphosphate (IP3), which in turn mediates the discharge of Ca from intracellular stores (components of the endoplasmic reticulum), allowing calcium to be released into the cytosol. In most of the cell, the fall in Ca concentration within the lumen of the Ca-storing organelles subsequently activates plasma membrane Ca channels.
CoRR hypothesis
Both the genetic and energy-converting systems of chloroplasts and mitochondria are descended, with little modification, from those of the free-living bacteria that these organelles once were. The existence of these cytoplasmic genomes is consistent with, and counts as evidence for, the endosymbiont hypothesis. Most genes for proteins of chloroplasts and mitochondria are, however, now located on chromosomes in the nuclei of eukaryotic cells. There they code for protein precursors that are made in the cytosol for subsequent import into the organelles.
Gloeocapsa magma
Gloeocapsa magma is a species of bacteria in the gloeocapsa genus of cyanobacteria, an ancient line of photosynthesizing bacteria, which photolyze water generating oxygen gas. Ancient cyanobacteria were ancestral to the chloroplasts of all plants on earth. "Gloeocapsa magma" may resemble "algae" in that they are green, but in fact cyanobacteria are bacteria whereas algae are single-celled eukaryotes (cells with nuclei) that are closely related to plants.
Cytokinesis
Plant cytokinesis differs from animal cytokinesis, partly because of the rigidity of plant cell walls. Instead of plant cells forming a cleavage furrow such as develops between animal daughter cells, a dividing structure known as the cell plate forms in the cytoplasm and grows into a new, doubled cell wall between plant daughter cells. It divides the cell into two daughter cells.
Valonia ventricosa
The entire cell contains several cytoplasmic domains with each domain having a nucleus and a few chloroplasts. Cytoplasmic domains are interconnected by cytoplasmic "bridges" that are supported by microtubules. The peripheral cytoplasm (whose membrane is overlaid by the cell wall), is only about 40 nm thick.
Light-dependent reactions
PS II, PS I, and cytochrome" are found in chloroplasts. All plants and all photosynthetic algae contain chloroplasts, which produce NADPH and ATP by the mechanisms described above. In essence, the same transmembrane structures are also found in "cyanobacteria".
Chloroplast
Chloroplasts are a special type of a plant cell organelle called a plastid, though the two terms are sometimes used interchangeably. There are many other types of plastids, which carry out various functions. All chloroplasts in a plant are descended from undifferentiated proplastids found in the zygote, or fertilized egg. Proplastids are commonly found in an adult plant's apical meristems. Chloroplasts do not normally develop from proplastids in root tip meristems—instead, the formation of starch-storing amyloplasts is more common.
Ascidiacea
The dramatic rearrangement of egg cytoplasm following fertilization, called ooplasmic segregation, determines the dorsoventral and anteroposterior axes of the embryo. There are at least three types of sea squirt egg cytoplasm: ectoplasm containing vesicles and fine particles, endoderm containing yolk platelets, and myoplasm containing pigment granules, mitochondria, and endoplasmic reticulum. In the first phase of ooplasmic segregation, the myoplasmic actin-filament network contracts to rapidly move the peripheral cytoplasm (including the myoplasm) to the vegetal pole, which marks the dorsal side of the embryo. In the second phase, the myoplasm moves to the subequatorial zone and extends into a crescent, which marks the future posterior of the embryo. The ectoplasm with the zygote nucleus ends up at the animal hemisphere while the endoplasm ends up in the vegetal hemisphere.
Cytoplasmic streaming
Cytoplasmic streaming, also called protoplasmic streaming and cyclosis, is where there is flow inside the cytoplasm. It is typically observed in large plant and animal cells. Here flow means that the cytoplasm is moving inside the cell, it is not stationary. The flow is driven by forces from the cytoskeleton, and it is likely that the function of flow is at least partly to speed up transport of molecules and organelles around the cell. Cytoplasmic streaming is usually found in unusually large cells, greater than approximately 0.1 mm. In smaller cells, diffusion of molecules will be rapid but diffusion slows rapidly as the size increases, and so larger cells may need flow to move nutrients etc inside them rapidly enough for efficient function.
Cytosol
Prior to this, other terms, including "hyaloplasm", were used for the cell fluid, not always synonymously, as its nature was not very clear (see protoplasm).
Myeloblast
Myeloblasts are rather small cells with a diameter between 14 and 18μm. The major part is occupied by a large oval nucleus composed of very fine nonaggregated chromatin and possesses 3 or more nucleoli. The cytoplasm has basophilic character and is devoid of granules, which is a major difference with its successor, the promyelocyte. The nucleolus is the site of assembly of ribosomal proteins, which are located in various particles dispersed over the cytoplasm. Mitochondria are present but have a rather small size.
Proximal tubule
The cytoplasm of the cells is densely packed with mitochondria, which are largely found in the basal region within the infoldings of the basal plasma membrane. The high quantity of mitochondria gives the cells an acidophilic appearance. The mitochondria are needed in order to supply the energy for the active transport of sodium ions out of the cells to create a concentration gradient which allows more sodium ions to enter the cell from the luminal side. Water passively follows the sodium out of the cell along its concentration gradient.
Protoplasm
Protoplasm is composed of a mixture of small molecules such as ions, amino acids, monosaccharides and water, and macromolecules such as nucleic acids, proteins, lipids and polysaccharides. In eukaryotes the protoplasm surrounding the cell nucleus is known as the cytoplasm and that inside the nucleus as the nucleoplasm. In prokaryotes the material inside the plasma membrane is the bacterial cytoplasm, while in Gram-negative bacteria the region outside the plasma membrane but inside the outer membrane is the periplasm.
Protoplasm
The idea that protoplasm of eukaryotes is simply divisible into a ground substance called "cytoplasm" and a structural body called the cell nucleus reflects the more primitive knowledge of cell structure that preceded the development of electron microscopy, when it seemed that cytoplasm was a homogeneous fluid and the existence of most sub-cellular compartments, or how cells maintain their shape, was unknown. Today, it is known that the cell contents are structurally very complex and contain multiple organelles.
List of types of proteins
exact_synonym: "protoplasm"
"The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm."
See the of Wikipedia.
Cytosol
The term "cytosol" is now used to refer to the liquid phase of the cytoplasm in an intact cell. This excludes any part of the cytoplasm that is contained within organelles. Due to the possibility of confusion between the use of the word "cytosol" to refer to both extracts of cells and the soluble part of the cytoplasm in intact cells, the phrase "aqueous cytoplasm" has been used to describe the liquid contents of the cytoplasm of living cells.
Chloroplast
Glyceraldehyde-3-phosphate can double up to form larger sugar molecules like glucose and fructose. These molecules are processed, and from them, the still larger sucrose, a disaccharide commonly known as table sugar, is made, though this process takes place outside of the chloroplast, in the cytoplasm.
Cytoplasm
There has been certain disagreement on the definition of cytoplasm, as some authors prefer to exclude from it some organelles, especially the vacuoles and sometimes the plastids.
Tegument (helminth)
The fine structure of tegument is essentially the same in both the cestodes and trematodes. A typical tegument is 7-16 μm thick, with distinct layers. It is a syncytium consisting of multinucleated tissues with no distinct cell boundaries. The outer zone of the syncytium, called the "distal cytoplasm," is lined with a plasma membrane. This plasma membrane is in turn associated with a layer of carbohydrate-containing macromolecules known as the glycocalyx, that varies in thickness from one species to another. The distal cytoplasm is connected to the inner layer called the "proximal cytoplasm", which is the "cellular region or cyton or perikarya" through cytoplasmic tubes that are composed of microtubules. The proximal cytoplasm contains nuclei, endoplasmic reticulum, Golgi complex, mitochondria, ribosomes, glycogen deposits, and numerous vesicles. The internal most layer is bounded by a layer of connective tissue known as the "basal lamina". The basal lamina is followed by a thick layer of muscle.
Endoplasm
The term granule refers to a small particle within the endoplasm, typically the secretory vesicles. The granule is the defining characteristic of the endoplasm, as they are typically not present within the ectoplasm. These offshoots of the endomembrane system are enclosed by a phospholipid bilayer and can fuse with other organelles as well as the plasma membrane. Their membrane is only semipermeable and allows them to house substances that could be harmful to the cell if they were allowed to flow freely within the cytosol. These granules give the cell a large amount of regulation and control over the wide variety of metabolic activities that take place within the endoplasm. There are many different types, characterized by the substance that the vesicle contains. These granules/vesicles can contain enzymes, neurotransmitters, hormones, and waste. Typically the contents are destined for another cell/tissue. These vesicles act as a form of storage and release their contents when needed, often prompted by a signaling pathway. Once signaled to move, the vesicles can travel along aspects of the cytoskeleton via motor proteins to reach their final destination.
Syncytium
The fine structure of tegument is essentially the same in both the cestodes and trematodes. A typical tegument is 7-16 μm thick, with distinct layers. It is a syncytium consisting of multinucleated tissues with no distinct cell boundaries. The outer zone of the syncytium, called the "distal cytoplasm," is lined with a plasma membrane. This plasma membrane is in turn associated with a layer of carbohydrate-containing macromolecules known as the glycocalyx, that varies in thickness from one species to another. The distal cytoplasm is connected to the inner layer called the "proximal cytoplasm", which is the "cellular region or cyton or perikarya" through cytoplasmic tubes that are composed of microtubules. The proximal cytoplasm contains nuclei, endoplasmic reticulum, Golgi complex, mitochondria, ribosomes, glycogen deposits, and numerous vesicles. The internal most layer is bounded by a layer of connective tissue known as the "basal lamina". The basal lamina is followed by a thick layer of muscle.
Metabolism
In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across the thylakoid membrane in the chloroplast. These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then either be used to reduce the coenzyme NADP, for use in the Calvin cycle, which is discussed below, or recycled for further ATP generation.
Cytoplast
Protoplasm = Cytoplasm + Nucleoplasm
Light-dependent reactions
This is a "cyclic" process in which electrons are removed from an excited chlorophyll molecule ("bacteriochlorophyll"; P870), passed through an electron transport chain to a proton pump (cytochrome ' complex, similar but not identical to cytochrome ' in chloroplasts), and then returned to the chlorophyll molecule. The result is a proton gradient, which is used to make ATP via ATP synthase. As in cyanobacteria and chloroplasts, this is a solid-state process that depends on the precise orientation of various functional groups within a complex transmembrane macromolecular structure.
Cytoplast
Protoplast = Protoplasm + Plasma membrane
Onion epidermal cell
The epidermal cells of onions provide a protective layer against viruses and fungi that may harm the sensitive tissues. Because of their simple structure and transparency they are often used to introduce students to plant anatomy or to demonstrate plasmolysis.
The clear epidermal cells exist in a single layer and do not contain chloroplasts, because the onion fruiting body (bulb) is used for storing energy, not photosynthesis.
Each plant cell has a cell wall, cell membrane, cytoplasm, nucleus, and a large vacuole. The nucleus is present at the periphery of the cytoplasm. The vacuole is prominent and present at the center of the cell, surrounded by cytoplasm.
Cytoplasmic hybrid
A cytoplasmic hybrid (or cybrid, a portmanteau of the two words) is a eukaryotic cell line produced by the fusion of a whole cell with a cytoplast. Cytoplasts are enucleated cells. This enucleation can be effected by simultaneous application of centrifugal force and treatment of the cell with an agent that disrupts the cytoskeleton. A special case of cybrid formation involves the use of "rho-zero" cells as the whole cell partner in the fusion. Rho-zero cells are cells which have been depleted of their own mitochondrial DNA by prolonged incubation with ethidium bromide, a chemical which inhibits mitochondrial DNA replication. The rho-zero cells do retain mitochondria and can grow in rich culture medium with certain supplements. They do retain their own nuclear genome. A cybrid is then a hybrid cell which mixes the nuclear genes from one cell with the mitochondrial genes from another cell. Using this powerful tool, it makes it possible to dissociate contribution from the mitochondrial genes vs that of the nuclear genes.
ATG16L1
Autophagy is the major intracellular degradation system delivering cytoplasmic components to lysosomes, and it accounts for degradation of most long-lived proteins and some organelles. Cytoplasmic constituents, including organelles, are sequestered into double-membraned autophagosomes, which subsequently fuse with lysosomes. ATG16L1 is a component of a large protein complex essential for autophagy.
Thixotropy
Both cytoplasm and the ground substance in the human body are thixotropic, as is semen.
Peter Michaelis
Michaelis firmly believed in complex unity in the cytoplasm, but he rejected simplistic notions such as the plasma gene or that the cause of cytoplasmic inheritance was solely due to plastids and mitochondria.
Cytoplasmic determinant
Cytoplasmic determinants are special molecules which play a very important role during oocyte maturation, in the female's ovary. During this period of time, some regions of the cytoplasm accumulate some of these cytoplasmic determinants, whose distribution is thus very heterogenic. They play a major role in the development of the embryo's organs. Each type of cell is determined by a particular determinant or group of determinants. Thus, all the organs of the future embryo are distributed and operating well thanks to the right position of the cytoplasmic determinants. The action of the determinants on the blastomeres is one of the most important ones. During the segmentation, cytoplasmic determinants are distributed among the blastomeres, at different times depending on the species and on the type of determinant. Therefore, the daughter cells resulting from the first divisions are totipotent : they can, independently, lead to a complete individual. That is not possible after the cytoplasmic determinants have been distributed in the differentiated blastomeres.
Endoplasm
The endoplasm, like the cytoplasm, is far from static. It is in a constant state of flux through intracellular transport, as vesicles are shuttled between organelles and to/from the plasma membrane. Materials are regularly both degraded and synthesized within the endoplasm based on the needs of the cell and/or organism. Some components of the cytoskeleton run throughout the endoplasm though most are concentrated in the ectoplasm - towards the cells edges, closer to the plasma membrane. The endoplasm’s granules are suspended in cytosol.
Chloroplast
Because so many chloroplast genes have been moved to the nucleus, many proteins that would originally have been translated in the chloroplast are now synthesized in the cytoplasm of the plant cell. These proteins must be directed back to the chloroplast, and imported through at least two chloroplast membranes.
Immunoblast
The majority of lymphocytes are small and have a thin rim of cytoplasm, 6-9 µm in diameter, about the same size as erythrocytes (diameter 7.5 µm). Large lymphocytes (12-18 µm in diameter) are probably activated, i.e. immunoblasts, cells with a paler and wider rim of cytoplasm and are often mistaken for monocytes. They have moderate-to-abundant basophilic cytoplasm and a prominent, centrally located, trapezoid-shaped single nucleolus which often has fine strands of chromatin attached to the nuclear membrane (‘spider legs’). In some cases, immunoblasts show some morphologic features of plasma cells. Centroblasts are distinguished from immunoblasts by being large lymphoid cells containing a moderate amount of cytoplasm, round to oval vesicular (i.e. containing small fluid-filled sacs) nuclei, vesicular chromatin, and 2–3 small nucleoli often located adjacent to the nuclear membrane. Both immunoblasts and centroblasts are defived from B cells.
Cytosol
The term "cytosol" was first introduced in 1965 by H. A. Lardy, and initially referred to the liquid that was produced by breaking cells apart and pelleting all the insoluble components by ultracentrifugation. Such a soluble cell extract is not identical to the soluble part of the cell cytoplasm and is usually called a cytoplasmic fraction.
Extranuclear inheritance
Extranuclear inheritance or cytoplasmic inheritance is the transmission of genes that occur outside the nucleus. It is found in most eukaryotes and is commonly known to occur in cytoplasmic organelles such as mitochondria and chloroplasts or from cellular parasites like viruses or bacteria.
Tracy Sonneborn
Sonneborn also showed the cytoplasmic inheritance of mitochondria and chloroplasts along with other internal cellular organelles (Kappa particles) which had their own DNA were inherited but limited by their distribution in the cytoplasm at the time of cell division. Only progeny from the 'half' of the cell with the mutant organelles inherited those organelles and thus the associated trait. Obviously, most cells had a distribution such that the organelles were in both halves but in cases where the new mutant arose and thus is rare then only those cell with cytoplasm containing the rare form inherited the traits associated with it.
Cell membrane
The cytoskeleton is found underlying the cell membrane in the cytoplasm and provides a scaffolding for membrane proteins to anchor to, as well as forming organelles that extend from the cell. Indeed, cytoskeletal elements interact extensively and intimately with the cell membrane. Anchoring proteins restricts them to a particular cell surface — for example, the apical surface of epithelial cells that line the vertebrate gut — and limits how far they may diffuse within the bilayer. The cytoskeleton is able to form appendage-like organelles, such as cilia, which are microtubule-based extensions covered by the cell membrane, and filopodia, which are actin-based extensions. These extensions are ensheathed in membrane and project from the surface of the cell in order to sense the external environment and/or make contact with the substrate or other cells. The apical surfaces of epithelial cells are dense with actin-based finger-like projections known as microvilli, which increase cell surface area and thereby increase the absorption rate of nutrients. Localized decoupling of the cytoskeleton and cell membrane results in formation of a bleb.
Cytohet
Mutations in the cytoplasmic genome occur spontaneously and at a much higher rate than in the nucleus, since the mitochondria and chloroplasts are exposed to high concentrations of reactive oxygen species (ROS, by-products of respiration and photosynthesis). Mitochondria and chloroplasts with mutant genes have the ability to cause wildtype alleles in other mitochondria and chloroplasts to become mutant as well; the way in which this is done is still not clear. A certain cell in which a mutant gene exists only in some of the organelles, whereas the wildtype allele exists in the rest, is a cytohet (or heteroplasmon).
Cytoplasmic streaming
"Neurospora crassa" is a multicellular fungus with many off shooting hyphae. Cells can be up to 10 cm long, and are separated by a small septum. Small holes in the septum allow cytoplasm and cytoplasmic contents to flow from cell to cell. Osmotic pressure gradients occur through the length of the cell to drive this cytoplasmic flow. Flows contribute to growth and the formation of cellular subcompartments.
Post-transcriptional regulation
Furthermore, RNA found in the nucleus is more complex than that found in the cytoplasm: more than 95% (bases) of the RNA synthesized by RNA polymerase II never reaches the cytoplasm. The main reason for this is due to the removal of introns which account for 80% of the total bases. Some studies have shown that even after processing the levels of mRNA between the cytoplasm and the nucleus differ greatly.
Axon
The axoplasm is the equivalent of cytoplasm in the cell. Microtubules form in the axoplasm at the axon hillock. They are arranged along the length of the axon, in overlapping sections, and all point in the same direction – towards the axon terminals. This is noted by the positive endings of the microtubules. This overlapping arrangement provides the routes for the transport of different materials from the cell body. Studies on the axoplasm has shown the movement of numerous vesicles of all sizes to be seen along cytoskeletal filaments – the microtubules, and neurofilaments, in both directions between the axon and its terminals and the cell body.
Cytosolic ciliogenesis
Cytosolic ciliogenesis is divided into three types: Primary cytosolic cilia are formed by exposing the axoneme of compartmentalized cilium (formed initially by compartmentalized ciliogenesis) to the cytoplasm. This type of cilia is found in the sperm of human and other mammals. Secondary cytosolic cilia are formed in parallels to the formation of the typical compartmentalized cilium. One end of the axoneme is exposed to the cytoplasm as the other end of the axoneme is formed as compartmentalized cilia. This type of cilia is found in insects. Tertiary cytosolic cilia are axonemes that form directly in the cytoplasm. This type of cilia is found in Plasmodium (the malaria parasite).
FITM2
Cytosolic lipid droplets are organelles that are composed of a core that is hydrophobic in nature containing neutral lipids (like triglycerides) as well as cholesteryl esters that have a phospholipid monolayer in addition to a distinctive set of expressed proteins that surrounds them. The most generally accepted view on the creation of lipid droplets is that the neutral lipids build up between the ER leaflets due to "de novo" synthesizing enzymes for both triglyceride phospholipids and cholesteryl esters. This leads to the budding lipid droplets growing into the cytoplasm space. There are two different groups of lipid droplets that are known: the first is characterized by its phospholipid leaflet in continuity with the membrane of the ER and the second is classified as definitively cytosolic without a connection to the ER.
Plasma cell
Plasma cells are large lymphocytes with a considerable nucleus-to-cytoplasm ratio and a characteristic appearance on light microscopy. They have amphophilic cytoplasm and an eccentric nucleus with heterochromatin in a characteristic cartwheel or clock face arrangement. Their cytoplasm also contains a pale zone that on electron microscopy contains an extensive Golgi apparatus and centrioles (EM picture). Abundant rough endoplasmic reticulum combined with a well-developed Golgi apparatus makes plasma cells well-suited for secreting immunoglobulins. Other organelles in a plasma cell include ribosomes, lysosomes, mitochondria, and the plasma membrane.
Centroblasts
Morphologically, centroblasts are large lymphoid cells containing a moderate amount of cytoplasm, round to oval vesicular (i.e. containing small fluid-filled sacs) nuclei, vesicular chromatin, and 2–3 small nucleoli often located adjacent to the nuclear membrane. They are derived from B cells. Immunoblasts are distguished from centroblasts by being B cell-derived lymphoid cells that have moderate-to-abundant basophilic cytoplasm and a prominent, centrally located, trapezoid-shaped single nucleolus which often has fine strands of chromatin attached to the nuclear membrane (‘spider legs’). In some cases, immunoblasts can show some morphologic features of plasma cells.
Cytochrome c
The sustained elevation in calcium levels precedes cyt "c" release from the mitochondria. The release of small amounts of cyt "c" leads to an interaction with the IP3 receptor (IP3R) on the endoplasmic reticulum (ER), causing ER calcium release. The overall increase in calcium triggers a massive release of cyt "c", which then acts in the positive feedback loop to maintain ER calcium release through the IP3Rs. This explains how the ER calcium release can reach cytotoxic levels. This release of cytochrome c in turn activates caspase 9, a cysteine protease. Caspase 9 can then go on to activate caspase 3 and caspase 7, which are responsible for destroying the cell from within.
Apoptosome
In mammalian cells, once cytochrome c is released, it binds to the cytosolic protein Apaf-1 to facilitate the formation of an apoptosome. An early biochemical study suggests a two-to-one ratio of cytochrome c to apaf-1 for apoptosome formation. However, recent structural studies suggest the cytochrome c to apaf-1 ratio is one-to-one. It has also been shown that the nucleotide dATP as third component binds to apaf-1, however its exact role is still debated. The mammalian apoptosome had never been crystallized, but a human APAF-1/cytochrome-c apoptosome has been imaged at lower (2 nm) resolution by cryogenic transmission electron microscopy in 2002, revealing a wheel-like particle with 7-fold symmetry. Recently, a medium resolution (9.5 Ångström) structure of human apoptosome was also solved by cryo-electron microscopy, which allows unambiguous inference for positions of all the APAF-1 domains (CARD, NBARC and WD40) and cytochrome c. There is also now a crystal structure of the monomeric, inactive Apaf-1 subunit (PDB 3SFZ).
Cytoplasm
The three major elements of the cytoplasm are the cytosol, organelles and inclusions.
Clear cell
In histology, a clear cell is a cell that shows a clear cytoplasm when stained with hematoxylin and eosin (H&E). Normally, clear cells are secretory cells in the epithelium, and are one of the components of eccrine sweat glands. A clear cell's plasma membrane is highly folded, more so on the apical and lateral surfaces. The cytoplasm of clear cells contains large amounts of glycogen and many mitochondria. Melanocytes appear as clear cells when in the stratum basale of the skin, and Langerhans' cells appear as clear cells in the stratum spinosum.
Chaetosphaeridium globosum
Chloroplasts are known to be captured (symbiotic) cyanobacteria with their own genome. Part of this genome has been transferred to the nucleus and part has been retained in the chloroplast for the continuation of metabolic processes. This symbiosis, now proven by modern genomics, has shown us how "Chaetosphaeridium globosum" links ancient cyanobacteria with modern green plants.
Cytoplasm
In plants, movement of the cytoplasm around vacuoles is known as cytoplasmic streaming.
Phragmosome
Initially, cytoplasmic strands form that penetrate the central vacuole and provide pathways for nuclear migration. Actin filaments along these cytoplasmic strands pull the nucleus into the center of the cell. These cytoplasmic strands fuse into a transverse sheet of cytoplasm along the plane of future cell division, forming the phragmosome. Phragmosome formation is only clearly visible in dividing plant cells that are highly vacuolated.
Cytoplasmic streaming
What is clearly visible in plants cells which exhibit cytoplasmic streaming is the motion of the chloroplasts moving with the cytoplasmic flow. This motion results from fluid being entrained by moving motor molecules of the plant cell. Myosin filaments connect cell organelles to actin filaments. These actin filaments are generally attached to the chloroplasts and/or membranes of plant cells. As the myosin molecules "walk" along the actin filaments dragging the organelles with them, the cytoplasmic fluid becomes entrained and is pushed/pulled along. Cytoplasmic flow rates can range between 1 and 100 micron/sec.
Chloroplast
The protein-rich, alkaline, aqueous fluid within the inner chloroplast membrane and outside of the thylakoid space is called the stroma, which corresponds to the cytosol of the original cyanobacterium. Nucleoids of chloroplast DNA, chloroplast ribosomes, the thylakoid system with plastoglobuli, starch granules, and many proteins can be found floating around in it. The Calvin cycle, which fixes CO into sugar takes place in the stroma.
Cytosolic ciliogenesis
Cytosolic ciliogenesis, otherwise cytoplasmic ciliogenesis, is a type of ciliogenesis where the cilium axoneme is formed in the cytoplasm or becomes exposed to the cytoplasm.
Extrachromosomal DNA
Extrachromosomal DNA was found to be structurally different from nuclear DNA. Cytoplasmic DNA is less methylated than DNA found within the nucleus. It was also confirmed that the sequences of cytoplasmic DNA was different from nuclear DNA in the same organism, showing that cytoplasmic DNAs are not simply fragments of nuclear DNA.
Cytoskeleton
A cytoskeleton is present in the cytoplasm of all cells, including bacteria, and archaea. It is a complex, dynamic network of interlinking protein filaments that extend from the cell nucleus to the cell membrane. The cytoskeletal systems of different organisms are composed of similar proteins. In eukaryotes, the cytoskeletal matrix is a dynamic structure composed of three main proteins, which are capable of rapid growth or disassembly dependent on the cell's requirements at a certain period of time.
Cytosol
The cytosol, also known as intracellular fluid (ICF) or cytoplasmic matrix, is the liquid found inside cells. It is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondrion into many compartments.
Hexactinellid
Glass sponges are different from other sponges in a variety of other ways. For example, most of the cytoplasm is not divided into separate cells by walls but forms a syncytium or continuous mass of cytoplasm with many nuclei (e.g., Reiswig and Mackie, 1983).
Cytoplast
So, Cytoplasm = Protoplasm - Nucleoplasm and
Cytoplasm
The cytosol is the portion of the cytoplasm not contained within membrane-bound organelles. Cytosol makes up about 70% of the cell volume and is a complex mixture of cytoskeleton filaments, dissolved molecules, and water. The cytosol's filaments include the protein filaments such as actin filaments and microtubules that make up the cytoskeleton, as well as soluble proteins and small structures such as ribosomes, proteasomes, and the mysterious vault complexes. The inner, granular and more fluid portion of the cytoplasm is referred to as endoplasm.
Cytosol
In the eukaryotic cell, the cytosol is surrounded by the cell membrane and is part of the cytoplasm, which also comprises the mitochondria, plastids, and other organelles (but not their internal fluids and structures); the cell nucleus is separate. The cytosol is thus a liquid matrix around the organelles. In prokaryotes, most of the chemical reactions of metabolism take place in the cytosol, while a few take place in membranes or in the periplasmic space. In eukaryotes, while many metabolic pathways still occur in the cytosol, others take place within organelles.
Cytoplasmic incompatibility
Cytoplasmic incompatibility (CI) is a phenomenon that results in sperm and eggs being unable to form viable offspring. The effect arises from changes in the gamete cells caused by intracellular parasites like "Wolbachia", which infect a wide range of insect species. As the reproductive incompatibility is caused by bacteria that reside in the cytoplasm of the host cells, it is referred to as cytoplasmic incompatibility. In 1971, Janice Yen and A. Ralph Barr of UCLA demonstrated the etiologic relationship of "Wolbachia" infection and cytoplasmic incompatibility in "Culex" mosquitos when they found that eggs were killed when the sperm of "Wolbachia"-infected males fertilized infection-free eggs.
Hepatocyte
Hepatocytes display an eosinophilic cytoplasm, reflecting numerous mitochondria, and basophilic stippling due to large amounts of rough endoplasmic reticulum and free ribosomes. Brown lipofuscin granules are also observed (with increasing age) together with irregular unstained areas of cytoplasm; these correspond to cytoplasmic glycogen and lipid stores removed during histological preparation. The average life span of the hepatocyte is 5 months; they are able to regenerate.
Intragenomic conflict
Anisogamy generally produces zygotes that inherit cytoplasmic elements exclusively from the female gamete. Thus, males represent dead-ends to these genes. Because of this fact, cytoplasmic genes have evolved a number of mechanisms to increase the production of female descendants and eliminate offspring not containing them.
Glycosome
Glycosomes are unique to kinetoplastids.
The term glycosome is also used for glycogen-containing structures found in hepatocytes responsible for storing sugar, but these are not membrane bound organelles. 
Glycosomes are composed of glycogen and proteins. The proteins are the enzymes that are associated with the metabolism of glycogen. These proteins and glycogen form a complex to make a distinct and separate organelle. The proteins for glycosomes are imported from free cytosolic ribosomes. The proteins imported into the organelle have a specific sequence, a PTS1 ending sequence to make sure they go to the right place. They are similar to alpha-granules in the cytosol of a cell that are filled with glycogen. Glycosomes are typically round-to-oval shape with size varying in each cell. Although glycogen is found in the cytoplasm, that in the glycosome is separate, surrounded by membrane. The membrane is a lipid bilayer. The glycogen that is found within the glycosome is identical to glycogen found freely in the cytosol. Glycosomes can be associated or attached to many different types of organelles. They have been found to be attached to the sarcoplasmic reticulum and its intermediate filaments. Other glycosomes have been found to be attached to myofibrils and mitochondria, rough endoplasmic reticulum, sarcolemma, polyribosomes, or the Golgi apparatus. Glycosome attachment may bestow a functional distinction between them; the glycosomes attached to the myofibrils seem to serve the myosin by providing energy substrates for generation of ATP through glycolysis. The glycosomes in the rough and smooth endoplasmic reticulum make use of its glycogen synthase and phosphorylase phosphatases.
Cytoplasm
Movement of calcium ions in and out of the cytoplasm is a signaling activity for metabolic processes.
Neutrophil
With the eosinophil and the basophil, they form the class of "polymorphonuclear cells", named for the nucleus' multilobulated shape (as compared to lymphocytes and monocytes, the other types of white cells). The nucleus has a characteristic lobed appearance, the separate lobes connected by chromatin. The nucleolus disappears as the neutrophil matures, which is something that happens in only a few other types of nucleated cells. In the cytoplasm, the Golgi apparatus is small, mitochondria and ribosomes are sparse, and the rough endoplasmic reticulum is absent. The cytoplasm also contains about 200 granules, of which a third are azurophilic.
Plasmodium (life cycle)
A plasmodium is a living structure of cytoplasm that contains many nuclei, rather than being divided into individual cells each with a single nucleus.
Deutoplasm
Deutoplasm refers to the food particles stored in the cytoplasm of an ovum or a cell, as distinguished from protoplasm, the yolk substance. Generally, the deutoplasm accumulates about the nucleus and is heavier than the surrounding cytoplasm. In chicken eggs, the cytoplasm and deutoplasm are separate.