Instruct: Given a question, retrieve relevant passages that can help answer the question.
Query: What is cytoplasm made off?
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.
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.
Autophagy was first observed by Keith R. Porter and his student Thomas Ashford at the Rockefeller Institute. In January 1962 they reported an increased number of lysosomes in rat liver cells after the addition of glucagon, and that some displaced lysosomes towards the centre of the cell contained other cell organelles such as mitochondria. They called this autolysis after Christian de Duve and Alex B. Novikoff. However Porter and Ashford wrongly interpreted their data as lysosome formation (ignoring the pre-existing organelles). Lysosomes could not be cell organelles, but part of cytoplasm such as mitochondria, and that hydrolytic enzymes were produced by microbodies. In 1963 Hruban, Spargo and colleagues published a detailed ultrastructural description of "focal cytoplasmic degradation," which referenced a 1955 German study of injury-induced sequestration. Hruban, Spargo and colleagues recognized three continuous stages of maturation of the sequestered cytoplasm to lysosomes, and that the process was not limited to injury states that functioned under physiological conditions for "reutilization of cellular materials," and the "disposal of organelles" during differentiation. Inspired by this discovery, de Duve christened the phenomena "autophagy". Unlike Porter and Ashford, de Duve conceived the term as a part of lysosomal function while describing the role of glucagon as a major inducer of cell degradation in the liver. With his student Russell Deter, he established that lysosomes are responsible for glucagon-induced autophagy. This was the first time the fact that lysosomes are the sites of intracellular autophagy are established.
Cell theory led biologists to re-envision individual organisms as interdependent assemblages of individual cells. Scientists in the rising field of cytology, armed with increasingly powerful microscopes and new staining methods, soon found that even single cells were far more complex than the homogeneous fluid-filled chambers described by earlier microscopists. Robert Brown had described the nucleus in 1831, and by the end of the 19th century cytologists identified many of the key cell components: chromosomes, centrosomes mitochondria, chloroplasts, and other structures made visible through staining. Between 1874 and 1884 Walther Flemming described the discrete stages of mitosis, showing that they were not artifacts of staining but occurred in living cells, and moreover, that chromosomes doubled in number just before the cell divided and a daughter cell was produced. Much of the research on cell reproduction came together in August Weismann's theory of heredity: he identified the nucleus (in particular chromosomes) as the hereditary material, proposed the distinction between somatic cells and germ cells (arguing that chromosome number must be halved for germ cells, a precursor to the concept of meiosis), and adopted Hugo de Vries's theory of pangenes. Weismannism was extremely influential, especially in the new field of experimental embryology.
The cytosolic, intermembrane space, compartment has a water content of 3.8 μl/mg protein, while the mitochondrial matrix 0.8 μl/mg protein. It is not known how mitochondria maintain osmotic balance across the inner mitochondrial membrane, although the membrane contains aquaporins that are believed to be conduits for regulated water transport. Mitochondrial matrix has a pH of about 7.8. Mitochondrial DNA was discovered by Nash and Margit in 1963. One to many double stranded mainly circular DNA is present in mitochondrial matrix. Mitochondrial DNA is 1% of total DNA of a cell. It is rich in Guanine and Cytosine content. Mitochondria of mammals have 55s ribosomes.
Cells in the body function because of DNA. DNA sits within the nucleus of a cell. Here, parts of DNA are copied and sent to the body of the cell via RNA. The RNA is then used to create proteins which form the basis for cells, their activity, and their products. Proteins dictate cell function and gene expression, a cell is able to self-regulate by the amount of proteins produced. However, not all cells have DNA – some cells such as mature red blood cells lose their nucleus as they mature.
Malonyl-CoA is then involved in a repeating series of reactions that lengthens the growing fatty acid chain by two carbons at a time. Almost all natural fatty acids, therefore, have even numbers of carbon atoms. When synthesis is complete the free fatty acids are nearly always combined with glycerol (three fatty acids to one glycerol molecule) to form triglycerides, the main storage form of fatty acids, and thus of energy in animals. However, fatty acids are also important components of the phospholipids that form the phospholipid bilayers out of which all the membranes of the cell are constructed (the cell wall, and the membranes that enclose all the organelles within the cells, such as the nucleus, the mitochondria, endoplasmic reticulum, and the Golgi apparatus).
The ova, which are the female sex cells, are much larger than the sperm and are normally formed within the ovaries of the fetus before its birth. They are mostly fixed in location within the ovary until their transit to the uterus, and contain nutrients for the later zygote and embryo. Over a regular interval, in response to hormonal signals, a process of oogenesis matures one ovum which is released and sent down the Fallopian tube. If not fertilized, this egg is released through menstruation in humans and other great apes, and reabsorbed in other mammals in the estrus cycle.
In eukaryotes, the enzymes in this electron transport system use the energy released from the oxidation of NADH to pump protons across the inner membrane of the mitochondrion. This causes protons to build up in the intermembrane space, and generates an electrochemical gradient across the membrane. The energy stored in this potential is then used by ATP synthase to produce ATP. Oxidative phosphorylation in the eukaryotic mitochondrion is the best-understood example of this process. The mitochondrion is present in almost all eukaryotes, with the exception of anaerobic protozoa such as "Trichomonas vaginalis" that instead reduce protons to hydrogen in a remnant mitochondrion called a hydrogenosome.
The first model known as the "syntrophic model" proposes that a symbiotic relationship between the archaea and bacteria created the nucleus-containing eukaryotic cell. (Organisms of the Archaea and Bacteria domain have no cell nucleus.) It is hypothesized that the symbiosis originated when ancient archaea, similar to modern methanogenic archaea, invaded and lived within bacteria similar to modern myxobacteria, eventually forming the early nucleus. This theory is analogous to the accepted theory for the origin of eukaryotic mitochondria and chloroplasts, which are thought to have developed from a similar endosymbiotic relationship between proto-eukaryotes and aerobic bacteria. The archaeal origin of the nucleus is supported by observations that archaea and eukarya have similar genes for certain proteins, including histones. Observations that myxobacteria are motile, can form multicellular complexes, and possess kinases and G proteins similar to eukarya, support a bacterial origin for the eukaryotic cell.
An artificial cell or minimal cell is an engineered particle that mimics one or many functions of a biological cell. The term does not refer to a specific physical entity, but rather to the idea that certain functions or structures of biological cells can be replaced or supplemented with a synthetic entity. Often, artificial cells are biological or polymeric membranes which enclose biologically active materials. As such, nanoparticles, liposomes, polymersomes, microcapsules and a number of other particles have qualified as artificial cells. Micro-encapsulation allows for metabolism within the membrane, exchange of small molecules and prevention of passage of large substances across it. The main advantages of encapsulation include improved mimicry in the body, increased solubility of the cargo and decreased immune responses. Notably, artificial cells have been clinically successful in hemoperfusion.
In biology, cell theory is the historic scientific theory, now universally accepted, that living organisms are made up of cells, that they are the basic structural/organizational unit of all organisms, and that all cells come from pre-existing cells. Cells are the basic unit of structure in all organisms and also the basic unit of reproduction. With continual improvements made to microscopes over time, magnification technology advanced enough to discover cells in the 17th century. This discovery is largely attributed to Robert Hooke, and began the scientific study of cells, also known as cell biology. Over a century later, many debates about cells began amongst scientists. Most of these debates involved the nature of cellular regeneration, and the idea of cells as a fundamental unit of life. Cell theory was eventually formulated in 1839. This is usually credited to Matthias Schleiden and Theodor Schwann. However, many other scientists like Rudolf Virchow contributed to the theory. It was an important step in the movement away from spontaneous generation.
Schmid and Seipel argue that the origin of muscle cells is a monophyletic trait that occurred concurrently with the development of the digestive and nervous systems of all animals and that this origin can be traced to a single metazoan ancestor in which muscle cells are present. They argue that molecular and morphological similarities between the muscles cells in cnidaria and ctenophora are similar enough to those of bilaterians that there would be one ancestor in metazoans from which muscle cells derive. In this case, Schmid and Seipel argue that the last common ancestor of bilateria, ctenophora, and cnidaria was a triploblast or an organism with three germ layers and that diploblasty, meaning an organism with two germ layers, evolved secondarily due to their observation of the lack of mesoderm or muscle found in most cnidarians and ctenophores. By comparing the morphology of cnidarians and ctenophores to bilaterians, Schmid and Seipel were able to conclude that there were myoblast-like structures in the tentacles and gut of some species of cnidarians and in the tentacles of ctenophores. Since this is a structure unique to muscle cells, these scientists determined based on the data collected by their peers that this is a marker for striated muscles similar to that observed in bilaterians. The authors also remark that the muscle cells found in cnidarians and ctenophores are often contests due to the origin of these muscle cells being the ectoderm rather than the mesoderm or mesendoderm. The origin of true muscles cells is argued by others to be the endoderm portion of the mesoderm and the endoderm. However, Schmid and Seipel counter this skepticism about whether or not the muscle cells found in ctenophores and cnidarians are true muscle cells by considering that cnidarians develop through a medusa stage and polyp stage. They observe that in the hydrozoan medusa stage there is a layer of cells that separate from the distal side of the ectoderm to form the striated muscle cells in a way that seems similar to that of the mesoderm and call this third separated layer of cells the ectocodon. They also argue that not all muscle cells are derived from the mesendoderm in bilaterians with key examples being that in both the eye muscles of vertebrates and the muscles of spiralians these cells derive from the ectodermal mesoderm rather than the endodermal mesoderm. Furthermore, Schmid and Seipel argue that since myogenesis does occur in cnidarians with the help of molecular regulatory elements found in the specification of muscles cells in bilaterians that there is evidence for a single origin for striated muscle.
In mammals, there are two broad types of stem cells: embryonic stem cells, which are isolated from the inner cell mass of blastocysts, and adult stem cells, which are found in various tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body, replenishing adult tissues. In a developing embryo, stem cells can differentiate into all the specialized cells—ectoderm, endoderm and mesoderm (see induced pluripotent stem cells)—but also maintain the normal turnover of regenerative organs, such as blood, skin, or intestinal tissues.
In biochemistry and metabolism, beta-oxidation is the catabolic process by which fatty acid molecules are broken down in the cytosol in prokaryotes and in the mitochondria in eukaryotes to generate acetyl-CoA, which enters the citric acid cycle, and NADH and FADH, which are co-enzymes used in the electron transport chain. It is named as such because the beta carbon of the fatty acid undergoes oxidation to a carbonyl group. Beta-oxidation is primarily facilitated by the mitochondrial trifunctional protein, an enzyme complex associated with the inner mitochondrial membrane, although very long chain fatty acids are oxidized in peroxisomes.
Most of the time, ‘artificial’ tissue is grown from the patient’s own cells. However, when the damage is so extreme that it is impossible to use the patient's own cells, artificial tissue cells are grown. The difficulty is in finding a scaffold that the cells can grow and organize on. The characteristics of the scaffold must be that it is biocompatible, cells can adhere to the scaffold, mechanically strong and biodegradable. One successful scaffold is a copolymer of lactic acid and glycolic acid.
Protein is a nutrient needed by the human body for growth and maintenance. Aside from water, proteins are the most abundant kind of molecules in the body. Protein can be found in all cells of the body and is the major structural component of all cells in the body, especially muscle. This also includes body organs, hair and skin. Proteins are also used in membranes, such as glycoproteins. When broken down into amino acids, they are used as precursors to nucleic acid, co-enzymes, hormones, immune response, cellular repair, and other molecules essential for life. Additionally, protein is needed to form blood cells.
In cells, DNA is housed in the nucleus and it never leaves. The DNA within the nucleus is transcribed by tRNA, and the transcriptions of the DNA become RNA. The RNA (ribonucleic acid) leaves the nucleus to float freely around the cytoplasm, and it contains the instructions of the DNA that are vital to the coding, decoding, regulation and expression of genes. The ribosomes then take the RNA messages and turn them into proteins that build cells. When a virus enters a cell and inserts its DNA code into the nucleus, it gets transcribed and released into the cell for the ribosome to make it into a protein. This is how viral infections occur. The cell then explodes with the overproduction of the virus, releasing it into the body to infect any and all other cells it finds. It is theorized that through evolution, cells developed a defense system called RNAi (RNA interference) to stop the production of the proteins that have suspicious mirror image messages of the RNA. They don’t just destroy the suspicious messages, but the correct messages as well to stop all production of that message. This is a cell’s self-destruct mechanism and every cell, plant and animal, have RNAi: a way to turn off the production of a certain gene inside the protein.
The act of reproduction, regarding the female, leads to an increase of digestive enzymes. This allows her to eat more prey and to stock more nutrients. The digestive enzymes then start to digest the inside of the organism itself, except for the heart, guts, and mostly the ovaries. Once the offspring are born, and until the mother dies, the mother regurgitates for two weeks the fluids stocked inside as highly nutritive food for the progeny. Ninety-five per cent of the mother's mass is digested by the offspring. They will grow to three times their original size between their birth and dispersion. During the period when female spiders are caring for their hatched offspring, the mothers do not eat, and their offspring only eat the food that the mother regurgitates along with the mother's body at the end of this time.
On December 29, 2011, chemists at Harvard University reported the creation of an artificial cell membrane.
The European Commission sponsored the development of the "Programmable Artificial Cell Evolution" (PACE) program from 2004-2008 whose goal was to lay the foundation for the creation of "microscopic self-organizing, self-replicating, and evolvable autonomous entities built from simple organic and inorganic substances that can be genetically programmed to perform specific functions" for the eventual integration into information systems. The PACE project developed the first Omega Machine, a microfluidic life support system for artificial cells that could complement chemically missing functionalities (as originally proposed by Norman Packard, Steen Rasmussen, Mark Beadau and John McCaskill). The ultimate aim was to attain an evolvable hybrid cell in a complex microscale programmable environment. The functions of the Omega Machine could then be removed stepwise, posing a series of solvable evolution challenges to the artificial cell chemistry. The project achieved chemical integration up to the level of pairs of the three core functions of artificial cells (a genetic subsystem, a containment system and a metabolic system), and generated novel spatially resolved programmable microfluidic environments for the integration of containment and genetic amplification."Programmable Artificial Cell Evolution" (PACE) The project led to the creation of the  European center for living technology] which is now continuing similar research.
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.
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.
"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.
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.