1.
Protein (nutrient)
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Proteins are essential nutrients for the human body. They are one of the blocks of body tissue. As a fuel, proteins provide as much energy density as carbohydrates,4 kcal per gram, in contrast, the most important aspect and defining characteristic of protein from a nutritional standpoint is its amino acid composition. Proteins are polymer chains made of amino acids linked together by peptide bonds, during human digestion, proteins are broken down in the stomach to smaller polypeptide chains via hydrochloric acid and protease actions. This is crucial for the synthesis of the amino acids that cannot be biosynthesized by the body. There are nine amino acids which humans must obtain from their diet in order to prevent protein-energy malnutrition. They are phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine, there are five dispensable amino acids which humans are able to synthesize in the body. These five are alanine, aspartic acid, asparagine, glutamic acid and these six are arginine, cysteine, glycine, glutamine, proline and tyrosine. Humans need the essential amino acids in certain ratios, some protein sources contain amino acids in a more or less complete sense. This has given rise to various ranking systems for protein sources, Dietary sources of protein include both animals and plants, meats, dairy products, fish and eggs as well as grains, legumes and nuts. Vegetarians and vegans can get enough essential amino acids by eating a variety of plant proteins and it is commonly believed that athletes should consume a higher-than-normal protein intake to maintain optimal physical performance. Protein is a nutrient needed by the body for growth. 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 acid, co-enzymes, hormones, immune response, cellular repair. Additionally, protein is needed to form blood cells, proteins are believed to increase performance in terms of athletics. Amino acids, the blocks of proteins, are used for building muscle tissue. Protein is only used as fuel when carbohydrates are low
2.
Myoglobin
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Myoglobin is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals. It is related to hemoglobin, which is the iron- and oxygen-binding protein in blood, in humans, myoglobin is only found in the bloodstream after muscle injury. It is a finding, and can be diagnostically relevant when found in blood. Myoglobin is the primary oxygen-carrying pigment of muscle tissues, high concentrations of myoglobin in muscle cells allow organisms to hold their breath for a longer period of time. Diving mammals such as whales and seals have muscles with high abundance of myoglobin. Myoglobin is found in Type I muscle, Type II A and Type II B, myoglobin was the first protein to have its three-dimensional structure revealed by X-ray crystallography. This achievement was reported in 1958 by John Kendrew and associates, for this discovery, John Kendrew shared the 1962 Nobel Prize in chemistry with Max Perutz. They adapted to this deficiency through natural reactions to inadequate oxygen supply, in humans myoglobin is encoded by the MB gene. Hemoglobin can take the forms of oxyhemoglobin, carboxyhemoglobin, and methemoglobin, similarly, myoglobin can take the forms of oxymyoglobin, carboxymyoglobin, like hemoglobin, myoglobin is a cytoplasmic protein that binds oxygen on a heme group. It harbors only one group, whereas hemoglobin has four. Although its heme group is identical to those in Hb, Mb has an affinity for oxygen than does hemoglobin. This difference is related to its different role, whereas hemoglobin transports oxygen, myoglobin contains hemes, pigments responsible for the colour of red meat. The colour that meat takes is partly determined by the degree of oxidation of the myoglobin, in fresh meat the iron atom is the ferrous oxidation state bound to an oxygen molecule. Meat cooked well done is brown because the atom is now in the ferric oxidation state. If meat has been exposed to nitrites, it will remain pink because the atom is bound to NO. Grilled meats can also take on a smoke ring that comes from the iron binding to a molecule of carbon monoxide. Raw meat packed in a carbon monoxide atmosphere also shows this same pink smoke ring due to the same principles, notably, the surface of this raw meat also displays the pink color, which is usually associated in consumers minds with fresh meat. This artificially induced pink color can persist, reportedly up to one year, hormel and Cargill are both reported to use this meat-packing process, and meat treated this way has been in the consumer market since 2003
3.
Alpha helix
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This secondary structure is also sometimes called a classic Pauling–Corey–Branson α-helix. The name 3. 613-helix is also used for type of helix, denoting the average number of residues per helical turn. Among types of structure in proteins, the α-helix is the most regular. In the early 1930s, William Astbury showed that there were changes in the X-ray fiber diffraction of moist wool or hair fibers upon significant stretching. The data suggested that the unstretched fibers had a molecular structure with a characteristic repeat of ~5.1 ångströms. Astbury initially proposed a structure for the fibers. He later joined other researchers in proposing that, the protein molecules formed a helix the stretching caused the helix to uncoil. Hans Neurath was the first to show that Astburys models could not be correct in detail, neuraths paper and Astburys data inspired H. S. Taylor, Maurice Huggins and Bragg and collaborators to propose models of keratin that somewhat resemble the modern α-helix. The pivotal moment came in the spring of 1948, when Pauling caught a cold. Being bored, he drew a polypeptide chain of roughly correct dimensions on a strip of paper and folded it into a helix, after a few attempts, he produced a model with physically plausible hydrogen bonds. Pauling then worked with Corey and Branson to confirm his model before publication. The amino acids in an α-helix are arranged in a helical structure where each amino acid residue corresponds to a 100° turn in the helix. Dunitz describes how Paulings first article on the theme in fact shows a left-handed helix, short pieces of left-handed helix sometimes occur with a large content of achiral glycine amino acids, but are unfavorable for the other normal, biological L-amino acids. The pitch of the alpha-helix is 5.4 Å, which is the product of 1.5 and 3.6, the alpha-helices can be identified in protein structure using several computational methods, one of which being DSSP. Similar structures include the 310 helix and the π-helix, the subscripts refer to the number of atoms in the closed loop formed by the hydrogen bond. Residues in α-helices typically adopt backbone dihedral angles around, as shown in the image at right, in more general terms, they adopt dihedral angles such that the ψ dihedral angle of one residue and the φ dihedral angle of the next residue sum to roughly -105°. As a consequence, α-helical dihedral angles, in general, fall on a stripe on the Ramachandran diagram. For comparison, the sum of the angles for a 310 helix is roughly -75°
4.
X-ray crystallography
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By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the positions of the atoms in the crystal can be determined, as well as their chemical bonds, their disorder. The method also revealed the structure and function of biological molecules, including vitamins, drugs, proteins. X-ray crystallography is still the method for characterizing the atomic structure of new materials. In a single-crystal X-ray diffraction measurement, a crystal is mounted on a goniometer, the goniometer is used to position the crystal at selected orientations. The crystal is illuminated with a finely focused monochromatic beam of X-rays, poor resolution or even errors may result if the crystals are too small, or not uniform enough in their internal makeup. X-ray crystallography is related to other methods for determining atomic structures. Similar diffraction patterns can be produced by scattering electrons or neutrons, for all above mentioned X-ray diffraction methods, the scattering is elastic, the scattered X-rays have the same wavelength as the incoming X-ray. By contrast, inelastic X-ray scattering methods are useful in studying excitations of the sample, Crystals, though long admired for their regularity and symmetry, were not investigated scientifically until the 17th century. Johannes Kepler hypothesized in his work Strena seu de Nive Sexangula that the symmetry of snowflake crystals was due to a regular packing of spherical water particles. The Danish scientist Nicolas Steno pioneered experimental investigations of crystal symmetry, hence, William Hallowes Miller in 1839 was able to give each face a unique label of three small integers, the Miller indices which remain in use today for identifying crystal faces. In the 19th century, a catalog of the possible symmetries of a crystal was worked out by Johan Hessel, Auguste Bravais, Evgraf Fedorov, Arthur Schönflies. Wilhelm Röntgen discovered X-rays in 1895, just as the studies of crystal symmetry were being concluded, physicists were initially uncertain of the nature of X-rays, but soon suspected that they were waves of electromagnetic radiation, in other words, another form of light. Single-slit experiments in the laboratory of Arnold Sommerfeld suggested that X-rays had a wavelength of about 1 angstrom, however, X-rays are composed of photons, and thus are not only waves of electromagnetic radiation but also exhibit particle-like properties. Albert Einstein introduced the concept in 1905, but it was not broadly accepted until 1922. Therefore, these properties of X-rays, such as their ionization of gases. Nevertheless, Braggs view was not broadly accepted and the observation of X-ray diffraction by Max von Laue in 1912 confirmed for most scientists that X-rays were a form of electromagnetic radiation, Crystals are regular arrays of atoms, and X-rays can be considered waves of electromagnetic radiation. Atoms scatter X-ray waves, primarily through the atoms electrons and this phenomenon is known as elastic scattering, and the electron is known as the scatterer
5.
Cofactor (biochemistry)
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A cofactor is a non-protein chemical compound or metallic ion that is required for a proteins biological activity to happen. These proteins are enzymes, and cofactors can be considered helper molecules that assist in biochemical transformations. A coenzyme that is tightly or even covalently bound is termed a prosthetic group, the two subcategories under coenzyme are cosubstrates and prosthetic groups. Cosubstrates are transiently bound to the protein and will be released at some point, the prosthetic groups, on the other hand, are bound permanently to the protein. Both of them have the function, which is to facilitate the reaction of enzymes. Additionally, some sources also limit the use of the cofactor to inorganic substances. An inactive enzyme without the cofactor is called an apoenzyme, while the enzyme with cofactor is called a holoenzyme. Some enzymes or enzyme complexes require several cofactors, organic cofactors are often vitamins or made from vitamins. Many contain the nucleotide adenosine monophosphate as part of their structures, such as ATP, coenzyme A, FAD and this common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the AMP part of the molecule can be considered to be a kind of handle by which the enzyme can grasp the coenzyme to switch it between different catalytic centers. Cofactors can be divided into two groups, organic cofactors, such as flavin or heme, and inorganic cofactors, such as the metal ions Mg2+, Cu+, Mn2+. Organic cofactors are sometimes divided into coenzymes and prosthetic groups. The term coenzyme refers specifically to enzymes and, as such, on the other hand, prosthetic group emphasizes the nature of the binding of a cofactor to a protein and, thus, refers to a structural property. Different sources give different definitions of coenzymes, cofactors. It should be noted that terms are often used loosely. However, the author could not arrive at a single all-encompassing definition of a coenzyme, the study of these cofactors falls under the area of bioinorganic chemistry. In nutrition, the list of essential trace elements reflects their role as cofactors, in humans this list commonly includes iron, magnesium, manganese, cobalt, copper, zinc, and molybdenum. Although chromium deficiency causes impaired glucose tolerance, no human enzyme that uses this metal as a cofactor has been identified, iodine is also an essential trace element, but this element is used as part of the structure of thyroid hormones rather than as an enzyme cofactor
6.
Heme
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Not all porphyrins contain iron, but a substantial fraction of porphyrin-containing metalloproteins have heme as their prosthetic group, these are known as hemoproteins. Hemoproteins have diverse functions including the transportation of diatomic gases, chemical catalysis, diatomic gas detection. The heme iron serves as a source or sink of electrons during electron transfer or redox chemistry, in peroxidase reactions, the porphyrin molecule also serves as an electron source. In the transportation or detection of gases, the gas binds to the heme iron. During the detection of gases, the binding of the gas ligand to the heme iron induces conformational changes in the surrounding protein. Hemoproteins achieve their remarkable diversity by modifying the environment of the heme macrocycle within the protein matrix. For example, the ability of hemoglobin to effectively deliver oxygen to tissues is due to amino acid residues located near the heme molecule. Hemoglobin reversibly binds to oxygen in the lungs when the pH is high, when the situation is reversed, hemoglobin will release oxygen into the tissues. This phenomenon, which states that hemoglobins oxygen binding affinity is inversely proportional to both acidity and concentration of carbon dioxide, is known as the Bohr effect. There are several biologically important kinds of heme, The most common type is heme B, other important types include heme A, isolated hemes are commonly designated by capital letters while hemes bound to proteins are designated by lower case letters. Cytochrome a refers to the heme A in specific combination with membrane protein forming a portion of cytochrome c oxidase, the following carbon numbering system of porphyrins is an older numbering used by biochemists and not the 1–24 numbering system recommended by IUPAC which is shown in the table above. Heme l is the derivative of heme B which is attached to the protein of lactoperoxidase, eosinophil peroxidase. The addition of peroxide with the glutamyl-375 and aspartyl-225 of lactoperoxidase forms ester bonds between amino acid residues and the heme 1- and 5-methyl groups, respectively. Similar ester bonds with two methyl groups are thought to form in eosinophil and thyroid peroxidases. Heme l is one important characteristic of animal peroxidases, plant peroxidases incorporate heme B, lactoperoxidase and eosinophil peroxidase are protective enzymes responsible for the destruction of invading bacteria and virus. Thyroid peroxidase is the enzyme catalyzing the biosynthesis of the important thyroid hormones, because lactoperoxidase destroys invading organisms in the lungs and excrement, it is thought to be an important protective enzyme. Heme m is the derivative of heme B covalently bound at the site of myeloperoxidase. Heme m contains the two ester bonds at the heme 1- and 5-methyls as in heme l found in other mammalian peroxidases, myeloperoxidase is present in mammalian neutrophils and is responsible for the destruction of invading bacteria and viruse
7.
Biomolecule
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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 or they may be totally synthetic. Biology and its subsets of biochemistry and molecular biology study biomolecules, most biomolecules are organic compounds, and just four elements—oxygen, carbon, hydrogen, and nitrogen—make up 96% of the human bodys mass. But many other elements, such as the various biometals, are present in small amounts, examples of these include cytidine, uridine, adenosine, guanosine, thymidine and inosine. 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 C, G, A, modified bases are fairly common, as found in ribosomal RNA or transfer RNAs or for discriminating the new from old strands of DNA after replication. Each nucleotide is made of a nitrogenous base, a pentose. They contain carbon, nitrogen, oxygen, hydrogen and phosphorus and they serve as sources of chemical energy, participate in cellular signaling, and are incorporated into important cofactors of enzymatic reactions. DNA structure is dominated by the 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 or as A-form or Z-form helices, 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, examples are tRNA, ribosomes, ribozymes, and riboswitches. Monosaccharides are the simplest form of carbohydrates with only one simple sugar and they essentially contain an aldehyde or ketone group in their structure. The presence of an group in a monosaccharide is indicated by the prefix aldo-. Similarly, a group is denoted by the prefix keto-. Examples of monosaccharides are the hexoses glucose, fructose, and galactose and pentoses, ribose, most saccharides eventually provide fuel for cellular respiration. Disaccharides are formed when two monosaccharides, or two 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, examples of disaccharides include sucrose, maltose, and lactose
8.
Macromolecule
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A macromolecule is a very large molecule, such as protein, commonly created by polymerization of smaller subunits. They are typically composed of thousands of atoms or more, the most common macromolecules in biochemistry are biopolymers and large non-polymeric molecules. Synthetic macromolecules include common plastics and synthetic fibres as well as materials such as carbon nanotubes. The term macromolecule was coined by Nobel laureate Hermann Staudinger in the 1920s, usage of the term to describe large molecules varies among the disciplines. According to the standard IUPAC definition, the term macromolecule as used in science refers only to a single molecule. For example, a polymeric molecule is appropriately described as a macromolecule or polymer molecule rather than a polymer. Because of their size, macromolecules are not conveniently described in terms of stoichiometry alone, the structure of simple macromolecules, such as homopolymers, may be described in terms of the individual monomer subunit and total molecular mass. Complicated biomacromolecules, on the hand, require multi-faceted structural description such as the hierarchy of structures used to describe proteins. In British English. Macromolecules often have physical properties that do not occur for smaller molecules. For example, DNA in a solution can be simply by sucking the solution through an ordinary straw because the physical forces on the molecule can overcome the strength of its covalent bonds. The 1964 edition of Linus Paulings College Chemistry asserted that DNA in nature is never longer than about 5,000 base pairs and this error arose because biochemists were inadvertently breaking their samples into fragments. In fact, the DNA of chromosomes can be hundreds of millions of base pairs long, another common macromolecular property that does not characterize smaller molecules is their relative insolubility in water and similar solvents, instead forming colloids. Many require salts or particular ions to dissolve in water, similarly, many proteins will denature if the solute concentration of their solution is too high or too low. High concentrations of macromolecules in a solution can alter the rates and equilibrium constants of the reactions of other macromolecules and this comes from macromolecules excluding other molecules from a large part of the volume of the solution, thereby increasing the effective concentrations of these molecules. All living organisms are dependent on three essential biopolymers for their functions, DNA, RNA and Proteins. Each of these molecules is required for life since each plays a distinct, the simple summary is that DNA makes RNA, and then RNA makes proteins. DNA, RNA and proteins all consist of a structure of related building blocks. In general, they are all unbranched polymers, and so can be represented in the form of a string
9.
Amino acid
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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, hydrogen, 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, cells 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, 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 also 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 also 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 also differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, 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, cysteine, 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
10.
Residue (chemistry)
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In chemistry residue is whatever remains or acts as a contaminant after a given class of events. Residue may be the material remaining after a process of preparation, separation, or purification, such as distillation, evaporation and it may also denote the undesired by-products of a chemical reaction. Toxic chemical residues, wastes or contamination from other processes, are a concern in food safety, for example, the U. S. Food and Drug Administration and the Canadian Food Inspection Agency have guidelines for detecting chemical residues that are possibly dangerous to consume. Residue may refer to an atom or a group of atoms that forms part of a molecule, in biochemistry and molecular biology, a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid. One might say, This protein consists of 118 amino acid residues or The histidine residue is considered to be basic because it contains an imidazole ring. Note that a residue is different from a moiety, which, a residue might be one amino acid in a polypeptide or one monosaccharide in a starch molecule
11.
Organism
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In biology, an organism is any contiguous living system, such as an animal, plant, fungus, protist, archaeon, or bacterium. All known types of organisms are capable of some degree of response to stimuli, reproduction, growth and development and homeostasis. An organism consists of one or more cells, when it has one cell it is known as an organism. Most unicellular organisms are of microscopic scale and are thus described as microorganisms. Humans are multicellular organisms composed of trillions of cells grouped into specialized tissues. An organism may be either a prokaryote or a eukaryote, prokaryotes are represented by two separate domains—bacteria and archaea. Eukaryotic organisms are characterized by the presence of a cell nucleus. Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes, estimates on the number of Earths current species range from 10 million to 14 million, of which only about 1.2 million have been documented. More than 99% of all species, amounting to five billion species. In 2016, a set of 355 genes from the last universal ancestor of all living organisms living was identified. The term organism first appeared in the English language in 1703 and it is directly related to the term organization. There is a tradition of defining organisms as self-organizing beings. An organism may be defined as an assembly of molecules functioning as a more or less stable whole that exhibits the properties of life. Dictionary definitions can be broad, using such as any living structure, such as a plant, animal, fungus or bacterium, capable of growth. Many definitions exclude viruses and possible man-made non-organic life forms, as viruses are dependent on the machinery of a host cell for reproduction. A superorganism is an organism consisting of individuals working together as a single functional or social unit. There has been controversy about the best way to define the organism, several contributions are responses to the suggestion that the category of organism may well not be adequate in biology. Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction and this controversy is problematic because some cellular organisms are also incapable of independent survival and live as obligatory intracellular parasites
12.
Enzyme catalysis
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Enzyme catalysis is the increase in the rate of a chemical reaction by the active site of a protein. The protein catalyst may be part of a complex, and/or may transiently or permanently associate with a Cofactor. Catalysis of biochemical reactions in the cell is vital due to the very low rates of the uncatalysed reactions at room temperature and pressure. A key driver of protein evolution is the optimization of such catalytic activities via protein dynamics, the mechanism of enzyme catalysis is similar in principle to other types of chemical catalysis. By providing an alternative reaction route the enzyme reduces the required to reach the highest energy transition state of the reaction. The reduction of activation increases the amount of reactant molecules that achieve a sufficient level of energy, such that they reach the activation energy. As with other catalysts, the enzyme is not consumed during the reaction but is recycled such that a single enzyme performs many rounds of catalysis, the favored model for the enzyme-substrate interaction is the induced fit model. The advantages of the induced fit mechanism arise due to the effect of strong enzyme binding. There are two different mechanisms of substrate binding, uniform binding, which has strong binding, and differential binding. The stabilizing effect of uniform binding increases both substrate and transition state binding affinity, while differential binding increases only transition state binding affinity, both are used by enzymes and have been evolutionarily chosen to minimize the activation energy of the reaction. It is important to clarify, however, that the induced fit concept cannot be used to rationalize catalysis and that is, the chemical catalysis is defined as the reduction of Ea‡ relative to Ea‡ in the uncatalyzed reaction in water. The induced fit only suggests that the barrier is lower in the form of the enzyme. Induced fit may be beneficial to the fidelity of molecular recognition in the presence of competition, →→→editor These conformational changes also bring catalytic residues in the active site close to the chemical bonds in the substrate that will be altered in the reaction. After binding takes place, one or more mechanisms of catalysis lowers the energy of the transition state. This effect is analogous to an increase in concentration of the reagents. The binding of the reagents to the enzyme gives the reaction intramolecular character, however, the situation might be more complex, since modern computational studies have established that traditional examples of proximity effects cannot be related directly to enzyme entropic effects. Also, the original proposal has been found to largely overestimate the contribution of orientation entropy to catalysis. Histidine is often the residue involved in these reactions, since it has a pKa close to neutral pH
13.
DNA replication
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In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. This process occurs in all living organisms and is the basis for biological inheritance, DNA is made up of a double helix of two complementary strands. During replication, these strands are separated, each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication, in a cell, DNA replication begins at specific locations, or origins of replication, in the genome. Unwinding of DNA at the origin and synthesis of new results in replication forks growing bi-directionally from the origin. A number of proteins are associated with the fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each strand, DNA replication occurs during the S-stage of interphase. DNA replication can also be performed in vitro, DNA polymerases isolated from cells and artificial DNA primers can be used to initiate DNA synthesis at known sequences in a template DNA molecule. The polymerase chain reaction, a laboratory technique, cyclically applies such artificial synthesis to amplify a specific target DNA fragment from a pool of DNA. DNA usually exists as a structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotides, nucleotides in DNA contain a deoxyribose sugar, a phosphate, and a nucleobase. These nucleotides form phosphodiester bonds, creating the phosphate-deoxyribose backbone of the DNA double helix with the bases pointing inward. Nucleotides are matched between strands through hydrogen bonds to form base pairs, adenine pairs with thymine, and guanine pairs with cytosine. DNA strands have a directionality, and the different ends of a single strand are called the 3 end and the 5 end. By convention, if the sequence of a single strand of DNA is given. The strands of the helix are anti-parallel with one being 5 to 3. These terms refer to the atom in deoxyribose to which the next phosphate in the chain attaches. Directionality has consequences in DNA synthesis, because DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3 end of a DNA strand, the pairing of complementary bases in DNA means that the information contained within each strand is redundant
14.
Cell signaling
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Cell signaling is part of any communication process that governs basic activities of cells and coordinates all cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, errors in signaling interactions and cellular information processing are responsible for diseases such as cancer, autoimmunity, and diabetes. By understanding cell signaling, diseases may be treated effectively and, theoretically. Traditional work in biology has focused on studying individual parts of cell signaling pathways, systems biology research helps us to understand the underlying structure of cell signaling networks and how changes in these networks may affect the transmission and flow of information. Such networks are complex systems in their organization and may exhibit a number of emergent properties including bistability and ultrasensitivity, analysis of cell signaling networks requires a combination of experimental and theoretical approaches including the development and analysis of simulations and modeling. Long-range allostery is often a significant component of signaling events. Cell signaling has been most extensively studied in the context of human diseases, however, cell signaling may also occur between the cells of two different organisms. In many mammals, early embryo cells exchange signals with cells of the uterus, in the human gastrointestinal tract, bacteria exchange signals with each other and with human epithelial and immune system cells. For the yeast Saccharomyces cerevisiae during mating, some cells send a signal into their environment. The mating factor peptide may bind to a surface receptor on other yeast cells. Cell signaling can be classified to be mechanical and biochemical based on the type of the signal, mechanical signals are the forces exerted on the cell and the forces produced by the cell. These forces can both be sensed and responded by the cells, biochemical signals are the biochemical molecules such as proteins, lipids, ions and gases. These signals can be categorized based on the distance between signaling and responder cells, Signaling within, between, and amongst cells is subdivided into the following classifications, Intracrine signals are produced by the target cell that stay within the target cell. Autocrine signals are produced by the cell, are secreted. Sometimes autocrine cells can target cells close by if they are the type of cell as the emitting cell. An example of this are immune cells and these signals are transmitted along cell membranes via protein or lipid components integral to the membrane and are capable of affecting either the emitting cell or cells immediately adjacent. Paracrine signals target cells in the vicinity of the emitting cell, endocrine cells produce hormones that travel through the blood to reach all parts of the body. Cells communicate with each other via direct contact, over short distances, some cell–cell communication requires direct cell–cell contact
15.
Nucleic acid sequence
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A nucleic acid sequence is a succession of letters that indicate the order of nucleotides within a DNA or RNA molecule. By convention, sequences are presented from the 5 end to the 3 end. For DNA, the strand is used. Because nucleic acids are linear polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure, the sequence has capacity to represent information. Biological deoxyribonucleic acid represents the information which directs the functions of a living thing, nucleic acids also have a secondary structure and tertiary structure. Primary structure is sometimes referred to as primary sequence. Conversely, there is no concept of secondary or tertiary sequence. Nucleic acids consist of a chain of linked units called nucleotides, each nucleotide consists of three subunits, a phosphate group and a sugar make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set of nucleobases. The nucleobases are important in base pairing of strands to form secondary and tertiary structure such as the famed double helix. The possible letters are A, C, G, and T, in the typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, read left to right in the 5 to 3 direction. With regards to transcription, a sequence is on the strand if it has the same order as the transcribed RNA. One sequence can be complementary to sequence, meaning that they have the base on each position in the complementary. For example, the sequence to TTAC is GTAA. If one strand of the double-stranded DNA is considered the sense strand, then the other strand, considered the antisense strand, will have the complementary sequence to the sense strand. Apart from adenine, cytosine, guanine, thymine and uracil, in DNA, the most common modified base is 5-methylcytidine. In RNA, there are many modified bases, including pseudouridine, dihydrouridine, inosine, ribothymidine and 7-methylguanosine, hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination. Hypoxanthine is produced from adenine, xanthine from guanine, similarly, deamination of cytosine results in uracil
16.
Gene
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A gene is a locus of DNA which is made up of nucleotides and is the molecular unit of heredity. The transmission of genes to an offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes, genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions, genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotypical traits, usage of the term having a gene typically refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection or survival of the fittest of the alleles, the concept of a gene continues to be refined as new phenomena are discovered. For example, regulatory regions of a gene can be far removed from its coding regions, some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. The existence of discrete inheritable units was first suggested by Gregor Mendel, from 1857 to 1864, in Brno, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring. He described these mathematically as 2n combinations where n is the number of differing characteristics in the original peas, although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured the distinction between genotype and phenotype, charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan and genesis / genos. Darwin used the term gemmule to describe hypothetical particles that would mix during reproduction, de Vries called these units pangenes, after Darwins 1868 pangenesis theory. In 1909 the Danish botanist Wilhelm Johannsen shortened the name to gene, advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid was shown to be the repository of genetic information by experiments in the 1940s to 1950s. In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities, indivisible by recombination, collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, which is transcribed from DNA. This dogma has since shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics, in 1972, Walter Fiers and his team at the University of Ghent were the first to determine the sequence of a gene, the gene for Bacteriophage MS2 coat protein. The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing, an automated version of the Sanger method was used in early phases of the Human Genome Project. The theories developed in the 1930s and 1940s to integrate molecular genetics with Darwinian evolution are called the evolutionary synthesis
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Protein folding
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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 also 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, however, 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
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Protein structure
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Protein structure is the three-dimensional arrangement of atoms in a protein molecule. Proteins are polymers — specifically polypeptides — formed from sequences of amino acids, a single amino acid monomer may also be called a residue indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, to understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. Protein structures range in size from tens to several amino acids. By physical size, proteins are classified as nanoparticles, between 1–100 nm, very large aggregates can be formed from protein subunits. For example, many thousands of actin molecules assemble into a microfilament, a protein may undergo reversible structural changes in performing its biological function. The alternative structures of the protein are referred to as different conformational isomers, or simply, conformations. There are four levels of protein structure. Each α-amino acid consists of a backbone that is present in all the amino acid types, an exception from this rule is proline. Because the carbon atom is bound to four different groups it is chiral, glycine however, is not chiral since its side chain is a hydrogen atom. A simple mnemonic for correct L-form is CORN, when the Cα atom is viewed with the H in front, the primary structure of a protein refers to the linear sequence of amino acids in the polypeptide chain. The primary structure is held together by covalent bonds such as peptide bonds, the two ends of the polypeptide chain are referred to as the carboxyl terminus and the amino terminus based on the nature of the free group on each extremity. Counting of residues always starts at the N-terminal end, which is the end where the group is not involved in a peptide bond. The primary structure of a protein is determined by the corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, the sequence of amino acids in insulin was discovered by Frederick Sanger, establishing that proteins have defining amino acid sequences. The sequence of a protein is unique to that protein, and defines the structure, the sequence of a protein can be determined by methods such as Edman degradation or tandem mass spectrometry. Often, however, it is directly from the sequence of the gene using the genetic code
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Peptide
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Peptides are biologically occurring short chains of amino acid monomers linked by peptide bonds. The covalent chemical bonds are formed when the group of one amino acid reacts with the amine group of another. The shortest peptides are dipeptides, consisting of 2 amino acids joined by a peptide bond, followed by tripeptides, tetrapeptides. A polypeptide is a long, continuous, and unbranched peptide chain, hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides and polysaccharides, etc. Peptides are distinguished from proteins on the basis of size, all peptides except cyclic peptides have an N-terminal and C-terminal residue at the end of the peptide. Ribosomal peptides Ribosomal peptides are synthesized by translation of mRNA and they are often subjected to proteolysis to generate the mature form. These function, typically in higher organisms, as hormones and signaling molecules, some organisms produce peptides as antibiotics, such as microcins. Since they are translated, the amino acid residues involved are restricted to those utilized by the ribosome, however, these peptides frequently have posttranslational modifications such as phosphorylation, hydroxylation, sulfonation, palmitoylation, glycosylation and disulfide formation. In general, they are linear, although lariat structures have been observed, more exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom. Nonribosomal peptides Nonribosomal peptides are assembled by enzymes that are specific to each peptide, the most common non-ribosomal peptide is glutathione, which is a component of the antioxidant defenses of most aerobic organisms. Other nonribosomal peptides are most common in organisms, plants. These complexes are often out in a similar fashion. These peptides are often cyclic and can have highly complex cyclic structures, since the system is closely related to the machinery for building fatty acids and polyketides, hybrid compounds are often found. The presence of oxazoles or thiazoles often indicates that the compound was synthesized in this fashion, Peptones See also Tryptone Peptones are derived from animal milk or meat digested by proteolysis. In addition to containing small peptides, the material includes fats, metals, salts, vitamins. Peptones are used in nutrient media for growing bacteria and fungi, Peptide fragments Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein. Peptides received prominence in molecular biology for several reasons, the first is that peptides allow the creation of peptide antibodies in animals without the need of purifying the protein of interest. This involves synthesizing antigenic peptides of sections of the protein of interest and these will then be used to make antibodies in a rabbit or mouse against the protein
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Oligopeptide
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An oligopeptide, often just called peptide, consists of two to twenty amino acids and can include dipeptides, tripeptides, tetrapeptides, and pentapeptides. Microcystins are best studied, because of their potential toxicity impact in drinking water, a review of some oligopeptides found that the largest class are the cyanopeptolins, followed by microcystins. Oligopeptide classes are produced by nonribosomal peptides synthases, except cyclamides, examples of oligopeptides include, Amanitins - Cyclic peptides taken from carpophores of several different mushroom species. They are potent inhibitors of RNA polymerases in most eukaryotic species and these peptides are important in the study of transcription. Alpha-amanitin is the toxin from the species Amanita phalloides, poisonous if ingested by humans or animals. Antipain - An oligopeptide produced by bacteria which acts as a protease inhibitor. Ceruletide - A specific decapeptide found in the skin of Hyla caerulea, ceruletide has very much in common with regards to action and composition to cholecystokinin. It stimulates gastric, biliary, and pancreatic secretion, and certain smooth muscle and it is used to induce pancreatitis in experimental animal models. Glutathione - A tripeptide with many roles in cells and it conjugates to drugs to make them more soluble for excretion, is a cofactor for some enzymes, is involved in protein disulfide bond rearrangement and reduces peroxides. Leupeptins - A group of acylated oligopeptides produced by Actinomycetes that function as protease inhibitors and they have been known to inhibit to varying degrees trypsin, plasmin, kallikreins, papain and the cathepsins. Netropsin - A basic polypeptide isolated from Streptomyces netropsis and it is cytotoxic and its strong, specific binding to A-T areas of DNA is useful to genetics research. Pepstatins - N-acylated oligopeptides isolated from culture filtrates of Actinomycetes, which act specifically to inhibit acid proteases such as pepsin and renin, octapeptide sharing sequence homology with HIV envelope protein gp120. It may be useful as antiviral agent in AIDS therapy, the core pentapeptide sequence, TTNYT, consisting of amino acids 4-8 in peptide T, is the HIV envelope sequence required for attachment to the CD4 receptor. Phalloidin - A very toxic polypeptide isolated mainly from Amanita phalloides or death cap, causes fatal liver, kidney and CNS damage in mushroom poisoning, teprotide - A man made nonapeptide which is exactly the same as the peptide from the venom of the snake, Bothrops jararaca. It inhibits kininase II and ANGIOTENSIN I and has proposed as an antihypertensive agent. A tetrapeptide manufactured in the spleen by enzymatic cleavage of a leukophilic gamma-globulin and it stimulates the phagocytic activity of blood polymorphonuclear leukocytes and neutrophils in particular. The peptide is located in the Fd fragment of the gamma-globulin molecule, oligoester Oligomer Oligopeptidase Peptide synthesis Protease Structural Biochemistry/Proteins/Amino Acids
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Peptide bond
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A peptide bond is a covalent chemical bond linking two consecutive amino acid monomers along a peptide or protein chain. When two amino acids form a dipeptide through a peptide bond it is called condensation, in condensation, two amino acids approach each other, with the acid moiety of one coming near the amino moiety of the other. One loses a hydrogen and oxygen from its group and the other loses a hydrogen from its amino group. This reaction produces a molecule of water and two amino acids joined by a peptide bond, the two joined amino acids are called a dipeptide. The formation of the peptide bond consumes energy, which, in living systems, is derived from ATP, polypeptides and proteins are chains of amino acids held together by peptide bonds. Living organisms employ enzymes to produce polypeptides, and ribosomes to produce proteins, peptides are synthesized by specific enzymes. For example, the tripeptide glutathione is synthesized in two steps from free amino acids, by two enzymes, gamma-glutamylcysteine synthetase and glutathione synthetase, a peptide bond can be broken by hydrolysis. In the presence of water they will break down and release 8–16 kilojoule/mol of free energy, in living organisms, the process is catalyzed by enzymes known as peptidases or proteases. The wavelength of absorption for a bond is 190–230 nm. Significant delocalisation of the pair of electrons on the nitrogen atom gives the group a partial double bond character. The partial double bond renders the amide group planar, occurring in either the cis or trans isomers. In the unfolded state of proteins, the groups are free to isomerize. The trans form is preferred overwhelmingly in most peptide bonds, however, X-Pro peptide groups tend to have a roughly 3,1 ratio, presumably because the symmetry between the C α and C δ atoms of proline makes the cis and trans isomers nearly equal in energy. The dihedral angle associated with the group is denoted ω, ω =0 ∘ for the cis isomer. Amide groups can isomerize about the C-N bond between the cis and trans forms, albeit slowly, the transition states ω = ±90 ∘ requires that the partial double bond be broken, so that the activation energy is roughly 80 kilojoule/mol. Conformational protein folding is much faster than cis-trans isomerization. A nonnative isomer of some groups can disrupt the conformational folding significantly. However, not all groups have the same effect on folding
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Protein primary structure
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Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the structure of a protein is reported starting from the amino-terminal end to the carboxyl-terminal end. Protein biosynthesis is most commonly performed by ribosomes in cells, peptides can also be synthesised in the laboratory. Protein primary structures can be sequenced, or inferred from DNA sequences. Amino acids are polymerised via peptide bonds to form a long backbone, in biological systems, proteins are produced during translation by a cells ribosomes. Some organisms can also make short peptides by non-ribosomal peptide synthesis, which often use amino acids other than the standard 20, peptides can be synthesised chemically via a range of laboratory methods. Chemical methods typically synthesise peptides in the order to biological protein synthesis. Protein sequence is typically notated as a string of letters, listing the amino acids starting at the end through to the carboxyl-terminal end. Either a three letter code or single letter code can be used to represent the 20 naturally occurring amino acids, peptides can be directly sequenced, or inferred from DNA sequences. Large sequence databases now exist that collate known protein sequences, in general, polypeptides are unbranched polymers, so their primary structure can often be specified by the sequence of amino acids along their backbone. The chiral centers of a chain can undergo racemization. Although it does not change the sequence, it affect the chemical properties of the sequence. In particular, the L-amino acids normally found in proteins can spontaneously isomerize at the C α atom to form D-amino acids, additionally, proline can form stable trans-isomers at the peptide bond. Finally, the protein can undergo a variety of posttranslational modifications, formylation − C H The N-terminal methionine usually found after translation has an N-terminus blocked with a formyl group. This formyl group is removed by the enzyme deformylase, pyroglutamate An N-terminal glutamine can attack itself, forming a cyclic pyroglutamate group. Myristoylation − C −12 − C H3 Similar to acetylation, instead of a simple methyl group, the myristoyl group has a tail of 14 hydrophobic carbons, which make it ideal for anchoring proteins to cellular membranes. The C-terminal carboxylate group of a polypeptide can also be modified, Glycosyl phosphatidylinositol attachment Glycosyl phosphatidylinositol is a large, hydrophobic phospholipid prosthetic group that achors proteins to cellular membranes. It is attached to the polypeptide C-terminus through a linkage that then connects to ethanolamine, thence to sundry sugars
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Genetic code
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The genetic code is the set of rules by which information encoded within genetic material is translated into proteins by living cells. Translation is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA molecules to carry amino acids, the genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The code defines how sequences of nucleotide triplets, called codons, with some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme and that scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes exist. While the genetic code determines a proteins amino acid sequence, other genomic regions determine when, efforts to understand how proteins are encoded began after DNAs structure was discovered in 1953. George Gamow postulated that sets of three bases must be employed to encode the 20 standard amino acids used by living cells to build proteins, the Crick, Brenner et al. experiment first demonstrated that codons consist of three DNA bases. Marshall Nirenberg and Heinrich J. Matthaei were the first to reveal the nature of a codon in 1961 and they used a cell-free system to translate a poly-uracil RNA sequence and discovered that the polypeptide that they had synthesized consisted of only the amino acid phenylalanine. They thereby deduced that the codon UUU specified the amino acid phenylalanine, therefore, the codon AAA specified the amino acid lysine, and the codon CCC specified the amino acid proline. Using various copolymers most of the remaining codons were then determined, subsequent work by Har Gobind Khorana identified the rest of the genetic code. Shortly thereafter, Robert W. Holley determined the structure of transfer RNA and this work was based upon Ochoas earlier studies, yielding the latter the Nobel Prize in Physiology or Medicine in 1959 for work on the enzymology of RNA synthesis. Extending this work, Nirenberg and Philip Leder revealed the triplet nature. In these experiments, various combinations of mRNA were passed through a filter that contained ribosomes, unique triplets promoted the binding of specific tRNAs to the ribosome. Leder and Nirenberg were able to determine the sequences of 54 out of 64 codons in their experiments, Khorana, Holley and Nirenberg received the 1968 Nobel for their work. The three stop codons were named by discoverers Richard Epstein and Charles Steinberg, amber was named after their friend Harris Bernstein, whose last name means amber in German. The other two stop codons were named ochre and opal in order to keep the color names theme, H. Murakami and M. Sisido extended some codons to have four and five bases. Steven A. Benner constructed a functional 65th codon, in 2016 the first stable semisynthetic organism was created. It was a bacterium with two synthetic bases, in 2017 a mouse engineered with an extended genetic code that can produce proteins with unnatural amino acids was reported. A codon is defined by the initial nucleotide from which starts and sets the frame for a run of successive triplets
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Selenocysteine
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Selenocysteine is the 21st proteinogenic amino acid. Selenocysteine exists naturally in three domains of life, but not in lineage, as a building block of selenoproteins. Selenocysteine is an analogue with a selenium-containing selenol group in place of the sulfur-containing thiol group. Selenocysteine is present in several enzymes, Selenocysteine was discovered by biochemist Thressa Stadtman at the National Institutes of Health. Selenocysteine has a similar to that of cysteine, but with an atom of selenium taking the place of the usual sulfur. Proteins that contain one or more residues are called selenoproteins. Most selenoproteins contain a single Sec residue, selenoproteins with catalytic activities which depend on selenocysteines biochemical activity are called selenoenzymes. The structurally characterized selenoenzymes have been found to employ catalytic triad structures that influence the nucleophilicity of the active site selenocysteine, Selenocysteine has both a lower pKa and a lower reduction potential than cysteine. These properties make it suitable in proteins that are involved in antioxidant activity. Although it is found in the three domains of life, it is not universal in all organisms, unlike other amino acids present in biological proteins, selenocysteine is not coded for directly in the genetic code. Instead, it is encoded in a way by a UGA codon. Such a mechanism is called translational recoding and its efficiency depends on the selenoprotein being synthesized, when cells are grown in the absence of selenium, translation of selenoproteins terminates at the UGA codon, resulting in a truncated, nonfunctional enzyme. The UGA codon is made to encode selenocysteine by the presence of an insertion sequence in the mRNA. The SECIS element is defined by nucleotide sequences and secondary structure base-pairing patterns. In bacteria, the SECIS element is located immediately following the UGA codon within the reading frame for the selenoprotein. In Archaea and in eukaryotes, the SECIS element is in the 3 untranslated region of the mRNA, again unlike the other amino acids, no free pool of selenocysteine exists in the cell. Its high reactivity would cause damage to cells, instead, cells store selenium in the less reactive selenide form. Selenocysteine synthesis occurs on a specialized tRNA, which functions to incorporate it into nascent polypeptides
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Archaea
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The Archaea constitute a domain and kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells, Archaea were initially classified as bacteria, receiving the name archaebacteria, but this classification is outdated. Archaeal cells have unique properties separating them from the two domains of life, Bacteria and Eukaryota. The Archaea are further divided into multiple recognized phyla, classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment. Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat, other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more energy sources than eukaryotes, these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea use sunlight as a source, and other species of archaea fix carbon, however, unlike plants and cyanobacteria. Archaea reproduce asexually by fission, fragmentation, or budding, unlike bacteria and eukaryotes. They are also found in the colon, oral cavity. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet, Archaea are a major part of Earths life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, one example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures. For much of the 20th century, prokaryotes were regarded as a group of organisms and classified based on their biochemistry, morphology. For example, microbiologists tried to classify based on the structures of their cell walls, their shapes. In 1965, Emile Zuckerkandl and Linus Pauling proposed instead using the sequences of the genes in different prokaryotes to work out how they are related to each other and this approach, known as phylogenetics, is the main method used today. Archaea were first classified as a group of prokaryotes in 1977 by Carl Woese. These two groups were named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese. Woese argued that group of prokaryotes is a fundamentally different sort of life
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Pyrrolysine
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Pyrrolysine is an ɑ-amino acid that is used in the biosynthesis of proteins in some methanogenic archaea and bacterium, it is not present in humans. It contains a group, a carboxylic acid group. Its pyrroline side-chain is similar to that of lysine in being basic, nearly all proteins are made using only 20 standard amino acid building blocks. Two unusual genetically-encoded amino acids are selenocysteine and pyrrolysine, pyrrolysine was discovered in 2002 at the active site of methyl-transferase enzyme from a methane-producing archeon, Methanosarcina barkeri. This amino acid is encoded by UAG, and its synthesis, as determined by X-ray crystallography and MALDI mass spectrometry, pyrrolysine is made up of 4-methylpyrroline-5-carboxylate in amide linkage with the ϵN of lysine. Pyrrolysine is synthesized in vivo by joining two molecules of L-lysine, one molecule of lysine is first converted to -3-methyl-D-ornithine, which is then ligated to a second lysine. An NH2 group is eliminated, followed by cyclization and dehydration step to yield L-pyrrolysine, the extra pyrroline ring is incorporated into the active site of several methyltransferases, where it is believed to rotate relatively freely. It is believed that the ring is involved in positioning and displaying the group of methylamine for attack by a corrinoid cofactor. In this way a net CH+3 is transferred to the cobalt atom with a change of oxidation state from I to III. The methylamine-derived ammonia is released, restoring the original imine. It is encoded in mRNA by the UAG codon, which in most organisms is the stop codon. The pylT and pylS genes are part of an operon of Methanosarcina barkeri, with homologues in other sequenced members of the Methanosarcinaceae family, M. acetivorans, M. mazei, pyrrolysine-containing genes are known to include monomethylamine methyltransferase, dimethylamine methyltransferase, and trimethylamine methyltransferase. Homologs of pylS and pylT have also found in an Antarctic archaeon, Methanosarcina barkeri. The occurrence in Desulfitobacterium is of special interest, because bacteria, when use of the amino acid appeared confined to the Methanosarcinaceae, the system was described as a late archaeal invention by which a 21st amino acid was added to the genetic code. Afterward it was concluded that PylRS was already present in the last universal common ancestor some 3 billion years ago, another possibility is that evolution of the system involved a horizontal gene transfer between unrelated microorganisms. The other genes of the Pyl operon mediate pyrrolysine biosynthesis, leading to description of the operon as a genetic code expansion cassette. Some differences exist between the bacterial and archaeal systems studied, homology to pylS is broken into two separate proteins in D. hafniense. Most notably, the UAG codon appears to act as a stop codon in many of that organisms proteins, by contrast, in methanogenic archaea it was not possible to identify any unambiguous UAG stop signal
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Post-translational modification
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Post-translational modification refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the protein product. PTMs are important components in cell signaling, post-translational modifications can occur on the amino acid side chains or at the proteins C- or N- termini. They can extend the chemical repertoire of the 20 standard amino acids by modifying an existing functional group or introducing a new one such as phosphate, phosphorylation is a very common mechanism for regulating the activity of enzymes and is the most common post-translational modification. Attachment of lipid molecules, known as lipidation, often targets a protein or part of an attached to the cell membrane. Other forms of post-translational modification consist of cleaving peptide bonds, as in processing a propeptide to a form or removing the initiator methionine residue. The formation of bonds from cysteine residues may also be referred to as a post-translational modification. Some types of modification are consequences of oxidative stress. Carbonylation is one example that targets the modified protein for degradation, specific amino acid modifications can be used as biomarkers indicating oxidative damage. In addition, although the amide of asparagine is a weak nucleophile, rarer modifications can occur at oxidized methionines and at some methylenes in side chains. Post-translational modification of proteins can be detected by a variety of techniques, including mass spectrometry, Eastern blotting. O-acylation, N-acylation, S-acylation acetylation, the addition of an acetyl group, formylation alkylation, the addition of an alkyl group, e. g. methyl, ethyl methylation the addition of a methyl group, usually at lysine or arginine residues. Formed by oxidative dissociation of a C-terminal Gly residue, amide bond formation amino acid addition arginylation, a tRNA-mediation addition polyglutamylation, covalent linkage of glutamic acid residues to the N-terminus of tubulin and some other proteins. Distinct from glycation, which is regarded as an attachment of sugars. Glycation, the addition of a molecule to a protein without the controlling action of an enzyme. Carbamylation the addition of Isocyanic acid to a proteins N-terminus or the side-chain of Lys. carbonylation the addition of carbon monoxide to other organic/inorganic compounds, biotinylation, covalent attachment of a biotin moiety using a biotinylation reagent, typically for the purpose of labeling a protein. Carbamylation, the addition of Isocyanic acid to a proteins N-terminus or the side-chain of Lys or Cys residues, oxidation, addition of one or more Oxygen atoms to a susceptible side-chain, principally of Met, Trp, His or Cys residues. Formation of disulfide bonds between Cys residues, pegylation, covalent attachment of polyethylene glycol using a pegylation reagent, typically to the N-terminus or the side-chains of Lys residues
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Protein complex
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A multiprotein complex is a group of two or more associated polypeptide chains. The different polypeptide chains may have different functions and this is distinct from a multienzyme polypeptide, in which multiple catalytic domains are found in a single polypeptide chain. Protein complexes are a form of quaternary structure, proteins in a protein complex are linked by non-covalent protein–protein interactions, and different protein complexes have different degrees of stability over time. These complexes are a cornerstone of many biological processes and together they form various types of machinery that perform a vast array of biological functions. Increasingly, scientists view the cell as composed of modular supramolecular complexes, each of which performs an independent, through proximity, the speed and selectivity of binding interactions between enzymatic complex and substrates can be vastly improved, leading to higher cellular efficiency. Examples of protein complexes include the proteasome for degradation and most RNA polymerases. In stable complexes, large hydrophobic interfaces between proteins typically bury surface areas larger than 2500 square angstroms, Protein complex formation sometimes serves to activate or inhibit one or more of the complex members and in this way, protein complex formation can be similar to phosphorylation. Individual proteins can participate in the formation of a variety of different protein complexes, different complexes perform different functions, and the same complex can perform very different functions that depend on a variety of factors. For this relatively simple organism, the study of protein complexes is now being performed genome wide, if a protein can form stable crystal structure of its own in vivo, then the complexes formed by such proteins are called non-obligate protein complex. On the other hand, some cant be found to create a crystal structure alone. Such protein complexes are called obligate protein complex, transient protein complexes form and break down transiently in vivo, whereas permanent complexes have a relatively long half-life. Typically, the interactions are permanent, whereas non-obligate interactions have been found to be either permanent or transient. Fuzzy protein complexes have more than one form or dynamic structural disorder in the bound state. This means that proteins may not fold completely in either transient or permanent complexes, consequently, specific complexes can have ambiguous interactions, which vary according to the environmental signals. Hence different ensemble of structures result in different biological functions, post-translational modifications, protein interactions or alternative splicing modulate the conformational ensembles of fuzzy complexes, to fine-tune affinity or specificity of interactions. These mechanisms are used for regulation within the eukaryotic transcription machinery. However, the correlation is robust for networks of stable cocomplex interactions, in fact, a disproportionate number of essential genes belong to protein complexes. This led to the conclusion that essentiality is a property of molecular machines rather than individual components, wang et al. noted that larger protein complexes are more likely to be essential, explaining why essential genes are more likely to have high cocomplex interaction degree
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Proteolysis
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Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years, proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion. Low pH or high temperatures can also cause proteolysis non-enzymatically and it is also important in the regulation of some physiological and cellular processes, as well as preventing the accumulation of unwanted or abnormal proteins in cells. Consequently, dis-regulation of proteolysis can cause diseases and is used in some venoms to damage their prey, proteolysis is important as an analytical tool for studying proteins in the laboratory, as well as industrially, for example in food processing and stain removal. Limited proteolysis of a polypeptide during or after translation in protein synthesis often occurs for many proteins and this may involve removal of the N-terminal methionine, signal peptide, and/or the conversion of an inactive or non-functional protein to an active one. The precursor to the functional form of protein is termed proprotein. For example, albumin is first synthesized as preproalbumin and contains a signal peptide. This forms the proalbumin after the signal peptide is cleaved, the initiating methionine may be removed during translation of the nascent protein. For E. coli, fMet is efficiently removed if the second residue is small and uncharged, in both prokaryotes and eukaryotes, the exposed N-terminal residue may determine the half-life of the protein according to the N-end rule. Proteins that are to be targeted to a particular organelle or for secretion have an N-terminal signal peptide directs the protein to its final destination. This signal peptide is removed by proteolysis after their transport through a membrane, the polyprotein pro-opiomelanocortin contains many polypeptide hormones. The cleavage pattern of POMC, however, may vary between different tissues, yielding different sets of polypeptide hormones from the same polyprotein, many viruses also produce their proteins initially as a single polypeptide chain that were translated from a polycistronic mRNA. This polypeptide is subsequently cleaved into individual polypeptide chains, many proteins and hormones are synthesized in the form of their precursors - zymogens, proenzymes, and prehormones. These proteins are cleaved to form their final active structures, insulin, for example, is synthesized as preproinsulin, which yields proinsulin after the signal peptide has been cleaved. The proinsulin is then cleaved at two positions to yield two polypeptide chains linked by two disulfide bonds, removal of two C-terminal residues from the B-chain then yields the mature insulin. Proteases in particular are synthesized in the form so that they may be safely stored in cells. This is to ensure that the protease is activated only in the location or context. Proteolysis can, therefore, be a method of regulating biological processes by turning inactive proteins into active ones, a good example is the blood clotting cascade whereby an initial event triggers a cascade of sequential proteolytic activation of many specific proteases, resulting in blood coagulation
30.
Half-life
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Half-life is the time required for a quantity to reduce to half its initial value. The term is used in nuclear physics to describe how quickly unstable atoms undergo. The term is used more generally to characterize any type of exponential or non-exponential decay. For example, the medical sciences refer to the biological half-life of drugs, the converse of half-life is doubling time. The original term, half-life period, dating to Ernest Rutherfords discovery of the principle in 1907, was shortened to half-life in the early 1950s. Rutherford applied the principle of a radioactive elements half-life to studies of age determination of rocks by measuring the period of radium to lead-206. Half-life is constant over the lifetime of an exponentially decaying quantity, the accompanying table shows the reduction of a quantity as a function of the number of half-lives elapsed. A half-life usually describes the decay of discrete entities, such as radioactive atoms, in that case, it does not work to use the definition that states half-life is the time required for exactly half of the entities to decay. For example, if there are 3 radioactive atoms with a half-life of one second, instead, the half-life is defined in terms of probability, Half-life is the time required for exactly half of the entities to decay on average. In other words, the probability of a radioactive atom decaying within its half-life is 50%, for example, the image on the right is a simulation of many identical atoms undergoing radioactive decay. Note that after one half-life there are not exactly one-half of the remaining, only approximately. Nevertheless, when there are many identical atoms decaying, the law of large numbers suggests that it is a good approximation to say that half of the atoms remain after one half-life. There are various simple exercises that demonstrate probabilistic decay, for example involving flipping coins or running a computer program. The three parameters t1⁄2, τ, and λ are all related in the following way. Amount approaches zero as t approaches infinity as expected, some quantities decay by two exponential-decay processes simultaneously. There is a half-life describing any exponential-decay process, for example, The current flowing through an RC circuit or RL circuit decays with a half-life of RCln or lnL/R, respectively. For this example, the half time might be used instead of half life. In a first-order chemical reaction, the half-life of the reactant is ln/λ, in radioactive decay, the half-life is the length of time after which there is a 50% chance that an atom will have undergone nuclear decay
31.
Polysaccharide
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They range in structure from linear to highly branched. Examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose, polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure, these macromolecules can have distinct properties from their building blocks. They may be amorphous or even insoluble in water, natural saccharides are generally of simple carbohydrates called monosaccharides with general formula n where n is three or more. Examples of monosaccharides are glucose, fructose, and glyceraldehyde, polysaccharides, meanwhile, have a general formula of Cxy where x is usually a large number between 200 and 2500. When the repeating units in the backbone are six-carbon monosaccharides, as is often the case, the general formula simplifies to n. Polysaccharides are an important class of biological polymers and their function in living organisms is usually either structure- or storage-related. Starch is used as a polysaccharide in plants, being found in the form of both amylose and the branched amylopectin. In animals, the structurally similar glucose polymer is the more densely branched glycogen, glycogens properties allow it to be metabolized more quickly, which suits the active lives of moving animals. Cellulose and chitin are examples of structural polysaccharides, cellulose is used in the cell walls of plants and other organisms, and is said to be the most abundant organic molecule on Earth. It has many such as a significant role in the paper and textile industries, and is used as a feedstock for the production of rayon, cellulose acetate, celluloid. Chitin has a structure, but has nitrogen-containing side branches. It is found in arthropod exoskeletons and in the walls of some fungi. It also has multiple uses, including surgical threads, polysaccharides also include callose or laminarin, chrysolaminarin, xylan, arabinoxylan, mannan, fucoidan and galactomannan. Nutrition polysaccharides are common sources of energy, many organisms can easily break down starches into glucose, however, most organisms cannot metabolize cellulose or other polysaccharides like chitin and arabinoxylans. These carbohydrate types can be metabolized by bacteria and protists. Ruminants and termites, for example, use microorganisms to process cellulose, even though these complex carbohydrates are not very digestible, they provide important dietary elements for humans. Called dietary fiber, these carbohydrates enhance digestion among other benefits, the main action of dietary fiber is to change the nature of the contents of the gastrointestinal tract, and to change how other nutrients and chemicals are absorbed
32.
Nucleic acid
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Nucleic acids are biopolymers, or large biomolecules, essential to all known forms of life. They are composed of monomers, which are made of three components, a 5-carbon sugar, a phosphate group, and a nitrogenous base. If the sugar is a simple ribose, the polymer is RNA, if the sugar is derived from ribose as deoxyribose, Nucleic acids are arguably the most important of all biomolecules. They are found in abundance in all living things, where they function to create and encode, the encoded information is contained and conveyed via the nucleic acid sequence, which provides the ladder-step ordering of nucleotides within the molecules of RNA and DNA. Using amino acids and the known as protein synthesis, the specific sequencing in DNA of these nucleobase-pairs enables storing and transmitting coded instructions as genes. In RNA, base-pair sequencing provides for manufacturing new proteins that determine the frames and parts, Nucleic acids were discovered by Friedrich Miescher in 1869. In 1889 Richard Altmann discovered that nuclein has acidic properties, and it became called nucleic acid In 1938 Astbury, in 1953 Watson and Crick determined the structure of DNA. The term nucleic acid is the name for DNA and RNA, members of a family of biopolymers. Nucleic acids were named for their initial discovery within the nucleus, all living cells contain both DNA and RNA, while viruses contain either DNA or RNA, but usually not both. The basic component of nucleic acids is the nucleotide, each of which contains a pentose sugar, a phosphate group. Nucleic acids are generated within the laboratory, through the use of enzymes. The chemical methods also enable the generation of altered nucleic acids that are not found in nature, Nucleic acids are generally very large molecules. Indeed, DNA molecules are probably the largest individual molecules known, well-studied biological nucleic acid molecules range in size from 21 nucleotides to large chromosomes. In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded, Nucleic acids are linear polymers of nucleotides. Each nucleotide consists of three components, a purine or pyrimidine nucleobase, a sugar, and a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside, Nucleic acid types differ in the structure of the sugar in their nucleotides–DNA contains 2-deoxyribose while RNA contains ribose. Also, the found in the two nucleic acid types are different, adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids are connected to other in an alternating chain through phosphodiester linkages
33.
Cell (biology)
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The cell is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life that can replicate independently, the study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many such as proteins. Organisms can be classified as unicellular or multicellular, while the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion cells. Most plant and animal cells are only under a microscope. The cell was discovered by Robert Hooke in 1665, who named the unit for its resemblance to cells inhabited by Christian monks in a monastery. Cells emerged on Earth at least 3.5 billion years ago, Cells are of two types, eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular, prokaryotic cells were the first form of life on Earth, characterised by having vital biological processes including cell signaling and being self-sustaining. They are simpler and smaller than eukaryotic cells, and lack membrane-bound organelles such as the nucleus, prokaryotes include two of the domains of life, bacteria and archaea. The DNA of a prokaryotic cell consists of a chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid, most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 µm in diameter. Though most prokaryotes have both a cell membrane and a wall, there are exceptions such as Mycoplasma and Thermoplasma which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, the cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting from osmotic pressure due to a hypotonic environment, some eukaryotic cells also have a cell wall. Inside the cell is the region that contains the genome, ribosomes. The genetic material is found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular, linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a nucleoid, plasmids encode additional genes, such as antibiotic resistance genes
34.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
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Catalysis
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Catalysis is the increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst. In most cases, reactions occur faster with a catalyst because they require less activation energy, furthermore, since they are not consumed in the catalyzed reaction, catalysts can continue to act repeatedly. Often only tiny amounts are required in principle, in the presence of a catalyst, less free energy is required to reach the transition state, but the total free energy from reactants to products does not change. A catalyst may participate in multiple chemical transformations, the effect of a catalyst may vary due to the presence of other substances known as inhibitors or poisons or promoters. Catalyzed reactions have an activation energy than the corresponding uncatalyzed reaction, resulting in a higher reaction rate at the same temperature. However, the mechanics of catalysis is complex. Usually, the catalyst participates in this slowest step, and rates are limited by amount of catalyst, in heterogeneous catalysis, the diffusion of reagents to the surface and diffusion of products from the surface can be rate determining. A nanomaterial-based catalyst is an example of a heterogeneous catalyst, analogous events associated with substrate binding and product dissociation apply to homogeneous catalysts. Although catalysts are not consumed by the reaction itself, they may be inhibited, deactivated, in heterogeneous catalysis, typical secondary processes include coking where the catalyst becomes covered by polymeric side products. Additionally, heterogeneous catalysts can dissolve into the solution in a system or sublimate in a solid–gas system. The production of most industrially important chemicals involves catalysis, similarly, most biochemically significant processes are catalysed. Research into catalysis is a field in applied science and involves many areas of chemistry, notably organometallic chemistry. Catalysis is relevant to aspects of environmental science, e. g. the catalytic converter in automobiles. Many transition metals and transition metal complexes are used in catalysis as well, Catalysts called enzymes are important in biology. A catalyst works by providing a reaction pathway to the reaction product. The rate of the reaction is increased as this route has a lower activation energy than the reaction route not mediated by the catalyst. The disproportionation of hydrogen peroxide creates water and oxygen, as shown below,2 H2O2 →2 H2O + O2 This reaction is preferable in the sense that the reaction products are more stable than the starting material, though the uncatalysed reaction is slow. In fact, the decomposition of hydrogen peroxide is so slow that hydrogen peroxide solutions are commercially available and this reaction is strongly affected by catalysts such as manganese dioxide, or the enzyme peroxidase in organisms
36.
Metabolism
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Metabolism is the set of life-sustaining chemical transformations within the cells of living organisms. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, usually, breaking down releases energy and building up consumes energy. The chemical reactions of metabolism are organized into metabolic pathways, in one chemical is transformed through a series of steps into another chemical. Enzymes act as catalysts that allow the reactions to proceed more rapidly, enzymes also allow the regulation of metabolic pathways in response to changes in the cells environment or to signals from other cells. The metabolic system of a particular organism determines which substances it will find nutritious, for example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The speed of metabolism, the rate, influences how much food an organism will require. A striking feature of metabolism is the similarity of the metabolic pathways. These striking similarities in metabolic pathways are likely due to their appearance in evolutionary history. Most of the structures that make up animals, plants and microbes are made from three classes of molecule, amino acids, carbohydrates and lipids. These biochemicals can be joined together to make such as DNA and proteins. Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds, many proteins are enzymes that catalyze the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle. Lipids are the most diverse group of biochemicals and their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of energy. Lipids are usually defined as hydrophobic or amphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform, the fats are a large group of compounds that contain fatty acids and glycerol, a glycerol molecule attached to three fatty acid esters is called a triacylglyceride. Several variations on this structure exist, including alternate backbones such as sphingosine in the sphingolipids. Steroids such as cholesterol are another class of lipids. Carbohydrates are aldehydes or ketones, with hydroxyl groups attached. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy, the basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose
37.
Actin
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Actin is a family of globular multi-functional proteins that form microfilaments. It is found in all eukaryotic cells, where it may be present at a concentration of over 100 μM. Many of these processes are mediated by extensive and intimate interactions of actin with cellular membranes, in vertebrates, three main groups of actin isoforms, alpha, beta, and gamma have been identified. The alpha actins, found in tissues, are a major constituent of the contractile apparatus. The beta and gamma actins coexist in most cell types as components of the cytoskeleton and it is believed that the diverse range of structures formed by actin enabling it to fulfill such a large range of functions is regulated through the binding of tropomyosin along the filaments. Other enzymes or organelles such as cilia can be anchored to this scaffolding in order to control the deformation of the cell membrane. It can also produce movement either by itself or with the help of molecular motors, Actin therefore contributes to processes such as the intracellular transport of vesicles and organelles as well as muscular contraction and cellular migration. It therefore plays an important role in embryogenesis, the healing of wounds, the evolutionary origin of actin can be traced to prokaryotic cells, which have equivalent proteins. Actin homologs from prokaryotes and archaea polymerize into different helical or linear filaments consisting of one or multiple strands, however the in-strand contacts and nucleotide binding sites are preserved in prokaryotes and in archaea. Lastly, actin plays an important role in the control of gene expression, a large number of illnesses and diseases are caused by mutations in alleles of the genes that regulate the production of actin or of its associated proteins. The production of actin is also key to the process of infection by some pathogenic microorganisms, mutations in the different genes that regulate actin production in humans can cause muscular diseases, variations in the size and function of the heart as well as deafness. The make-up of the cytoskeleton is also related to the pathogenicity of bacteria and viruses. Actin was first observed experimentally in 1887 by W. D. Halliburton, in 1942, Straub developed a novel technique for extracting muscle protein that allowed him to isolate substantial amounts of relatively pure actin. Straubs method is essentially the same as used in laboratories today. Adding ATP to a mixture of both proteins causes a decrease in viscosity, the hostilities of World War II meant Szent-Gyorgyi and Straub were unable to publish the work in Western scientific journals. Actin therefore only became known in the West in 1945. Straub suggested that the transformation of ATP-bound actin to ADP-bound actin played a role in muscular contraction, in fact, this is true only in smooth muscle, and was not supported through experimentation until 2001. The amino acid sequencing of actin was completed by M. Elzinga, the crystal structure of G-actin was solved in 1990 by Kabsch and colleagues
38.
Myosin
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Myosins comprise a superfamily of ATP-dependent motor proteins and are best known for their role in muscle contraction and their involvement in a wide range of other motility processes in eukaryotes. They are responsible for actin-based motility, the term was originally used to describe a group of similar ATPases found in the cells of both striated muscle tissue and smooth muscle tissue. Following the discovery by Pollard and Korn of enzymes with myosin-like function in Acanthamoeba castellanii, virtually all eukaryotic cells contain myosin isoforms. Some isoforms have specialized functions in cell types, while other isoforms are ubiquitous. The structure and function of myosin is strongly conserved across species, most myosin molecules are composed of a head, neck, and tail domain. The head domain binds the actin, and uses ATP hydrolysis to generate force. The neck domain acts as a linker and as an arm for transducing force generated by the catalytic motor domain. The neck domain can also serve as a site for myosin light chains which are distinct proteins that form part of a macromolecular complex. The tail domain generally mediates interaction with cargo molecules and/or other myosin subunits, in some cases, the tail domain may play a role in regulating motor activity. Multiple myosin II molecules generate force in skeletal muscle through a power stroke mechanism fuelled by the energy released from ATP hydrolysis, the power stroke occurs at the release of phosphate from the myosin molecule after the ATP hydrolysis while myosin is tightly bound to actin. The effect of release is a conformational change in the molecule that pulls against the actin. The release of the ADP molecule leads to the rigor state of myosin. The binding of a new ATP molecule will release myosin from actin, ATP hydrolysis within the myosin will cause it to bind to actin again to repeat the cycle. The combined effect of the power strokes causes the muscle to contract. The wide variety of genes found throughout the eukaryotic phyla were named according to different schemes as they were discovered. The nomenclature can therefore be somewhat confusing when attempting to compare the functions of proteins within. Skeletal muscle myosin, the most conspicuous of the myosin superfamily due to its abundance in muscle fibers, was the first to be discovered and this protein makes up part of the sarcomere and forms macromolecular filaments composed of multiple myosin subunits. Similar filament-forming myosin proteins were found in muscle, smooth muscle
39.
Cytoskeleton
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A cytoskeleton is present in all cells of all domains of life. It is a network of interlinking filaments and tubules that extend throughout the cytoplasm. The cytoskeletal systems of different organisms are composed of similar proteins, the structure, function and dynamic behaviour of the cytoskeleton can be very different, depending on organism and cell type. Even within one cell the cytoskeleton can change through association with other proteins, there is a multitude of functions that the cytoskeleton can perform. Primarily, it gives the cell its shape and mechanical resistance to deformation, the cytoskeleton can also actively contract, thereby deforming the cell and the cells environment and allowing cells to migrate. Furthermore, it forms specialized structures, such as flagella, cilia, lamellipodia, a large-scale example of an action performed by the cytoskeleton is muscle contraction. During contraction of a muscle, within each cell, myosin molecular motors collectively exert forces on parallel actin filaments. This action contracts the muscle cell, and through the process in many muscle cells. In 1903, Nikolai K. Koltsov proposed that the shape of cells was determined by a network of tubules that he termed the cytoskeleton, eukaryotic cells contain three main kinds of cytoskeletal filaments, microfilaments, microtubules, and intermediate filaments. Each cytoskeletal filament has a shape and intracellular distribution, additionally, the filaments are formed by polymerization of different types of sub-units. The microfilament consist of the polymers of the protein actin which has a diameter of 7 nm, the microtubules are made up of the protein called tubulin which has a diameter of 25 nm. Intermediate filaments are made up of proteins which varies depending on the cell type. These type of filament normally have diameters ranging from 8-12 nm, the cytoskeleton provides the cell with structure and shape, and by excluding macromolecules from some of the cytosol, it adds to the level of macromolecular crowding in this compartment. Cytoskeletal elements interact extensively and intimately with cellular membranes, a number of small molecule cytoskeletal drugs have been discovered that interact with actin and microtubules. These compounds have proven useful in studying the cytoskeleton and several have clinical applications, all filaments interact with accessory proteins that regulate and link the filaments to other cell compounds and each other. The accessory proteins are essential for controlled assembly of cytoskeletal filaments in particular locations, microfilaments are composed of linear polymers of G-actin proteins, and generate force when the growing end of the filament pushes against a barrier, such as the cell membrane. They also act as tracks for the movement of molecules that attach to the microfilament. Myosin motoring along F-actin filaments generates contractile forces in so-called actomyosin fibers, actin structures are controlled by the Rho family of small GTP-binding proteins such as Rho itself for contractile acto-myosin filaments, Rac for lamellipodia and Cdc42 for filopodia
40.
Scaffolding
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Bamboo scaffolding is a type of scaffolding made from bamboo and widely used in construction work for centuries. Many famous landmarks, notably The Great Wall of China, were built using bamboo scaffolding and it was first introduced into the building industry in Hong Kong immediately after colonization in the 1800s. It was widely used in the building of houses and multi-story buildings prior to the development of metal scaffolding and it was also useful for short-term construction projects, such as framework for temporary sheds for Cantonese Opera performances. There is three types of scaffolding in Hong Kong,1, in 2013, there were 1,751 registered bamboo scaffolders and roughly 200 scaffolding companies in Hong Kong. The use of scaffolding is diminishing due to shortages in labor. Despite the lack of force and material, recently the safety problem has become another serious concern. The labor shortage may be due to the reluctance of younger generations to become scaffolders, “They even think that it’s a dirty and dangerous job. “They refuse to step in, although we give them high pay. Young generations do not like jobs that involve hard work. ”Another reason fewer people are becoming scaffolders is that new recruits need to undergo training with the Hong Kong Construction Industry Council in order to acquire a license. Older scaffolders generally learned in apprenticeships, and may have been able to gather more hands-on experience, material shortages are also a contributing factor to the decline. The bamboo scaffolding material was imported from mainland China, bamboo—which matures after three years to the wide diameter and thick skin perfect for scaffolding—came from the Shaoxing area in Guangdong. Over the past two decades, firms have had to look to Guangxi instead, the industrys fear is that one day supplies will be blocked due to export embargoes and environmental concerns. Attempts to import bamboo from Thailand, or switch to synthetic or plastic bamboo, have so far proved unsuccessful, in many African countries, notably Nigeria, bamboo scaffolding is still used in small scale construction in urban areas. In rural areas, the use of scaffolding for construction is common. Some of the structures in relaxation and recreation centres both in urban and rural areas of Nigeria are put in place using bamboo materials and this is not for reasons of poverty but to add more aesthetics to these centres. Bamboo materials are used in the construction of some bukas in rural areas. Content about specifications Double-row Scaffold Only double-row bamboo scaffold is allowed to use for working at height, nylon Mesh The perimeter of bamboo scaffold shall be covered by nylon mesh against falling objects. The lapping of nylon mesh should be at least 100mm wide, access and Egress Suitable means of access shall be provided from the building or ground level to the scaffold such as gangway, stairs and ladder etc
41.
Antibody
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An antibody, also 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, therefore, 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
42.
Cell adhesion
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Cell adhesion is the process by which cells interact and attach to a surface, substrate or another cell, mediated by interactions between molecules of the cell surface. Cell adhesion occurs from the action of transmembrane glycoproteins, called cell adhesion molecules, examples of these proteins include selectins, integrins, syndecans, and cadherins. Cellular adhesion is essential in maintaining multicellular structure, cellular adhesion can link cells in different ways and can be involved in signal transduction. Cell adhesion is essential for the pathogenesis of infectious organisms. Mammalian cells express many different types of adhesion molecules, the major classes are named integrins, Ig superfamily members, cadherins, and selectins. Each of these molecules has a different function and recognizes different ligands. Defects in cell adhesion are usually attributable to defects in expression of adhesion molecules, Cell junctions allow cells to adhere to one another in multicellular organisms. The cadherin subunit, β-catenin plays a role in adhesion by controlling cadherin-mediated cell adhesion at the plasma membrane. Cell–matrix adhesions however, are mediated by integrins. Selective cell–cell adhesion enables vertebrate cells to assemble into organised tissues, homophilic attachment allows selective recognition resulting. Cells of a similar type stick together whereas cells of a different type stay segregated, fungal adhesion allows fungi to bind to host tissues. There are human genetic diseases caused by an inability to express a specific adhesion molecule, an example is leukocyte adhesion deficiency-I, where patients do not express the β2-integrin subunit precursor. This integrin is required for leukocytes to adhere to the vessel wall during inflammation in order to fight infection. The leukocytes from LAD-I patients fail to adhere and patients exhibit serious episodes of infection that can be life-threatening, cancer metastasis tumors that spread through the circulatory system use mechanisms of cell adhesion to establish new tumors in the body. Release of epoxyeicosatrienoic acid is believed to increase this propensity, prokaryotes have adhesion molecules usually termed adhesins. Adhesins may occur on pili, flagella, or the cell surface, Adhesion of bacteria is the first step in colonization and regulates tropism. Viruses also have adhesion molecules required for binding to host cells. For example, influenza virus has a hemagglutinin on its surface that is required for recognition of the sialic acid on host cell surface molecules
43.
Cell cycle
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The cell cycle or cell-division cycle is the series of events that take place in a cell leading to its division and duplication of its DNA to produce two daughter cells. In bacteria, which lack a nucleus, the cell cycle is divided into the B, C. The B period extends from the end of cell division to the beginning of DNA replication, DNA replication occurs during the C period. The D period refers to the stage between the end of DNA replication and the splitting of the cell into two daughter cells. In cells with a nucleus, as in eukaryotes, the cycle is also divided into three periods, interphase, the mitotic phase, and cytokinesis. During interphase, the cell grows, accumulating nutrients needed for mitosis, preparing it for cell division, during the mitotic phase, the chromosomes separate. During the final stage, cytokinesis, the chromosomes and cytoplasm separate into two new daughter cells, to ensure the proper division of the cell, there are control mechanisms known as cell cycle checkpoints. After cell division, each of the cells begin the interphase of a new cycle. The cell cycle consists of four phases, G1 phase, S phase, G2 phase. Activation of each phase is dependent on the progression and completion of the previous one. Cells that have temporarily or reversibly stopped dividing are said to have entered a state of quiescence called G0 phase, after cell division, each of the daughter cells begin the interphase of a new cycle. G0 is a phase where the cell has left the cycle and has stopped dividing. The cell cycle starts with this phase, the word post-mitotic is sometimes used to refer to both quiescent and senescent cells. Non proliferative cells in multicellular eukaryotes generally enter the quiescent G0 state from G1 and may remain quiescent for long periods of time and this is very common for cells that are fully differentiated. Cellular senescence occurs in response to DNA damage and external stress, some cells enter the G0 phase semi-permanently, and are considered post-mitotic e. g. some liver, kidney, stomach cells. Many cells do not enter G0 and continue to divide throughout an organisms life, before a cell can enter cell division, it needs to take in nutrients. All of the preparations are done during interphase, interphase is a series of changes that takes place in a newly formed cell and its nucleus, before it becomes capable of division again. It is also called preparatory phase or intermitosis, previously it was called resting stage because there is no apparent activity related to cell division. Typically interphase lasts for at least 90% of the total time required for the cell cycle
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Diet (nutrition)
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In nutrition, diet is the sum of food consumed by a person or other organism. The word diet often implies the use of intake of nutrition for health or weight-management reasons. Although humans are omnivores, each culture and each person holds some food preferences or some food taboos and this may be due to personal tastes or ethical reasons. Individual dietary choices may be more or less healthy, complete nutrition requires ingestion and absorption of vitamins, minerals, and food energy in the form of carbohydrates, proteins, and fats. Dietary habits and choices play a significant role in the quality of life, health, some cultures and religions have restrictions concerning what foods are acceptable in their diet. For example, only Kosher foods are permitted by Judaism, although Buddhists are generally vegetarians, the practice varies and meat-eating may be permitted depending on the sects. In Hinduism, vegetarianism is the ideal, jains are strictly vegetarian and consumption of roots is not permitted. Raw foodism is another contemporary trend and these diets may require tuning or supplementation such as vitamins to meet ordinary nutritional needs. A particular diet may be chosen to seek weight loss or weight gain, changing a subjects dietary intake, or going on a diet, can change the energy balance and increase or decrease the amount of fat stored by the body. Some foods are recommended, or even altered, for conformity to the requirements of a particular diet. These diets are recommended in conjunction with exercise. Specific weight loss programs can be harmful to health, while others may be beneficial, the terms healthy diet and diet for weight management are often related, as the two promote healthy weight management. Having a healthy diet is a way to prevent health problems, and will provide the body with the balance of vitamins, minerals. An eating disorder is a disorder that interferes with normal food consumption. It is defined by abnormal eating habits that may involve either insufficient or excessive diet, a healthy diet may improve or maintain optimal health. In developed countries, affluence enables unconstrained caloric intake and possibly inappropriate food choices, health agencies recommend that people maintain a normal weight by limiting consumption of energy-dense foods and sugary drinks, eat plant-based food, limit red and processed meat, and limit alcohol. Diet food Dieting Dessert crop Nutrition psychology The dictionary definition of diet at Wiktionary
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Essential amino acid
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An essential amino acid, or indispensable amino acid, is an amino acid that cannot be synthesized de novo by the organism, and thus must be supplied in its diet. The nine amino acids humans cannot synthesize are phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine and these six are arginine, cysteine, glycine, glutamine, proline, and tyrosine. Five amino acids are dispensable in humans, meaning they can be synthesized in the body and these five are alanine, aspartic acid, asparagine, glutamic acid and serine. Pyrrolysine, sometimes considered the 22nd amino acid, is not used by humans, eukaryotes can synthesize some of the amino acids from other substrates. Consequently, only a subset of the amino acids used in protein synthesis are essential nutrients, estimating the daily requirement for the indispensable amino acids has proven to be difficult, these numbers have undergone considerable revision over the last 20 years. The following table lists the WHO recommended daily amounts currently in use for essential amino acids in adult humans, food sources are identified based on the USDA National Nutrient Database Release. The recommended daily intakes for children aged three years and older is 10% to 20% higher than adult levels and those for infants can be as much as 150% higher in the first year of life, cysteine, tyrosine, and arginine are always required by infants and growing children. Various attempts have been made to express the quality or value of various kinds of protein, measures include the biological value, net protein utilization, protein efficiency ratio, protein digestibility-corrected amino acid score and complete proteins concept. Thus, various feedstuffs may be fed in combination to increase net protein utilization, eating various plant foods in combination can provide a protein of higher biological value. Certain native combinations of foods, such as corn and beans, soybeans and rice, or red beans and rice, for example, while 100 g of raw broccoli only provides 28 kcal and 3 g of protein, it has over 100 mg of protein per kcal. An egg contains five times as many calories but only four times as much protein, however, a carrot has only 23 mg protein per kcal or twice the minimum recommendation, a banana meets the minimum, and an apple is below recommendation. It is recommended that adult humans obtain 10–35% of their calories as protein, the US FDA daily reference value of 50 g protein per 2000 kcal is 25 mg/kcal per day. This led William Cumming Rose to the discovery of the amino acid threonine. Roses later work showed that eight amino acids are essential for human beings. Longer term studies established histidine as also essential for adult humans, the distinction between essential and non-essential amino acids is somewhat unclear, as some amino acids can be produced from others. The sulfur-containing amino acids, methionine and homocysteine, can be converted into each other but neither can be synthesized de novo in humans, likewise, cysteine can be made from homocysteine but cannot be synthesized on its own. So, for convenience, sulfur-containing amino acids are considered a single pool of nutritionally equivalent amino acids as are the aromatic amino acid pair. Likewise arginine, ornithine, and citrulline, which are interconvertible by the cycle, are considered a single group
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Digestion
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Digestion is the breakdown of large insoluble food molecules into small water-soluble food molecules so that they can be absorbed into the watery blood plasma. In certain organisms, these substances are absorbed through the small intestine into the blood stream. Digestion is a form of catabolism that is divided into two processes based on how food is broken down, mechanical and chemical digestion. The term mechanical digestion refers to the breakdown of large pieces of food into smaller pieces which can subsequently be accessed by digestive enzymes. In chemical digestion, enzymes break down food into the small molecules the body can use. In the human system, food enters the mouth and mechanical digestion of the food starts by the action of mastication, a form of mechanical digestion. After undergoing mastication and starch digestion, the food will be in the form of a small and it will then travel down the esophagus and into the stomach by the action of peristalsis. Gastric juice in the stomach starts protein digestion, gastric juice mainly contains hydrochloric acid and pepsin. As these two chemicals may damage the stomach wall, mucus is secreted by the stomach, providing a slimy layer that acts as a shield against the effects of the chemicals. At the same time protein digestion is occurring, mechanical mixing occurs by peristalsis and this allows the mass of food to further mix with the digestive enzymes. After some time, the resulting liquid is called chyme. When the chyme is fully digested, it is absorbed into the blood, 95% of absorption of nutrients occurs in the small intestine. Water and minerals are reabsorbed back into the blood in the colon where the pH is slightly acidic about 5.6 ~6.9, some vitamins, such as biotin and vitamin K produced by bacteria in the colon are also absorbed into the blood in the colon. Waste material is eliminated from the rectum during defecation, there is a fundamental distinction between internal and external digestion. External digestion developed earlier in history, and most fungi still rely on it. In this process, enzymes are secreted into the environment surrounding the organism, where they break down an organic material, some organisms, including nearly all spiders, simply secrete biotoxins and digestive chemicals into the extracellular environment prior to ingestion of the consequent soup. Bacteria use several systems to obtain nutrients from other organisms in the environments, in a channel transupport system, several proteins form a contiguous channel traversing the inner and outer membranes of the bacteria. It is a system, which consists of only three protein subunits, the ABC protein, membrane fusion protein, and outer membrane protein
. PMID 24114984.
