The cytosol or cytoplasmic matrix is the liquid found inside cells. It constitutes most of the intracellular fluid and it is separated into compartments by membranes. For example, the mitochondrial matrix separates the mitochondrion into many compartments, in the eukaryotic cell, the cytosol is within the cell membrane and is part of the cytoplasm, which comprises the mitochondria and other organelles, 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 occur in the cytosol. The cytosol is a mixture of substances dissolved in water. Although water forms the majority of the cytosol, its structure. The cytosol contains amounts of macromolecules, which can alter how molecules behave. Although it was thought to be a simple solution of molecules. Such a soluble cell extract is not identical to the part of the cell cytoplasm and is usually called a cytoplasmic fraction.
The term cytosol is now used to refer to the phase of the cytoplasm in an intact cell. This excludes any part of the cytoplasm that is contained within organelles, prior to this, other terms were used for the cell fluid, not always synonymously, as its nature was not very clear. The cytosol consists mostly of water, dissolved ions, small molecules, the majority of these non-protein molecules have a molecular mass of less than 300 Da. This mixture of molecules is extraordinarily complex, as the variety of molecules that are involved in metabolism is immense. For example, up to 200,000 different small molecules might be made in plants, although not all these will be present in the same species, or in a single cell. Estimates of the number of metabolites in single cells such as E. coli, most of the cytosol is water, which makes up about 70% of the total volume of a typical cell. The pH of the fluid is 7.4. While human cytosolic pH ranges between 7.0 -7.4, and is higher if a cell is growing
It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil. Each protein exists as a polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks any stable three-dimensional structure, as the polypeptide chain is being synthesized by the ribosome, the linear chain begins to fold into its three dimensional structure. Folding begins to occur even during translation of the polypeptide chain, amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein, known as the native state. The resulting three-dimensional structure is determined by the amino acid sequence or primary structure, the energy landscape describes the folding pathways in which the unfolded protein is able to assume its native state. Experiments beginning in the 1980s indicate the codon for an acid can influence protein structure. The correct three-dimensional structure is essential to function, although parts of functional proteins may remain unfolded.
Failure to fold into native structure generally produces inactive proteins, several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins. Many allergies are caused by folding of some proteins, because the immune system does not produce antibodies for certain protein structures. The primary structure of a protein, its linear amino-acid sequence, the amino acid composition is not as important as the sequence. The essential fact of folding, remains that the amino acid sequence of protein contains the information that specifies both the native structure and the pathway to attain that state. This is not to say that nearly identical amino acid sequences always fold similarly, conformations differ based on environmental factors as well, similar proteins fold differently based on where they are found. Formation of a structure is the first step in the folding process that a protein takes to assume its native structure. Formation of intramolecular hydrogen bonds provides another important contribution to protein stability, alpha helices are formed by hydrogen bonding of the backbone to form a spiral shape.
The beta pleated sheet is a structure forms with the backbone bending over itself to form the hydrogen bonds. The hydrogen bonds are between the hydrogen and carbonyl carbon of the peptide bond. The alpha helices and beta pleated sheets can be amphipathic in nature, or contain a hydrophilic portion, secondary structure hierarchically gives way to tertiary structure formation. Tertiary structure of a protein involves a single chain, however
The Golgi apparatus, known as the Golgi complex, Golgi body, or simply the Golgi, is an organelle found in most eukaryotic cells. It was identified in 1897 by the Italian scientist Camillo Golgi, part of the cellular endomembrane system, the Golgi apparatus packages proteins into membrane-bound vesicles inside the cell before the vesicles are sent to their destination. The Golgi apparatus resides at the intersection of the secretory, owing to its large size and distinctive structure, the Golgi apparatus was one of the first organelles to be discovered and observed in detail. It was discovered in 1898 by Italian physician Camillo Golgi during an investigation of the nervous system, after first observing it under his microscope, he termed the structure the internal reticular apparatus. Some doubted the discovery at first, arguing that the appearance of the structure was merely an illusion created by the observation technique used by Golgi. With the development of modern microscopes in the 20th century, the discovery was confirmed, early references to the Golgi referred to it by various names including the Golgi–Holmgren apparatus, Golgi–Holmgren ducts, and Golgi–Kopsch apparatus.
The term Golgi apparatus was used in 1910 and first appeared in the literature in 1913. Among eukaryotes, the localization of the Golgi apparatus differs. In mammals, a single Golgi apparatus complex is located near the cell nucleus. Tubular connections are responsible for linking the stacks together and tubular connections of the Golgi apparatus are dependent on microtubules. If microtubules are experimentally depolymerized, the Golgi apparatus loses connections, in yeast, multiple Golgi apparatuses are scattered throughout the cytoplasm. In plants, Golgi stacks are not concentrated at the centrosomal region, organization of the plant Golgi depends on actin cables and not microtubules. The common feature among Golgi is that they are adjacent to endoplasmic reticulum exit sites, in most eukaryotes, the Golgi apparatus is made up of a series of compartments consisting of two main networks, the cis Golgi network and the trans Golgi network. The CGN is a collection of fused, flattened membrane-enclosed disks known as cisternae, a mammalian cell typically contains 40 to 100 stacks.
Between four and eight cisternae are usually present in a stack and this collection of cisternae is broken down into cis and trans compartments. The TGN is the final structure, from which proteins are packaged into vesicles destined to lysosomes, secretory vesicles. The TGN is usually positioned adjacent to the stacks of the Golgi apparatus, the TGN may act as an early endosome in yeast and plants. There are structural and organizational differences in the Golgi apparatus among eukaryotes, in some yeasts, Golgi stacking is not observed
White blood cell
White blood cells, called leukocytes or leucocytes, are the cells of the immune system that are involved in protecting the body against both infectious disease and foreign invaders. All white blood cells are produced and derived from multipotent cells in the bone known as hematopoietic stem cells. Leukocytes are found throughout the body, including the blood and lymphatic system, all white blood cells have nuclei, which distinguishes them from the other blood cells, the anucleated red blood cells and platelets. Types of white cells can be classified in standard ways. Two pairs of broadest categories classify them either by structure or by cell division lineage and these broadest categories can be further divided into the five main types, eosinophils, basophils and monocytes. These types are distinguished by their physical and functional characteristics, further subtypes can be classified, for example, among lymphocytes, there are B cells, T cells, and NK cells. The number of leukocytes in the blood is often an indicator of disease, the normal white cell count is usually between 4 × 109/L and 11 × 109/L.
In the US this is expressed as 4,000 to 11,000 white blood cells per microliter of blood. They make up approximately 1% of the blood volume in a healthy adult. However, this 1% of the blood makes a difference to health. An increase in the number of leukocytes over the limits is called leukocytosis. It is normal when it is part of immune responses. It is occasionally abnormal, when it is neoplastic or autoimmune in origin, a decrease below the lower limit is called leukopenia. The name white blood cell derives from the appearance of a blood sample after centrifugation. White cells are found in the buff, a thin, typically white layer of nucleated cells between the red blood cells and the blood plasma. The scientific term leukocyte directly reflects its description and it is derived from the Greek roots leuk- meaning white and cyt- meaning cell. The buffy coat may sometimes be green if there are large amounts of neutrophils in the sample, all white blood cells are nucleated, which distinguishes them from the anucleated red blood cells and platelets.
Types of leukocytes can be classified in standard ways, two pairs of broadest categories classify them either by structure or by cell lineage
Platelets, called thrombocytes, are a component of blood whose function is to stop bleeding by clumping and clotting blood vessel injuries. Platelets have no nucleus, they are fragments of cytoplasm that are derived from the megakaryocytes of the bone marrow. These unactivated platelets are biconvex discoid structures, 2–3 µm in greatest diameter, platelets are found only in mammals, whereas in other animals thrombocytes circulate as intact mononuclear cells. On a stained blood smear, platelets appear as purple spots. The smear is used to examine platelets for size, qualitative number, the ratio of platelets to red blood cells in a healthy adult is 1,10 to 1,20. The main function of platelets is to contribute to hemostasis, the process of stopping bleeding at the site of interrupted endothelium and they gather at the site and unless the interruption is physically too large, they plug the hole. First, platelets attach to substances outside the interrupted endothelium, second, they change shape, turn on receptors and secrete chemical messengers, activation.
Third, they connect to each other through receptor bridges, formation of this platelet plug is associated with activation of the coagulation cascade with resultant fibrin deposition and linking. These processes may overlap, the spectrum is from a predominantly platelet plug, or white clot to a predominantly fibrin clot, the final result is the clot. Some would add the subsequent clot retraction and platelet inhibition as fourth and fifth steps to the completion of the process, low platelet concentration is thrombocytopenia and is due to either decreased production or increased destruction. Elevated platelet concentration is thrombocytosis and is either congenital, reactive, or due to unregulated production, a disorder of platelet function is a thrombocytopathy. An arterial thrombus may partially obstruct blood flow, causing downstream ischemia, or may completely obstruct it, george Gulliver in 1841 drew pictures of platelets using the twin lens microscope invented in 1830 by Joseph Jackson Lister.
This microscope improved resolution sufficiently to make it possible to see platelets for the first time, william Addison in 1842 drew pictures of a platelet-fibrin clot. Lionel Beale in 1864 was the first to publish a drawing showing platelets, max Schultze in 1865 described what he called spherules, which he noted were much smaller than red blood cells, occasionally clumped, and were sometimes found in collections of fibrin material. Queens College, Birmingham physician Dr Richard Hill Norris was the first to describe the action of platelets in 1880, giulio Bizzozero in 1882 studied the blood of amphibians microscopically in vivo. He named Schultzs spherules piastrine, little plates, william Osler observed them and, in published lectures in 1886, called them a third corpuscle and a blood plaque and described them as a colorless protoplasmic disc. Thrombocytes are cells found in the blood of non-mammalian vertebrates and they are the functional equivalents of platelets, but circulate as intact mononuclear cells, and are not simply cytoplasmic fragments of bone marrow megakaryocytes.
In some contexts, the thrombus is used interchangeably with the word clot
A T cell, or T lymphocyte, is a type of lymphocyte that plays a central role in cell-mediated immunity. T cells can be distinguished from other lymphocytes, such as B cells and natural killer cells and they are called T cells because they mature in the thymus from thymocytes. The several subsets of T cells each have a distinct function, the majority of human T cells rearrange their alpha and beta chains on the cell receptor and are termed alpha beta T cells and are part of the adaptive immune system. The category of effector T cell is a one that includes various T cell types that actively respond to a stimulus. This includes helper, killer and potentially other T cell types, T helper cells assist other white blood cells in immunologic processes, including maturation of B cells into plasma cells and memory B cells, and activation of cytotoxic T cells and macrophages. These cells are known as CD4+ T cells because they express the CD4 glycoprotein on their surfaces. Helper T cells become activated when they are presented with peptide antigens by MHC class II molecules, once activated, they divide rapidly and secrete small proteins called cytokines that regulate or assist in the active immune response.
These cells can differentiate one of several subtypes, including TH1, TH2, TH3, TH17, TH9, or TFH. Signalling from the APC directs T cells into particular subtypes, cytotoxic T cells destroy virus-infected cells and tumor cells, and are implicated in transplant rejection. These cells are known as CD8+ T cells since they express the CD8 glycoprotein at their surfaces. These cells recognize their targets by binding to antigen associated with MHC class I molecules, through IL-10, and other molecules secreted by regulatory T cells, the CD8+ cells can be inactivated to an anergic state, which prevents autoimmune diseases. Appropriate co-stimulation must be present at the time of encounter for this process to occur. Historically, memory T cells were thought to belong to either the effector or central memory subtypes, numerous new populations of memory T cells were discovered including tissue-resident memory T cells, stem memory TSCM cells, and virtual memory T cells. The single unifying theme for all memory T cell subtypes is that they are long-lived, by this mechanism they provide the immune system with memory against previously encountered pathogens.
Memory T cells may be either CD4+ or CD8+ and usually express CD45RO, memory T cell subtypes, Central memory T cells express CD45RO, C-C chemokine receptor type 7, and L-selectin. Central memory T cells have intermediate to high expression of CD44 and this memory subpopulation is commonly found in the lymph nodes and in the peripheral circulation. Effector memory T cells express CD45RO but lack expression of CCR7 and they have intermediate to high expression of CD44. These memory T cells lack lymph node-homing receptors and are found in the peripheral circulation
Sialic acid is a generic term for the N- or O-substituted derivatives of neuraminic acid, a monosaccharide with a nine-carbon backbone. It is the name for the most common member of this group, Sialic acids are found widely distributed in animal tissues and to a lesser extent in other organisms, ranging from plants and fungi to yeasts and bacteria, mostly in glycoproteins and gangliosides. That is because it seems to have appeared late in evolution, however, it has been observed in Drosophila embryos and other insects and in the capsular polysaccharides of certain strains of bacteria. In humans the brain has the highest sialic acid concentration, where these acids play an important role in neural transmission, in general, the amino group bears either an acetyl or a glycolyl group, but other modifications have been described. The hydroxyl substituents may vary considerably, lactyl, sulfate, the term sialic acid was first introduced by Swedish biochemist Gunnar Blix in 1952. The sialic acid family includes 43 derivatives of the nine-carbon sugar neuraminic acid, the numbering of the sialic acid structure begins at the carboxylate carbon and continues around the chain.
The configuration that places the carboxylate in the position is the alpha-anomer. The alpha-anomer is the form that is found when sialic acid is bound to glycans, however, in solution, it is mainly in the beta-anomeric form. Sialic acid is synthesized by glucosamine 6 phosphate and acetyl CoA through a transferase and this becomes N-acetylmannosamine-6-P through epimerization, which reacts with phosphoenolpyruvate producing N-acetylneuraminic-9-P. This compound is synthesized in the nucleus of the animal cell, in bacterial systems, sialic acids are biosynthesized by an aldolase enzyme. The enzyme uses a derivative as a substrate, inserting three carbons from pyruvate into the resulting sialic acid structure. These enzymes can be used for synthesis of sialic acid derivatives. Sialic acid-rich glycoproteins bind selectin in humans and other organisms, metastatic cancer cells often express a high density of sialic acid-rich glycoproteins. This overexpression of sialic acid on surfaces creates a charge on cell membranes.
This creates repulsion between cells and helps these late-stage cancer cells enter the blood stream, many bacteria use sialic acid in their biology, although this is usually limited to bacteria that live in association with higher animals. Many of these incorporate sialic acid into cell surface features like their lipopolysaccharide and capsule, other bacteria simply use sialic acid as a good nutrient source, as it contains both carbon and nitrogen and can be converted to fructose-6-phosphate, which can enter central metabolism. Sialic acid-rich oligosaccharides on the glycoconjugates found on surface membranes help keep water at the surface of cells, the sialic acid-rich regions contribute to creating a negative charge on the cells surfaces. Since water is a molecule with partial positive charges on both hydrogen atoms, it is attracted to cell surfaces and membranes
An antibody, known as an immunoglobulin, is a large, Y-shaped protein produced mainly by plasma cells that is used by the immune system to neutralize pathogens such as bacteria and viruses. The antibody recognizes a molecule of the harmful agent, called an antigen. Each tip of the Y of an antibody contains a paratope that is specific for one particular epitope on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can tag a microbe or a cell for attack by other parts of the immune system. Depending on the antigen, the binding may impede the process causing the disease or may activate macrophages to destroy the foreign substance. The ability of an antibody to communicate with the components of the immune system is mediated via its Fc region. The production of antibodies is the function of the humoral immune system. Antibodies are secreted by B cells of the immune system. In most cases, interaction of the B cell with a T helper cell is necessary to produce full activation of the B cell and, soluble antibodies are released into the blood and tissue fluids, as well as many secretions to continue to survey for invading microorganisms.
Antibodies are glycoproteins belonging to the immunoglobulin superfamily and they constitute most of the gamma globulin fraction of the blood proteins. They are typically made of basic structural units—each with two heavy chains and two small light chains. There are several different types of heavy chains that define the five different types of crystallisable fragments that may be attached to the antigen-binding fragments. The five different types of Fc regions allow antibodies to be grouped into five isotypes, each Fc region of a particular antibody isotype is able to bind to its specific Fc Receptor, thus allowing the antigen-antibody complex to mediate different roles depending on which FcR it binds. The ability of an antibody to bind to its corresponding FcR is further modulated by the structure of the present at conserved sites within its Fc region. The ability of antibodies to bind to FcRs helps to direct the immune response for each different type of foreign object they encounter. For example, IgE is responsible for an allergic response consisting of mast cell degranulation, igEs Fab paratope binds to allergic antigen, for example house dust mite particles, while its Fc region binds to Fc receptor ε.
The allergen-IgE-FcRε interaction mediates allergic signal transduction to induce conditions such as asthma and this region is known as the hypervariable region. Each of these variants can bind to a different antigen and this enormous diversity of antibody paratopes on the antigen-binding fragments allows the immune system to recognize an equally wide variety of antigens
The endoplasmic reticulum is a type of organelle in eukaryotic cells that forms an interconnected network of flattened, membrane-enclosed sacs or tube-like structures known as cisternae. The membranes of the ER are continuous with the nuclear membrane. The endoplasmic reticulum occurs in most types of cells, including Giardia. There are two types of endoplasmic reticulum and smooth, the outer face of the rough endoplasmic reticulum is studded with ribosomes that are the sites of protein synthesis. The rough endoplasmic reticulum is especially prominent in such as hepatocytes. The smooth endoplasmic reticulum lacks ribosomes and functions in lipid manufacture and metabolism, the production of steroid hormones, the smooth ER is especially abundant in mammalian liver and gonad cells. The lacy membranes of the endoplasmic reticulum were first seen in 1945 using electron microscopy, the lacy membranes of the endoplasmic reticulum were first seen in 1945 by Keith R. Porter, Albert Claude, Brody Meskers and Ernest F.
Fullam, using electron microscopy. The word reticulum, which network, was applied to describe this fabric of membranes. The general structure of the reticulum is a network of membranes called cisternae. These sac-like structures are held together by the cytoskeleton, the phospholipid membrane encloses the cisternal space, which is continuous with the perinuclear space but separate from the cytosol. The functions of the reticulum can be summarized as the synthesis and export of proteins and membrane lipids. The quantity of both rough and smooth endoplasmic reticulum in a cell can slowly interchange from one type to the other, transformation can include embedding of new proteins in membrane as well as structural changes. Changes in protein content may occur without noticeable structural changes, the surface of the rough endoplasmic reticulum is studded with protein-manufacturing ribosomes giving it a rough appearance. The binding site of the ribosome on the endoplasmic reticulum is the translocon.
However, the ribosomes are not a part of this organelles structure as they are constantly being bound. A ribosome only binds to the RER once a specific protein-nucleic acid complex forms in the cytosol and this special complex forms when a free ribosome begins translating the mRNA of a protein destined for the secretory pathway. The first 5-30 amino acids polymerized encode a signal peptide, a message that is recognized. Translation pauses and the complex binds to the RER translocon where translation continues with the nascent protein forming into the RER lumen and/or membrane
The Maillard reaction is a chemical reaction between amino acids and reducing sugars that gives browned food its distinctive flavor. Seared steaks, pan-fried dumplings and other kinds of biscuits, toasted marshmallows and it is named after French chemist Louis-Camille Maillard, who first described it in 1912 while attempting to reproduce biological protein synthesis. The reaction is a form of non-enzymatic browning which typically proceeds rapidly from around 140 to 165 °C, at higher temperatures and subsequently pyrolysis become more pronounced. This process is accelerated in an environment, as the amino groups are deprotonated and. The type of the acid determines the resulting flavor. This reaction is the basis for many of the flavoring industrys recipes, at high temperatures, a potential carcinogen called acrylamide can be formed. In the process, hundreds of different flavor compounds are created and these compounds, in turn, break down to form yet more new flavor compounds, and so on. Each type of food has a distinctive set of flavor compounds that are formed during the Maillard reaction.
It is these same compounds that flavor scientists have used over the years to make artificial flavors, in 1913 Maillard published a paper to explain what happens when amino acids react with sugars at elevated temperatures. However, it was chemist John E. Hodge, working at the U. S. Department of Agriculture in Peoria, who published a paper in 1953 that established a mechanism for the Maillard reaction. The structurally related compound 2-acetyl-1-pyrroline has a smell, and occurs naturally without heating and gives varieties of cooked rice. Both compounds have odor thresholds below 0.06 ng/l, caramelization is an entirely different process from Maillard browning, though the results of the two processes are sometimes similar to the naked eye. Caramelization may sometimes cause browning in the foods in which the Maillard reaction occurs. They both are promoted by heating, but the Maillard reaction involves amino acids, as discussed above, in making silage, excess heat causes the Maillard reaction to occur, which reduces the amount of energy and protein available to the animals who feed on it.
Dicarbonyls react with amine to produce Strecker aldehyde through Strecker degradation, the Maillard reaction occurs in the human body. It is a step in the formation of advanced glycation endproducts and it is tracked by measuring pentosidine. Although the Maillard reaction has been studied most extensively in foods, it has shown a correlation in numerous different diseases in the human body. In general, these diseases are due to the accumulation of AGEs on nucleic acids, though AGEs have numerous origins, they can form from the oxidation and dehydration of Amadori adducts, which themselves are products of nonenzymatic Maillard reactions
Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an acid are carbon, oxygen. About 500 amino acids are known and can be classified in many ways, in the form of proteins, amino acids comprise the second-largest component of human muscles and other tissues. Outside proteins, amino acids perform critical roles in such as neurotransmitter transport. In biochemistry, amino acids having both the amine and the acid groups attached to the first carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids and they include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins. These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as standard amino acids.
The other two are selenocysteine, and pyrrolysine and selenocysteine are encoded via variant codons, for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine is generally considered as a form of methionine rather than as a separate proteinogenic amino acid, codon–tRNA combinations not found in nature can be used to expand the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids play critical roles within the body. Nine proteinogenic amino acids are called essential for humans because they cannot be created from other compounds by the human body, others may be conditionally essential for certain ages or medical conditions. Essential amino acids may differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements and food technology. Industrial uses include the production of drugs, biodegradable plastics, the first few amino acids were discovered in the early 19th century.
In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, cystine was discovered in 1810, although its monomer, remained undiscovered until 1884. Glycine and leucine were discovered in 1820, usage of the term amino acid in the English language is from 1898. Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis, in the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as amino acids