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.[1]

The submicroscopic ground cell substance, or cytoplasmatic matrix which remains after exclusion the cell organelles and particles is groundplasm. It is the hyaloplasm of light microscopy, and high complex, polyphasic system in which all of resolvable cytoplasmic elements of are suspended, including the larger organelles such as the ribosomes, mitochondria, the plant plastids, lipid droplets, and vacuoles.

Most cellular activities take place within the cytoplasm, such as many metabolic pathways including glycolysis, and processes such as cell division. The concentrated inner area is called the endoplasm and the outer layer is called the cell cortex or the ectoplasm.

Movement of calcium ions in and out of the cytoplasm is a signaling activity for metabolic processes.[2]

In plants, movement of the cytoplasm around vacuoles is known as cytoplasmic streaming.

Cell biology
The animal cell
Animal Cell
Components of a typical animal cell:
  1. Nucleolus
  2. Nucleus
  3. Ribosome (little dots)
  4. Vesicle
  5. Rough endoplasmic reticulum
  6. Golgi apparatus (or "Golgi body")
  7. Cytoskeleton
  8. Smooth endoplasmic reticulum
  9. Mitochondrion
  10. Vacuole
  11. Cytosol (fluid that contains organelles, comprising the cytoplasm)
  12. Lysosome
  13. Centrosome
  14. Cell membrane

History

The term was introduced by Rudolf von Kölliker in 1863, originally as a synonym for protoplasm, but later it has come to mean the cell substance and organelles outside the nucleus.[3][4]

There has been certain disagreement on the definition of cytoplasm, as some authors prefer to exclude from it some organelles, especially the vacuoles[5] and sometimes the plastids.[6]

Physical nature

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.[7] 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.[8] 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.[9] The irregular dynamics of such particles have given rise to various theories on the nature of the cytoplasm.

As a sol-gel

There has long been evidence that the cytoplasm behaves like a sol-gel.[10] It is thought that the component molecules and structures of the cytoplasm behave at times like a disordered colloidal solution (sol) and at other times like an integrated network, forming a solid mass (gel). This theory thus proposes that the cytoplasm exists in distinct fluid and solid phases depending on the level of interaction between cytoplasmic components, which may explain the differential dynamics of different particles observed moving through the cytoplasm.

As a glass

Recently it has been proposed that the cytoplasm behaves like a glass-forming liquid approaching the glass transition.[9] In this theory, the greater the concentration of cytoplasmic components, the less the cytoplasm behaves like a liquid and the more it behaves as a solid glass, freezing larger cytoplasmic components in place (it is thought that the cell's metabolic activity is able to fluidize the cytoplasm to allow the movement of such larger cytoplasmic components).[9] A cell's ability to vitrify in the absence of metabolic activity, as in dormant periods, may be beneficial as a defence strategy. A solid glass cytoplasm would freeze subcellular structures in place, preventing damage, while allowing the transmission of very small proteins and metabolites, helping to kickstart growth upon the cell's revival from dormancy.[9]

Other perspectives

There has been research examining the motion of cytoplasmic particles independent of the nature of the cytoplasm. In such an alternative approach, the aggregate random forces within the cell caused by motor proteins explain the non-Brownian motion of cytoplasmic constituents.[11]

Constituents

The three major elements of the cytoplasm are the cytosol, organelles and inclusions.

Cytosol

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.[12] The inner, granular and more fluid portion of the cytoplasm is referred to as endoplasm.

Localisations02eng
Proteins in different cellular compartments and structures tagged with green fluorescent protein

Due to this network of fibres and high concentrations of dissolved macromolecules, such as proteins, an effect called macromolecular crowding occurs and the cytosol does not act as an ideal solution. This crowding effect alters how the components of the cytosol interact with each other.

Organelles

Organelles (literally "little organs"), are usually membrane-bound structures inside the cell that have specific functions. Some major organelles that are suspended in the cytosol are the mitochondria, the endoplasmic reticulum, the Golgi apparatus, vacuoles, lysosomes, and in plant cells, chloroplasts.

Cytoplasmic inclusions

The inclusions are small particles of insoluble substances suspended in the cytosol. A huge range of inclusions exist in different cell types, and range from crystals of calcium oxalate or silicon dioxide in plants,[13][14] to granules of energy-storage materials such as starch,[15] glycogen,[16] or polyhydroxybutyrate.[17] A particularly widespread example are lipid droplets, which are spherical droplets composed of lipids and proteins that are used in both prokaryotes and eukaryotes as a way of storing lipids such as fatty acids and sterols.[18] Lipid droplets make up much of the volume of adipocytes, which are specialized lipid-storage cells, but they are also found in a range of other cell types.

Controversy and research

The cytoplasm, mitochondria and most organelles are contributions to the cell from the maternal gamete. Contrary to the older information that disregards any notion of the cytoplasm being active, new research has shown it to be in control of movement and flow of nutrients in and out of the cell by viscoplastic behavior and a measure of the reciprocal rate of bond breakage within the cytoplasmic network.[19]

The material properties of the cytoplasm remain an ongoing investigation. Recent measurements using force spectrum microscopy reveal that the cytoplasm can be likened to an elastic solid, rather than a viscoelastic fluid.

See also

References

  1. ^ Shepherd, V. A. (2006). The cytomatrix as a cooperative system of macromolecular and water networks. Current Topics in Developmental Biology. 75. pp. 171–223. doi:10.1016/S0070-2153(06)75006-2. ISBN 9780121531751. PMID 16984813.
  2. ^ Hogan, C. Michael (2010). "Calcium" Archived 12 June 2012 at the Wayback Machine in Encyclopedia of Earth. A. Jorgensen, C. Cleveland (eds.). National Council for Science and the Environment.
  3. ^ Kölliker, R. A. v. (1863). Handbuch der Gewebelehre des Menschen. 4. Auflage. Leipzig: Wilhelm Engelmann.
  4. ^ Bynum, W. F., Browne, E. J. and Porter, Ray (1981). Dictionary of the history of science. Princeton University Press.
  5. ^ Parker, J. (1972). "Protoplasmic resistance to water deficits", pp. 125–176 in Kozlowski, T. T. (ed.), Water deficits and plant growth. Vol. III. Plant responses and control of water balance. Academic Press, New York, p. 144, [1].
  6. ^ Strasburger, E. (1882). "Ueber den Theilungsvorgang der Zellkerne und das Verhältnis der Kernteilung zur Zellteilung". Arch Mikr Anat. 21: 476–590. Archived from the original on 27 August 2017.
  7. ^ Cowan AE, Moraru II, Schaff JC, Slepchenko BM, Loew LM (2012). Spatial Modeling of Cell Signaling Networks. Methods in Cell Biology. 110. pp. 195–221. doi:10.1016/B978-0-12-388403-9.00008-4. ISBN 9780123884039. PMC 3519356. PMID 22482950.
  8. ^ Holcman, David; Korenbrot, Juan I. (2004). "Longitudinal Diffusion in Retinal Rod and Cone Outer Segment Cytoplasm: The Consequence of Cell Structure". Biophysical Journal. 86 (4): 2566–2582. Bibcode:2004BpJ....86.2566H. doi:10.1016/S0006-3495(04)74312-X. PMC 1304104. PMID 15041693.
  9. ^ a b c d Parry, Bradley R.; Surovtsev, Ivan V.; Cabeen, Matthew T.; o'Hern, Corey S.; Dufresne, Eric R.; Jacobs-Wagner, Christine (2014). "The Bacterial Cytoplasm Has Glass-like Properties and is Fluidized by Metabolic Activity". Cell. 156 (1–2): 183–94. doi:10.1016/j.cell.2013.11.028. PMC 3956598. PMID 24361104.
  10. ^ Taylor, C. V. (1923). "The contractile vacuole in Euplotes: An example of the sol-gel reversibility of cytoplasm". Journal of Experimental Zoology. 37 (3): 259–289. doi:10.1002/jez.1400370302.
  11. ^ Guo, Ming; Ehrlicher, Allen J.; Jensen, Mikkel H.; Renz, Malte; Moore, Jeffrey R.; Goldman, Robert D.; Lippincott-Schwartz, Jennifer; MacKintosh, Frederick C.; Weitz, David A. (2014). "Probing the Stochastic, Motor-Driven Properties of the Cytoplasm Using Force Spectrum Microscopy". Cell. 158 (4): 822–32. doi:10.1016/j.cell.2014.06.051. PMC 4183065. PMID 25126787.
  12. ^ van Zon A, Mossink MH, Scheper RJ, Sonneveld P, Wiemer EA (September 2003). "The vault complex". Cell. Mol. Life Sci. 60 (9): 1828–37. doi:10.1007/s00018-003-3030-y. PMID 14523546.
  13. ^ Prychid, Christina J.; Rudall, Paula J. (1999). "Calcium Oxalate Crystals in Monocotyledons: A Review of their Structure and Systematics" (PDF). Annals of Botany. 84 (6): 725–739. doi:10.1006/anbo.1999.0975.
  14. ^ Prychid, C. J.; Rudall, P. J.; Gregory, M. (2004). "Systematics and Biology of Silica Bodies in Monocotyledons". The Botanical Review. 69 (4): 377–440. doi:10.1663/0006-8101(2004)069[0377:SABOSB]2.0.CO;2. JSTOR 4354467.
  15. ^ Ball SG, Morell MK (2003). "From bacterial glycogen to starch: understanding the biogenesis of the plant starch granule". Annu Rev Plant Biol. 54: 207–33. doi:10.1146/annurev.arplant.54.031902.134927. PMID 14502990.
  16. ^ Shearer J, Graham TE (April 2002). "New perspectives on the storage and organization of muscle glycogen". Can J Appl Physiol. 27 (2): 179–203. doi:10.1139/h02-012. PMID 12179957.
  17. ^ Anderson AJ, Dawes EA (1 December 1990). "Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates". Microbiol. Rev. 54 (4): 450–72. PMC 372789. PMID 2087222.
  18. ^ Murphy DJ (September 2001). "The biogenesis and functions of lipid bodies in animals, growth and microorganisms". Prog. Lipid Res. 40 (5): 325–438. doi:10.1016/S0163-7827(01)00013-3. PMID 11470496.
  19. ^ Feneberg, Wolfgang; Sackmann, Erich; Westphal, Monika (2001). "Dictyostelium cells' cytoplasm as an active viscoplastic body". European Biophysics Journal. 30 (4): 284–94. doi:10.1007/s002490100135. PMID 11548131.

External links

Alphaflexiviridae

Alphaflexiviridae is a family of viruses in the order Tymovirales. Plants and fungi serve as natural hosts. There are currently 51 species in this family, divided among 6 genera. Diseases associated with this family include: mosaic and ringspot symptoms.

Betaflexiviridae

Betaflexiviridae is a family of viruses in the order Tymovirales. Plants and fungi serve as natural hosts. There are currently 87 species in this family, divided among 7 genera. Diseases associated with this family include: mosaic and ringspot symptoms.

Bromoviridae

Bromoviridae is a family of viruses. Plants serve as natural hosts. There are currently 33 species in this family, divided among 6 genera.

Cell (biology)

The cell (from Latin cella, meaning "small room") is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life. Cells are often called the "building blocks of life". The study of cells is called cell biology.

Cells consist of cytoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic acids. Organisms can be classified as unicellular (consisting of a single cell; including bacteria) or multicellular (including plants and animals). While the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion (1013) cells. Most plant and animal cells are visible only under a microscope, with dimensions between 1 and 100 micrometres.Cells were discovered by Robert Hooke in 1665, who named them for their resemblance to cells inhabited by Christian monks in a monastery. Cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that cells are the fundamental unit of structure and function in all living organisms, and that all cells come from pre-existing cells. Cells emerged on Earth at least 3.5 billion years ago.

Cell nucleus

In cell biology, the nucleus (pl. nuclei; from Latin nucleus or nuculeus, meaning kernel or seed) is a membrane-enclosed organelle found in eukaryotic cells. Eukaryotes usually have a single nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei, and a few others including osteoclasts have many.

Cell nuclei contain most of the cell's genetic material, organized as multiple long linear DNA molecules in a complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these chromosomes are the cell's nuclear genome and are structured in such a way to promote cell function. The nucleus maintains the integrity of genes and controls the activities of the cell by regulating gene expression—the nucleus is, therefore, the control center of the cell. The main structures making up the nucleus are the nuclear envelope, a double membrane that encloses the entire organelle and isolates its contents from the cellular cytoplasm, and the nuclear matrix (which includes the nuclear lamina), a network within the nucleus that adds mechanical support, much like the cytoskeleton, which supports the cell as a whole.

Because the nuclear envelope is impermeable to large molecules, nuclear pores are required to regulate nuclear transport of molecules across the envelope. The pores cross both nuclear membranes, providing a channel through which larger molecules must be actively transported by carrier proteins while allowing free movement of small molecules and ions. Movement of large molecules such as proteins and RNA through the pores is required for both gene expression and the maintenance of chromosomes. Although the interior of the nucleus does not contain any membrane-bound subcompartments, its contents are not uniform, and a number of sub-nuclear bodies exist, made up of unique proteins, RNA molecules, and particular parts of the chromosomes. The best-known of these is the nucleolus, which is mainly involved in the assembly of ribosomes. After being produced in the nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA.

Closteroviridae

Closteroviridae is a family of viruses. Plants serve as natural hosts. There are currently 39 species in this family, divided among 4 genera. Diseases associated with this family include: yellowing and necrosis, particularly affecting the phloem.

Cyst

A cyst is a closed sac, having a distinct membrane and division compared with the nearby tissue. Hence, it is a cluster of cells that has grouped together to form a sac (not unlike the manner in which water molecules group together, forming a bubble); however, the distinguishing aspect of a cyst is that the cells forming the "shell" of such a sac are distinctly abnormal (in both appearance and behaviour) when compared with all surrounding cells for that given location. It may contain air, fluids, or semi-solid material. A collection of pus is called an abscess, not a cyst. Once formed, sometimes a cyst may resolve on its own. When a cyst fails to resolve, it may need to be removed surgically, but that would depend upon its type and location.

Cancer-related cysts are formed as a defense mechanism for the body, following the development of mutations that lead to an uncontrolled cellular division. Once that mutation has occurred, the affected cells divide incessantly (and become known as cancerous), forming a tumour. The body encapsulates those cells to try to prevent them from continuing their division and to try to contain the tumour, which becomes known as a cyst. That said, the cancerous cells still may mutate further and gain the ability to form their own blood vessels, from which they receive nourishment before being contained. Once that happens, the capsule becomes useless and the tumour may advance from benign to a cancer.

Some cysts are neoplastic and thus, are called cystic tumors; many types are not neoplastic. Some are dysplastic or metaplastic. Pseudocysts are similar to cysts (having a sac filled with fluid), but lack an epithelial lining.

Myoviridae

The Myoviridae is a family of bacteriophages in the order Caudovirales. Bacteria and archaea serve as natural hosts. There are currently 93 species in this family, divided among four subfamilies and 30 genera.

Picornavirus

A picornavirus is a virus belonging to the family Picornaviridae, a family of viruses in the order Picornavirales. Vertebrates, including humans, serve as natural hosts. Picornaviruses are nonenveloped viruses that represent a large family of small, cytoplasmic, plus-strand RNA (~7.5kb) viruses with a 30-nm icosahedral capsid. Its genome does not have a lipid membrane. Picornaviruses are found in mammals and birds. There are currently 80 species in this family, divided among 35 genera. Notable example are Enterovirus (including Rhinovirus and Poliovirus), Aphthovirus, Cardiovirus, and Hepatovirus genera. The viruses in this family can cause a range of diseases including paralysis, meningitis, hepatitis and poliomyelitis. Picornaviruses are in Baltimore IV class. Their genome single-stranded (+) sense RNA is what functions as mRNA after entry into the cell and all viral mRNA synthesized is of genome polarity. The mRNA encodes RNA dependent RNA polymerase. This polymerase makes complementary minus strands of RNA, then uses them as templates to make more plus strands. So, an overview of the steps in picornavirus replication are in order: attachment, entry, translation, transcription/genome replication (one and the same process), assembly and exit.The name has a dual etymology. First, picorna- is an acronym for poliovirus, insensitivity to ether, coxsackievirus, orphan virus, rhinovirus, and ribonucleic acid. Secondly, pico-, meaning extremely small, combines with RNA to describe these very small RNA viruses.

Podoviridae

Podoviridae is a family of viruses in the order Caudovirales. Bacteria serve as natural hosts. There are currently 50 species in this family, divided among 20 genera. This family is characterized by having very short, noncontractile tails.

Potyviridae

The Potyviridae are a family of viruses that encompasses more than 30% of known plant viruses, many of which are of great agricultural significance. Currently, more than 190 species are placed in this family, divided among eight genera.

Poxviridae

Poxviridae is a family of viruses. Humans, vertebrates, and arthropods serve as natural hosts. There are currently 69 species in this family, divided among 28 genera, which are divided into two subfamilies. Diseases associated with this family include smallpox.Four genera of poxviruses may infect humans: orthopoxvirus, parapoxvirus, yatapoxvirus, molluscipoxvirus.

Orthopox: smallpox virus (variola), vaccinia virus, cowpox virus, monkeypox virus;

Parapox: orf virus, pseudocowpox, bovine papular stomatitis virus;

Yatapox: tanapox virus, yaba monkey tumor virus;

Molluscipox: molluscum contagiosum virus (MCV).

The most common are vaccinia (seen on Indian subcontinent) and molluscum contagiosum, but monkeypox infections are rising (seen in west and central African rainforest countries). The similarly named disease chickenpox is not a true poxvirus and is actually caused by the herpesvirus varicella zoster.

Reoviridae

Reoviridae is a family of viruses. They have a wide host range, including vertebrates, invertebrates, plants, protists and fungi. They are unique in that they lack lipid envelopes and package their genomes of discrete double-stranded segments of RNA within multi-layered capsids. Lack of a lipid envelope has allowed three-dimensional structures of these large complex viruses (diameter,∼60–100 nm) to be obtained. There are currently 87 species in this family, divided among 30 genera. Reoviruses can affect the gastrointestinal system (such as Rotavirus) and respiratory tract. The name "Reo-" is derived from respiratory enteric orphan viruses. The term "orphan virus" refers to the fact that some of these viruses have been observed not associated with any known disease. Even though viruses in the family Reoviridae have more recently been identified with various diseases, the original name is still used.

Reovirus infection occurs often in humans, but most cases are mild or subclinical. Rotavirus, however, can cause severe diarrhea and intestinal distress in children, and lab studies in mice have implicated Orthoreovirus in the expression of coeliac disease in pre-disposed individuals. The virus can be readily detected in feces, and may also be recovered from pharyngeal or nasal secretions, urine, cerebrospinal fluid, and blood. Despite the ease of finding Reovirus in clinical specimens, their role in human disease or treatment is still uncertain.

Some viruses of this family, such as Phytoreovirus and Oryzavirus, infect plants. Most of the plant-infecting reoviruses are transmitted between plants by insect vectors. The viruses replicate in both the plant and the insect, generally causing disease in the plant, but little or no harm to the infected insect.

Rhabdoviridae

The Rhabdoviridae are a family of viruses in the order Mononegavirales. Vertebrates (including mammals and humans), invertebrates, and plants serve as natural hosts. Currently, 18 genera are recognised. Diseases associated with viruses of this family include rabies fatal encephalitis caused by rabies virus, and vesicular diseases and encephalitis flu-like symptoms in humans caused by vesiculoviruses. The name is derived from the Greek rhabdos, meaning rod, referring to the shape of the viral particles.

Secoviridae

Secoviridae is a family of viruses in the order Picornavirales. Plants serve as natural hosts. There are currently 81 species in this family, divided among 8 genera or not assigned to a genus.

Siphoviridae

Siphoviridae is a family of double-stranded DNA viruses in the order Caudovirales. Bacteria and archaea serve as natural hosts. There are currently 313 species in this family, divided among 47 genera. The characteristic structural features of this family are a nonenveloped head and noncontractile tail.

Tombusviridae

Tombusviridae is a family of single-stranded positive sense RNA plant viruses. There are currently 71 species in this family, divided among 13 genera. The name is derived from the type species of the genus Tombusvirus, tomato bushy stunt virus (TBSV).

Totiviridae

Totiviridae is a family of viruses. Giardia lamblia, leishmania, trichomonas vaginalis, and fungi serve as natural hosts. There are currently 28 species in this family, divided among 5 genera.

Virgaviridae

Virgaviridae is a family of positive sense, single-stranded RNA viruses. Plants serve as natural hosts. There are currently 59 species in this family, divided among 7 genera. The name of the family is derived from the Latin word virga (rod), as all viruses in this family are rod-shaped.

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