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Monday, June 25, 2018

Stem cell

From Wikipedia, the free encyclopedia

Stem cell
MSC high magnification.jpg
Transmission electron micrograph of an adult stem cell displaying typical ultrastructural characteristics.
Details
Identifiers
Latin Cellula praecursoria
MeSH D013234
TH H1.00.01.0.00028, H2.00.01.0.00001
FMA 63368

Stem cells are biological cells that can differentiate into other types of cells and can divide to produce more of the same type of stem cells. They are found in multicellular organisms.

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.

There are three known accessible sources of autologous adult stem cells in humans:
  1. Bone marrow, which requires extraction by harvesting, that is, drilling into bone (typically the femur or iliac crest).
  2. Adipose tissue (fat cells), which requires extraction by liposuction.[citation needed]
  3. Blood, which requires extraction through apheresis, wherein blood is drawn from the donor (similar to a blood donation), and passed through a machine that extracts the stem cells and returns other portions of the blood to the donor.
Stem cells can also be taken from umbilical cord blood just after birth. Of all stem cell types, autologous harvesting involves the least risk. By definition, autologous cells are obtained from one's own body, just as one may bank his or her own blood for elective surgical procedures.

Adult stem cells are frequently used in various medical therapies (e.g., bone marrow transplantation). Stem cells can now be artificially grown and transformed (differentiated) into specialized cell types with characteristics consistent with cells of various tissues such as muscles or nerves. Embryonic cell lines and autologous embryonic stem cells generated through somatic cell nuclear transfer or dedifferentiation have also been proposed as promising candidates for future therapies.[1] Research into stem cells grew out of findings by Ernest A. McCulloch and James E. Till at the University of Toronto in the 1960s.[2][3]

Properties

The classical definition of a stem cell requires that it possesses two properties:
  • Self-renewal: the ability to go through numerous cycles of cell division while maintaining the undifferentiated state.
  • Potency: the capacity to differentiate into specialized cell types. In the strictest sense, this requires stem cells to be either totipotent or pluripotent—to be able to give rise to any mature cell type, although multipotent or unipotent progenitor cells are sometimes referred to as stem cells. Apart from this it is said that stem cell function is regulated in a feed back mechanism.

Self-renewal

Two mechanisms exist to ensure that a stem cell population is maintained:

1. Obligatory asymmetric replication: a stem cell divides into one mother cell that is identical to the original stem cell, and another daughter cell that is differentiated.

When a stem cell self-renews it divides and does not disrupt the undifferentiated state. This self-renewal demands control of cell cycle as well as upkeep of multipotency or pluripotency, which all depends on the stem cell.[4]

2. Stochastic differentiation: when one stem cell develops into two differentiated daughter cells, another stem cell undergoes mitosis and produces two stem cells identical to the original.

Potency definition


Pluripotent, embryonic stem cells originate as
inner cell mass (ICM) cells within a blastocyst.
These stem cells can become any tissue in the
body, excluding a placenta. Only cells from an
earlier stage of the embryo, known as the
morula, are totipotent, able to become all
tissues in the body and the extraembryonic
placenta.

Human embryonic stem cells
A: Stem cell colonies that are not yet differentiated.
B: Nerve cells, an example of a cell type after differentiation.

Potency specifies the differentiation potential (the potential to differentiate into different cell types) of the stem cell.[5]
  • Totipotent (a.k.a. omnipotent) stem cells can differentiate into embryonic and extraembryonic cell types. Such cells can construct a complete, viable organism.[5] These cells are produced from the fusion of an egg and sperm cell. Cells produced by the first few divisions of the fertilized egg are also totipotent.[6]
  • Pluripotent stem cells are the descendants of totipotent cells and can differentiate into nearly all cells,[5] i.e. cells derived from any of the three germ layers.[7]
  • Multipotent stem cells can differentiate into a number of cell types, but only those of a closely related family of cells.[5]
  • Oligopotent stem cells can differentiate into only a few cell types, such as lymphoid or myeloid stem cells.[5]
  • Unipotent cells can produce only one cell type, their own,[5] but have the property of self-renewal, which distinguishes them from non-stem cells (e.g. progenitor cells, which cannot self-renew).

Identification

In practice, stem cells are identified by whether they can regenerate tissue. For example, the defining test for bone marrow or hematopoietic stem cells (HSCs) is the ability to transplant the cells and save an individual without HSCs. This demonstrates that the cells can produce new blood cells over a long term. It should also be possible to isolate stem cells from the transplanted individual, which can themselves be transplanted into another individual without HSCs, demonstrating that the stem cell was able to self-renew.

Properties of stem cells can be illustrated in vitro, using methods such as clonogenic assays, in which single cells are assessed for their ability to differentiate and self-renew.[8][9] Stem cells can also be isolated by their possession of a distinctive set of cell surface markers. However, in vitro culture conditions can alter the behavior of cells, making it unclear whether the cells shall behave in a similar manner in vivo. There is considerable debate as to whether some proposed adult cell populations are truly stem cells.[citation needed]

Embryonic

Embryonic stem (ES) cells are the cells of the inner cell mass of a blastocyst, an early-stage embryo.[10] Human embryos reach the blastocyst stage 4–5 days post fertilization, at which time they consist of 50–150 cells. ES cells are pluripotent and give rise during development to all derivatives of the three primary germ layers: ectoderm, endoderm and mesoderm. In other words, they can develop into each of the more than 200 cell types of the adult body when given sufficient and necessary stimulation for a specific cell type. They do not contribute to the extra-embryonic membranes or the placenta.
During embryonic development these inner cell mass cells continuously divide and become more specialized. For example, a portion of the ectoderm in the dorsal part of the embryo specializes as 'neurectoderm', which will become the future central nervous system.[11] Later in development, neurulation causes the neurectoderm to form the neural tube. At the neural tube stage, the anterior portion undergoes encephalization to generate or 'pattern' the basic form of the brain. At this stage of development, the principal cell type of the CNS is considered a neural stem cell. These neural stem cells are pluripotent, as they can generate a large diversity of many different neuron types, each with unique gene expression, morphological, and functional characteristics. The process of generating neurons from stem cells is called neurogenesis. One prominent example of a neural stem cell is the radial glial cell, so named because it has a distinctive bipolar morphology with highly elongated processes spanning the thickness of the neural tube wall, and because historically it shared some glial characteristics, most notably the expression of glial fibrillary acidic protein (GFAP).[12][13] The radial glial cell is the primary neural stem cell of the developing vertebrate CNS, and its cell body resides in the ventricular zone, adjacent to the developing ventricular system. Neural stem cells are committed to the neuronal lineages (neurons, astrocytes, and oligodendrocytes), and thus their potency is restricted.[11]

Nearly all research to date has made use of mouse embryonic stem cells (mES) or human embryonic stem cells (hES) derived from the early inner cell mass. Both have the essential stem cell characteristics, yet they require very different environments in order to maintain an undifferentiated state. Mouse ES cells are grown on a layer of gelatin as an extracellular matrix (for support) and require the presence of leukemia inhibitory factor (LIF) in serum media. A drug cocktail containing inhibitors to GSK3B and the MAPK/ERK pathway, called 2i, has also been shown to maintain pluripotency in stem cell culture.[14] Human ES cells are grown on a feeder layer of mouse embryonic fibroblasts (MEFs) and require the presence of basic fibroblast growth factor (bFGF or FGF-2).[15] Without optimal culture conditions or genetic manipulation,[16] embryonic stem cells will rapidly differentiate.

A human embryonic stem cell is also defined by the expression of several transcription factors and cell surface proteins. The transcription factors Oct-4, Nanog, and Sox2 form the core regulatory network that ensures the suppression of genes that lead to differentiation and the maintenance of pluripotency.[17] The cell surface antigens most commonly used to identify hES cells are the glycolipids stage specific embryonic antigen 3 and 4 and the keratan sulfate antigens Tra-1-60 and Tra-1-81. By using human embryonic stem cells to produce specialized cells like nerve cells or heart cells in the lab, scientists can gain access to adult human cells without taking tissue from patients. They can then study these specialized adult cells in detail to try and catch complications of diseases, or to study cells reactions to potentially new drugs. The molecular definition of a stem cell includes many more proteins and continues to be a topic of research.[18]

There are currently no approved treatments using embryonic stem cells. The first human trial was approved by the US Food and Drug Administration in January 2009.[19] However, the human trial was not initiated until October 13, 2010 in Atlanta for spinal cord injury research. On November 14, 2011 the company conducting the trial (Geron Corporation) announced that it will discontinue further development of its stem cell programs.[20] ES cells, being pluripotent cells, require specific signals for correct differentiation—if injected directly into another body, ES cells will differentiate into many different types of cells, causing a teratoma. Differentiating ES cells into usable cells while avoiding transplant rejection are just a few of the hurdles that embryonic stem cell researchers still face.[21] Due to ethical considerations, many nations currently have moratoria or limitations on either human ES cell research or the production of new human ES cell lines. Because of their combined abilities of unlimited expansion and pluripotency, embryonic stem cells remain a theoretically potential source for regenerative medicine and tissue replacement after injury or disease.[22]

Fetal

The primitive stem cells located in the organs of fetuses are referred to as fetal stem cells.[23] There are two types of fetal stem cells:
  1. Fetal proper stem cells come from the tissue of the fetus proper, and are generally obtained after an abortion. These stem cells are not immortal but have a high level of division and are multipotent.
  2. Extraembryonic fetal stem cells come from extraembryonic membranes, and are generally not distinguished from adult stem cells. These stem cells are acquired after birth, they are not immortal but have a high level of cell division, and are pluripotent.[24]

Adult


Stem cell division and differentiation. A: stem cell; B: progenitor cell; C: differentiated cell; 1: symmetric stem cell division; 2: asymmetric stem cell division; 3: progenitor division; 4: terminal differentiation

Adult stem cells, also called somatic (from Greek σωματικóς, "of the body") stem cells, are stem cells which maintain and repair the tissue in which they are found.[25] They can be found in children, as well as adults.[26]

Pluripotent adult stem cells are rare and generally small in number, but they can be found in umbilical cord blood and other tissues.[27] Bone marrow is a rich source of adult stem cells,[28] which have been used in treating several conditions including liver cirrhosis,[29] chronic limb ischemia [30] and endstage heart failure.[31] The quantity of bone marrow stem cells declines with age and is greater in males than females during reproductive years.[32] Much adult stem cell research to date has aimed to characterize their potency and self-renewal capabilities.[33] DNA damage accumulates with age in both stem cells and the cells that comprise the stem cell environment. This accumulation is considered to be responsible, at least in part, for increasing stem cell dysfunction with aging (see DNA damage theory of aging).[34]

Most adult stem cells are lineage-restricted (multipotent) and are generally referred to by their tissue origin (mesenchymal stem cell, adipose-derived stem cell, endothelial stem cell, dental pulp stem cell, etc.).[35][36] Muse cells (multi-lineage differentiating stress enduring cells) are a recently discovered pluripotent stem cell type found in multiple adult tissues, including adipose, dermal fibroblasts, and bone marrow. While rare, muse cells are identifiable by their expression of SSEA-3, a marker for undifferentiated stem cells, and general mesenchymal stem cells markers such as CD105. When subjected to single cell suspension culture, the cells will generate clusters that are similar to embryoid bodies in morphology as well as gene expression, including canonical pluripotency markers Oct4, Sox2, and Nanog.[37]

Adult stem cell treatments have been successfully used for many years to treat leukemia and related bone/blood cancers through bone marrow transplants.[38] Adult stem cells are also used in veterinary medicine to treat tendon and ligament injuries in horses.[39]

The use of adult stem cells in research and therapy is not as controversial as the use of embryonic stem cells, because the production of adult stem cells does not require the destruction of an embryo. Additionally, in instances where adult stem cells are obtained from the intended recipient (an autograft), the risk of rejection is essentially non-existent. Consequently, more US government funding is being provided for adult stem cell research.[40]

Amniotic

Multipotent stem cells are also found in amniotic fluid. These stem cells are very active, expand extensively without feeders and are not tumorigenic. Amniotic stem cells are multipotent and can differentiate in cells of adipogenic, osteogenic, myogenic, endothelial, hepatic and also neuronal lines.[41] Amniotic stem cells are a topic of active research.

Use of stem cells from amniotic fluid overcomes the ethical objections to using human embryos as a source of cells. Roman Catholic teaching forbids the use of embryonic stem cells in experimentation; accordingly, the Vatican newspaper "Osservatore Romano" called amniotic stem cells "the future of medicine".[42]

It is possible to collect amniotic stem cells for donors or for autologuous use: the first US amniotic stem cells bank [43][44] was opened in 2009 in Medford, MA, by Biocell Center Corporation[45][46][47] and collaborates with various hospitals and universities all over the world.[48]

Induced pluripotent

Adult stem cells have limitations with their potency; unlike ESCs, they are not able to differentiate into cells from all three germ layers. As such, they are deemed multipotent.
However, reprogramming allows for the creation of pluripotent cells, induced pluripotent stem cells, from adult cells. It is important to note that these are not adult stem cells, but adult cells (e.g. epithelial cells) reprogrammed to give rise to cells with pluripotent capabilities. Using genetic reprogramming with protein transcription factors, pluripotent stem cells with ESC-like capabilities have been derived.[49][50][51] The first demonstration of Induced Pluripotent Stem Cells was conducted by Shinya Yamanaka and his colleagues at Kyoto University.[52] They used the transcription factors Oct3/4, Sox2, c-Myc, and Klf4 to reprogram mouse fibroblast cells into pluripotent cells.[49][53] Subsequent work used these factors to induce pluripotency in human fibroblast cells.[54] Junying Yu, James Thomson, and their colleagues at the University of Wisconsin–Madison used a different set of factors, Oct4, Sox2, Nanog and Lin28, and carried out their experiments using cells from human foreskin.[49][55] However, they were able to replicate Yamanaka's finding that inducing pluripotency in human cells was possible.

It is important to note that iPSCs and ESCs are not equivalent. They have many similar properties, such as pluripotency and differentiation potential, the expression of pluripotency genes, epigenetic patterns, embryoid body and teratoma formation, and viable chimera formation.[52][53] However, similar does not mean they are the same. In fact, there are many differences within these properties. Importantly, the chromatin of iPSCs appears to be more "closed" or methylated than that of ESCs.[52][53] Similarly, the gene expression pattern between ESCs and iPSCs, or even iPSCs sourced from different origins.[52] There are thus questions about the "completeness" of reprogramming and the somatic memory of induced pluripotent stem cells. Despite this, inducing adult cells to be pluripotent appears to be viable.

As a result of the success of these experiments, Ian Wilmut, who helped create the first cloned animal Dolly the Sheep, has announced that he will abandon somatic cell nuclear transfer as an avenue of research.[56]

Furthermore, induced pluripotent stem cells provide several therapeutic advantages. Like ESCs, they are pluripotent. They thus have great differentiation potential; theoretically, they could produce any cell within the human body (if reprogramming to pluripotency was "complete").[52] Moreover, unlike ESCs, they potentially could allow doctors to create a pluripotent stem cell line for each individual patient.[57] In fact, frozen blood samples can be used as a source of induced pluripotent stem cells, opening a new avenue for obtaining the valued cells.[58] Patient specific stem cells allow for the screening for side effects before drug treatment, as well as the reduced risk of transplantation rejection.[57] Despite their current limited use therapeutically, iPSCs hold create potential for future use in medical treatment and research.

Lineage

To ensure self-renewal, stem cells undergo two types of cell division (see Stem cell division and differentiation diagram). Symmetric division gives rise to two identical daughter cells both endowed with stem cell properties. Asymmetric division, on the other hand, produces only one stem cell and a progenitor cell with limited self-renewal potential. Progenitors can go through several rounds of cell division before terminally differentiating into a mature cell. It is possible that the molecular distinction between symmetric and asymmetric divisions lies in differential segregation of cell membrane proteins (such as receptors) between the daughter cells.[59]

An alternative theory is that stem cells remain undifferentiated due to environmental cues in their particular niche. Stem cells differentiate when they leave that niche or no longer receive those signals. Studies in Drosophila germarium have identified the signals decapentaplegic and adherens junctions that prevent germarium stem cells from differentiating.[60][61]

Treatments

Stem cell therapy is the use of stem cells to treat or prevent a disease or condition. Bone marrow transplant is a form of stem cell therapy that has been used for many years without controversy. No stem cell therapies other than bone marrow transplant are widely used.[62][63]

Advantages

Stem cell treatments may lower symptoms of the disease or condition that is being treated. The lowering of symptoms may allow patients to reduce the drug intake of the disease or condition. Stem cell treatment may also provide knowledge for society to further stem cell understanding and future treatments.[64]

Disadvantages

Stem cell treatments may require immunosuppression because of a requirement for radiation before the transplant to remove the person's previous cells, or because the patient's immune system may target the stem cells. One approach to avoid the second possibility is to use stem cells from the same patient who is being treated.

Pluripotency in certain stem cells could also make it difficult to obtain a specific cell type. It is also difficult to obtain the exact cell type needed, because not all cells in a population differentiate uniformly. Undifferentiated cells can create tissues other than desired types.[65]

Some stem cells form tumors after transplantation;[66] pluripotency is linked to tumor formation especially in embryonic stem cells, fetal proper stem cells, induced pluripotent stem cells. Fetal proper stem cells form tumors despite multipotency.[67]

Research

Some of the fundamental patents covering human embryonic stem cells are owned by the Wisconsin Alumni Research Foundation (WARF) – they are patents 5,843,780, 6,200,806, and 7,029,913 invented by James A. Thomson. WARF does not enforce these patents against academic scientists, but does enforce them against companies.[68]

In 2006, a request for the US Patent and Trademark Office (USPTO) to re-examine the three patents was filed by the Public Patent Foundation on behalf of its client, the non-profit patent-watchdog group Consumer Watchdog (formerly the Foundation for Taxpayer and Consumer Rights).[68] In the re-examination process, which involves several rounds of discussion between the USPTO and the parties, the USPTO initially agreed with Consumer Watchdog and rejected all the claims in all three patents,[69] however in response, WARF amended the claims of all three patents to make them more narrow, and in 2008 the USPTO found the amended claims in all three patents to be patentable. The decision on one of the patents (7,029,913) was appealable, while the decisions on the other two were not.[70][71] Consumer Watchdog appealed the granting of the '913 patent to the USPTO's Board of Patent Appeals and Interferences (BPAI) which granted the appeal, and in 2010 the BPAI decided that the amended claims of the '913 patent were not patentable.[72] However, WARF was able to re-open prosecution of the case and did so, amending the claims of the '913 patent again to make them more narrow, and in January 2013 the amended claims were allowed.[73]

In July 2013, Consumer Watchdog announced that it would appeal the decision to allow the claims of the '913 patent to the US Court of Appeals for the Federal Circuit (CAFC), the federal appeals court that hears patent cases.[74] At a hearing in December 2013, the CAFC raised the question of whether Consumer Watchdog had legal standing to appeal; the case could not proceed until that issue was resolved.[75]

Treatment


Diseases and conditions where stem cell treatment is being investigated.

Diseases and conditions where stem cell treatment is being investigated include:
Research is underway to develop various sources for stem cells, and to apply stem cell treatments for neurodegenerative diseases and conditions, diabetes, heart disease, and other conditions.[91] Research is also underway in generating organoids using stem cells, which would allow for further understanding of human development, organogenesis, and modeling of human diseases.[92]

In more recent years, with the ability of scientists to isolate and culture embryonic stem cells, and with scientists' growing ability to create stem cells using somatic cell nuclear transfer and techniques to create induced pluripotent stem cells, controversy has crept in, both related to abortion politics and to human cloning.

Hepatotoxicity and drug-induced liver injury account for a substantial number of failures of new drugs in development and market withdrawal, highlighting the need for screening assays such as stem cell-derived hepatocyte-like cells, that are capable of detecting toxicity early in the drug development process.[93]

Biomolecule

From Wikipedia, the free encyclopedia

A representation of the 3d structure of myoglobin, showing alpha helices, represented by ribbons. This protein was the first to have its structure solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a Nobel Prize in Chemistry.

A biomolecule or biological molecule is a loosely used term for molecules and ions that are present in organisms, essential to some typically biological process such as cell division, morphogenesis, or development.[1] Biomolecules include large macromolecules (or polyanions) such as proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules such as primary metabolites, secondary metabolites, and natural products. A more general name for this class of material is biological materials. Biomolecules are usually endogenous but may also be exogenous. For example, pharmaceutical drugs may be natural products or semisynthetic (biopharmaceuticals) or they may be totally synthetic.

Biology and its subsets of biochemistry and molecular biology study biomolecules and their reactions. Most biomolecules are organic compounds, and just four elementsoxygen, carbon, hydrogen, and nitrogen—make up 96% of the human body's mass. But many other elements, such as the various biometals, are present in small amounts.

The uniformity of specific types of molecules (the biomolecules) and of some metabolic pathways as invariant features between the diversity of life forms is called "biochemical universals"[2] or "theory of material unity of the living beings", a unifying concept in biology, along with cell theory and evolution theory.[3]

Types of biomolecules

A diverse range of biomolecules exist, including:
Biomonomers Bio-oligo Biopolymers Polymerization process Covalent bond name between monomers
Amino acids Oligopeptides Polypeptides, proteins (hemoglobin...) Polycondensation Peptide bond
Monosaccharides Oligosaccharides Polysaccharides (cellulose...) Polycondensation Glycosidic bond
Isoprene Terpenes Polyterpenes: cis-1,4-polyisoprene natural rubber and trans-1,4-polyisoprene gutta-percha Polyaddition
Nucleotides Oligonucleotides Polynucleotides, nucleic acids (DNA, RNA)
Phosphodiester bond

Nucleosides and nucleotides

Nucleosides are molecules formed by attaching a nucleobase to a ribose or deoxyribose ring. Examples of these include cytidine (C), uridine (U), adenosine (A), guanosine (G), thymidine (T) and inosine (I).

Nucleosides can be phosphorylated by specific kinases in the cell, producing nucleotides. Both DNA and RNA are polymers, consisting of long, linear molecules assembled by polymerase enzymes from repeating structural units, or monomers, of mononucleotides. DNA uses the deoxynucleotides C, G, A, and T, while RNA uses the ribonucleotides (which have an extra hydroxyl(OH) group on the pentose ring) C, G, A, and U. Modified bases are fairly common (such as with methyl groups on the base ring), as found in ribosomal RNA or transfer RNAs or for discriminating the new from old strands of DNA after replication.[4]

Each nucleotide is made of an acyclic nitrogenous base, a pentose and one to three phosphate groups. They contain carbon, nitrogen, oxygen, hydrogen and phosphorus. They serve as sources of chemical energy (adenosine triphosphate and guanosine triphosphate), participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into important cofactors of enzymatic reactions (coenzyme A, flavin adenine dinucleotide, flavin mononucleotide, and nicotinamide adenine dinucleotide phosphate).[5]

DNA and RNA structure

DNA structure is dominated by the well-known double helix formed by Watson-Crick base-pairing of C with G and A with T. This is known as B-form DNA, and is overwhelmingly the most favorable and common state of DNA; its highly specific and stable base-pairing is the basis of reliable genetic information storage. DNA can sometimes occur as single strands (often needing to be stabilized by single-strand binding proteins) or as A-form or Z-form helices, and occasionally in more complex 3D structures such as the crossover at Holliday junctions during DNA replication.[5]
 

Stereo 3D image of a group I intron ribozyme (PDB file 1Y0Q); gray lines show base pairs; ribbon arrows show double-helix regions, blue to red from 5' to 3' end; white ribbon is an RNA product.

RNA, in contrast, forms large and complex 3D tertiary structures reminiscent of proteins, as well as the loose single strands with locally folded regions that constitute messenger RNA molecules. Those RNA structures contain many stretches of A-form double helix, connected into definite 3D arrangements by single-stranded loops, bulges, and junctions.[6] Examples are tRNA, ribosomes, ribozymes, and riboswitches. These complex structures are facilitated by the fact that RNA backbone has less local flexibility than DNA but a large set of distinct conformations, apparently because of both positive and negative interactions of the extra OH on the ribose.[7] Structured RNA molecules can do highly specific binding of other molecules and can themselves be recognized specifically; in addition, they can perform enzymatic catalysis (when they are known as "ribozymes", as initially discovered by Tom Cech and colleagues.[8]

Saccharides

Monosaccharides are the simplest form of carbohydrates with only one simple sugar. They essentially contain an aldehyde or ketone group in their structure.[9] The presence of an aldehyde group in a monosaccharide is indicated by the prefix aldo-. Similarly, a ketone group is denoted by the prefix keto-.[4] Examples of monosaccharides are the hexoses, glucose, fructose, TriosesTetroses, Heptoses, galactose, pentoses, ribose, and deoxyribose. Consumed fructose and glucose have different rates of gastric emptying, are differentially absorbed and have different metabolic fates, providing multiple opportunities for 2 different saccharides to differentially affect food intake.[9] Most saccharides eventually provide fuel for cellular respiration.

Disaccharides are formed when two monosaccharides, or two single simple sugars, form a bond with removal of water. They can be hydrolyzed to yield their saccharin building blocks by boiling with dilute acid or reacting them with appropriate enzymes.[4] Examples of disaccharides include sucrose, maltose, and lactose.

Polysaccharides are polymerized monosaccharides, or complex carbohydrates. They have multiple simple sugars. Examples are starch, cellulose, and glycogen. They are generally large and often have a complex branched connectivity. Because of their size, polysaccharides are not water-soluble, but their many hydroxy groups become hydrated individually when exposed to water, and some polysaccharides form thick colloidal dispersions when heated in water.[4] Shorter polysaccharides, with 3 - 10 monomers, are called oligosaccharides.[10] A fluorescent indicator-displacement molecular imprinting sensor was developed for discriminating saccharides. It successfully discriminated three brands of orange juice beverage.[11] The change in fluorescence intensity of the sensing films resulting is directly related to the saccharide concentration.[12]

Lignin

Lignin is a complex polyphenolic macromolecule composed mainly of beta-O4-aryl linkages. After cellulose, lignin is the second most abundant biopolymer and is one of the primary structural components of most plants. It contains subunits derived from p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol[13] and is unusual among biomolecules in that it is racemic. The lack of optical activity is due to the polymerization of lignin which occurs via free radical coupling reactions in which there is no preference for either configuration at a chiral center.

Lipids

Lipids (oleaginous) are chiefly fatty acid esters, and are the basic building blocks of biological membranes. Another biological role is energy storage (e.g., triglycerides). Most lipids consist of a polar or hydrophilic head (typically glycerol) and one to three nonpolar or hydrophobic fatty acid tails, and therefore they are amphiphilic. Fatty acids consist of unbranched chains of carbon atoms that are connected by single bonds alone (saturated fatty acids) or by both single and double bonds (unsaturated fatty acids). The chains are usually 14-24 carbon groups long, but it is always an even number.

For lipids present in biological membranes, the hydrophilic head is from one of three classes:
  • Glycolipids, whose heads contain an oligosaccharide with 1-15 saccharide residues.
  • Phospholipids, whose heads contain a positively charged group that is linked to the tail by a negatively charged phosphate group.
  • Sterols, whose heads contain a planar steroid ring, for example, cholesterol.
Other lipids include prostaglandins and leukotrienes which are both 20-carbon fatty acyl units synthesized from arachidonic acid. They are also known as fatty acids

Amino acids

Amino acids contain both amino and carboxylic acid functional groups. (In biochemistry, the term amino acid is used when referring to those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, plus proline which is not actually an amino acid).

Modified amino acids are sometimes observed in proteins; this is usually the result of enzymatic modification after translation (protein synthesis). For example, phosphorylation of serine by kinases and dephosphorylation by phosphatases is an important control mechanism in the cell cycle. Only two amino acids other than the standard twenty are known to be incorporated into proteins during translation, in certain organisms:
  • Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.
  • Pyrrolysine is incorporated into some proteins at a UAG codon. For instance, in some methanogens in enzymes that are used to produce methane.
Besides those used in protein synthesis, other biologically important amino acids include carnitine (used in lipid transport within a cell), ornithine, GABA and taurine.

Protein structure

The particular series of amino acids that form a protein is known as that protein's primary structure. This sequence is determined by the genetic makeup of the individual. It specifies the order of side-chain groups along the linear polypeptide "backbone".

Proteins have two types of well-classified, frequently occurring elements of local structure defined by a particular pattern of hydrogen bonds along the backbone: alpha helix and beta sheet. Their number and arrangement is called the secondary structure of the protein. Alpha helices are regular spirals stabilized by hydrogen bonds between the backbone CO group (carbonyl) of one amino acid residue and the backbone NH group (amide) of the i+4 residue. The spiral has about 3.6 amino acids per turn, and the amino acid side chains stick out from the cylinder of the helix. Beta pleated sheets are formed by backbone hydrogen bonds between individual beta strands each of which is in an "extended", or fully stretched-out, conformation. The strands may lie parallel or antiparallel to each other, and the side-chain direction alternates above and below the sheet. Hemoglobin contains only helices, natural silk is formed of beta pleated sheets, and many enzymes have a pattern of alternating helices and beta-strands. The secondary-structure elements are connected by "loop" or "coil" regions of non-repetitive conformation, which are sometimes quite mobile or disordered but usually adopt a well-defined, stable arrangement.[14]

The overall, compact, 3D structure of a protein is termed its tertiary structure or its "fold". It is formed as result of various attractive forces like hydrogen bonding, disulfide bridges, hydrophobic interactions, hydrophilic interactions, van der Waals force etc.

When two or more polypeptide chains (either of identical or of different sequence) cluster to form a protein, quaternary structure of protein is formed. Quaternary structure is an attribute of polymeric (same-sequence chains) or heteromeric (different-sequence chains) proteins like hemoglobin, which consists of two "alpha" and two "beta" polypeptide chains.

Apoenzymes

An apoenzyme (or, generally, an apoprotein) is the protein without any small-molecule cofactors, substrates, or inhibitors bound. It is often important as an inactive storage, transport, or secretory form of a protein. This is required, for instance, to protect the secretory cell from the activity of that protein. Apoenzymes becomes active enzymes on addition of a cofactor. Cofactors can be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds, (e.g., [Flavin group|flavin] and heme). Organic cofactors can be either prosthetic groups, which are tightly bound to an enzyme, or coenzymes, which are released from the enzyme's active site during the reaction.

Isoenzymes

Isoenzymes, or isozymes, are multiple forms of an enzyme, with slightly different protein sequence and closely similar but usually not identical functions. They are either products of different genes, or else different products of alternative splicing. They may either be produced in different organs or cell types to perform the same function, or several isoenzymes may be produced in the same cell type under differential regulation to suit the needs of changing development or environment. LDH (lactate dehydrogenase) has multiple isozymes, while fetal hemoglobin is an example of a developmentally regulated isoform of a non-enzymatic protein. The relative levels of isoenzymes in blood can be used to diagnose problems in the organ of secretion .

Operator (computer programming)

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