1.
Hydrogen bond
–
Hydrogen bonds can occur between molecules or within different parts of a single molecule. Depending on geometry and environment, the hydrogen bond free energy content is between 1 and 5 kcal/mol and this makes it stronger than a van der Waals interaction, but weaker than covalent or ionic bonds. This type of bond can occur in molecules such as water and in organic molecules like DNA. Intermolecular hydrogen bonding is responsible for the boiling point of water compared to the other group 16 hydrides that have much weaker hydrogen bonds. Intramolecular hydrogen bonding is responsible for the secondary and tertiary structures of proteins. It also plays an important role in the structure of polymers, in 2011, an IUPAC Task Group recommended a modern evidence-based definition of hydrogen bonding, which was published in the IUPAC journal Pure and Applied Chemistry. An accompanying detailed technical report provides the rationale behind the new definition, a hydrogen atom attached to a relatively electronegative atom will play the role of the hydrogen bond donor. This electronegative atom is usually fluorine, oxygen, or nitrogen, a hydrogen attached to carbon can also participate in hydrogen bonding when the carbon atom is bound to electronegative atoms, as is the case in chloroform, CHCl3. An example of a hydrogen donor is the hydrogen from the hydroxyl group of ethanol. In a hydrogen bond, the electronegative atom not covalently attached to the hydrogen is named proton acceptor, because of the small size of hydrogen relative to other atoms and molecules, the resulting charge, though only partial, represents a large charge density. A hydrogen bond results when this positive charge density attracts a lone pair of electrons on another heteroatom. The hydrogen bond is described as an electrostatic dipole-dipole interaction. These covalent features are more substantial when acceptors bind hydrogens from more electronegative donors, the partially covalent nature of a hydrogen bond raises the following questions, To which molecule or atom does the hydrogen nucleus belong. And Which should be labeled donor and which acceptor, liquids that display hydrogen bonding are called associated liquids. Hydrogen bonds can vary in strength from weak to extremely strong. For example, the central interresidue N−H···N hydrogen bond between guanine and cytosine is much stronger in comparison to the N−H···N bond between the adenine-thymine pair, the length of hydrogen bonds depends on bond strength, temperature, and pressure. The bond strength itself is dependent on temperature, pressure, bond angle, the typical length of a hydrogen bond in water is 197 pm. The ideal bond angle depends on the nature of the hydrogen bond donor, moore and Winmill used the hydrogen bond to account for the fact that trimethylammonium hydroxide is a weaker base than tetramethylammonium hydroxide
2.
Molecular biology
–
Writing in Nature in 1961, William Astbury described molecular biology as. It is concerned particularly with the forms of biological molecules and is predominantly three-dimensional and structural—which does not mean, however and it must at the same time inquire into genesis and function. Researchers in molecular biology use specific techniques native to molecular biology but increasingly combine these techniques and ideas from genetics. There is not a line between these disciplines. Biochemists focus heavily on the role, function, and structure of biomolecules, the study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry. Genetics is the study of the effect of differences on organisms. This can often be inferred by the absence of a normal component, the study of mutants – organisms which lack one or more functional components with respect to the so-called wild type or normal phenotype. Genetic interactions can often confound simple interpretations of such knockout studies, molecular biology is the study of molecular underpinnings of the processes of replication, transcription, translation, and cell function. This picture, however, is undergoing revision in light of emerging novel roles for RNA, much of molecular biology is quantitative, and recently much work has been done at its interface with computer science in bioinformatics and computational biology. In the early 2000s, the study of structure and function. There is also a tradition of studying biomolecules from the ground up in biophysics. One of the most basic techniques of molecular biology to study protein function is molecular cloning, in this technique, DNA coding for a protein of interest is cloned using PCR and/or restriction enzymes into a plasmid. A vector has 3 distinctive features, an origin of replication, a multiple cloning site, the origin of replication will have promoter regions upstream from the replication/transcription start site. This plasmid can be inserted into either bacterial or animal cells, introducing DNA into bacterial cells can be done by transformation via uptake of naked DNA, conjugation via cell-cell contact or by transduction via viral vector. Introducing DNA into eukaryotic cells, such as cells, by physical or chemical means is called transfection. Several different transfection techniques are available, such as calcium phosphate transfection, electroporation, microinjection, the plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection. DNA coding for a protein of interest is now inside a cell, a variety of systems, such as inducible promoters and specific cell-signaling factors, are available to help express the protein of interest at high levels. Large quantities of a protein can then be extracted from the bacterial or eukaryotic cell, polymerase chain reaction is an extremely versatile technique for copying DNA
3.
Genetics
–
Genetics is the study of genes, genetic variation, and heredity in living organisms. It is generally considered a field of biology, but intersects frequently with other life sciences and is strongly linked with the study of information systems. The father of genetics is Gregor Mendel, a late 19th-century scientist, Mendel studied trait inheritance, patterns in the way traits are handed down from parents to offspring. He observed that organisms inherit traits by way of discrete units of inheritance and this term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism, genetics has given rise to a number of subfields, including epigenetics and population genetics. Organisms studied within the broad field span the domain of life, including bacteria, plants, animals, genetic processes work in combination with an organisms environment and experiences to influence development and behavior, often referred to as nature versus nurture. The intracellular or extracellular environment of a cell or organism may switch gene transcription on or off, a classic example is two seeds of genetically identical corn, one placed in a temperate climate and one in an arid climate. The word genetics stems from the ancient Greek γενετικός genetikos meaning genitive/generative, the observation that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals through selective breeding. The modern science of genetics, seeking to understand this process, prior to Mendel, Imre Festetics, a Hungarian noble, who lived in Kőszeg before Mendel, was the first who used the word genetics. He described several rules of inheritance in his work The genetic law of the Nature. His second law is the same as what Mendel published, in his third law, he developed the basic principles of mutation. Other theories of inheritance preceded his work, a popular theory during Mendels time was the concept of blending inheritance, the idea that individuals inherit a smooth blend of traits from their parents. Mendels work provided examples where traits were not blended after hybridization. Blending of traits in the progeny is now explained by the action of genes with quantitative effects. Another theory that had some support at that time was the inheritance of acquired characteristics, other theories included the pangenesis of Charles Darwin and Francis Galtons reformulation of pangenesis as both particulate and inherited. Modern genetics started with Gregor Johann Mendel, a scientist and Augustinian friar who studied the nature of inheritance in plants, the importance of Mendels work did not gain wide understanding until the 1890s, after his death, when other scientists working on similar problems re-discovered his research. William Bateson, a proponent of Mendels work, coined the word genetics in 1905, Bateson popularized the usage of the word genetics to describe the study of inheritance in his inaugural address to the Third International Conference on Plant Hybridization in London in 1906. After the rediscovery of Mendels work, scientists tried to determine which molecules in the cell were responsible for inheritance, in 1911, Thomas Hunt Morgan argued that genes are on chromosomes, based on observations of a sex-linked white eye mutation in fruit flies
4.
Nitrogenous base
–
A nitrogenous base, or nitrogen-containing base, is an organic molecule with a nitrogen atom that has the chemical properties of a base. The main biological function of a base is to bond nucleic acids together. A nitrogenous base owes its properties to the lone pair of electrons of a nitrogen atom. Nitrogenous bases are classified as the derivatives of two parent compounds, pyrimidine and purine. They are non-polar and due to their aromaticity, planar, both pyrimidines and purines resemble pyridine and are thus weak bases and relatively unreactive towards electrophilic aromatic substitution. A set of five nitrogenous bases is used in the construction of nucleotides and these nitrogenous bases are adenine, uracil, guanine, thymine, and cytosine. These nitrogenous bases hydrogen bond between opposing DNA strands to form the rungs of the ladder or double helix of DNA or a biological catalyst that is found in the nucleotides. Adenine is always paired with thymine, and guanine is paired with cytosine. These are known as base pairs, uracil is only present in RNA, replacing thymine. Pyrimidines include thymine, cytosine, and uracil and they have a single ring structure. They have a ring structure
5.
DNA
–
Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids, alongside proteins, lipids and complex carbohydrates, most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are termed polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases—cytosine, guanine, adenine, or thymine —a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison the total mass of the biosphere has been estimated to be as much as 4 trillion tons of carbon. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information and this information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences, the two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases and it is the sequence of these four nucleobases along the backbone that encodes biological information. RNA strands are created using DNA strands as a template in a process called transcription, under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells DNA is organized into structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, eukaryotic organisms store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast prokaryotes store their DNA only in the cytoplasm, within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed, DNA was first isolated by Friedrich Miescher in 1869. DNA is used by researchers as a tool to explore physical laws and theories, such as the ergodic theorem. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro-, among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a polymer made from repeating units called nucleotides
6.
RNA
–
Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome, some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these processes is protein synthesis, a universal function where RNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA molecules to deliver amino acids to the ribosome, analysis of these RNAs has revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices, in this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA. Each nucleotide in RNA contains a sugar, with carbons numbered 1 through 5. A base is attached to the 1 position, in general, adenine, cytosine, guanine, adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3 position of one ribose, the phosphate groups have a negative charge each, making RNA a charged molecule. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil, however, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural feature of RNA that distinguishes it from DNA is the presence of a group at the 2 position of the ribose sugar. The A-form geometry results in a deep and narrow major groove. RNA is transcribed with only four bases, but these bases, pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine are found in various places. Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine, inosine plays a key role in the wobble hypothesis of the genetic code. The specific roles of many of these modifications in RNA are not fully understood, the functional form of single-stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule and this leads to several recognizable domains of secondary structure like hairpin loops, bulges, and internal loops
7.
Guanine
–
Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine. In DNA, guanine is paired with cytosine, the guanine nucleoside is called guanosine. With the formula C5H5N5O, guanine is a derivative of purine, being unsaturated, the bicyclic molecule is planar. Guanine, along with adenine and cytosine, is present in both DNA and RNA, whereas thymine is usually only in DNA, and uracil only in RNA. Guanine has two forms, the major keto form and rare enol form. It binds to cytosine through three hydrogen bonds, in cytosine, the amino group acts as the hydrogen bond donor and the C-2 carbonyl and the N-3 amine as the hydrogen-bond acceptors. Guanine has the C-6 carbonyl group that acts as the hydrogen acceptor, while a group at N-1. Guanine can be hydrolyzed with strong acid to glycine, ammonia, carbon dioxide, first, guanine gets deaminated to become xanthine. Guanine oxidizes more readily than adenine, the other purine-derivative base in DNA and its high melting point of 350 °C reflects the intermolecular hydrogen bonding between the oxo and amino groups in the molecules in the crystal. Because of this bonding, guanine is relatively insoluble in water. Between 1882 and 1906, Fischer determined the structure and also showed that uric acid can be converted to guanine, trace amounts of guanine form by the polymerization of ammonium cyanide. These results indicate guanine could arise in frozen regions of the primitive earth. In 1984, Yuasa reported a 0. 00017% yield of guanine after the discharge of NH3, CH4, C 2H6. However, it is whether the presence of guanine was not simply a resultant contaminant of the reaction. 10NH3 + 2CH4 + 4C2H6 + 2H2O → 2C5H8N5O + 25H2 A Fischer-Tropsch synthesis can also be used to form guanine, along with adenine, uracil, traubes synthesis involves heating 2,4, 5-triamino-1, 6-dihydro-6-oxypyrimidine with formic acid for several hours. The word guanine derives from the Spanish loanword guano, which itself is from the Quechua word wanu, as the Oxford English Dictionary notes, guanine is A white amorphous substance obtained abundantly from guano, forming a constituent of the excrement of birds. In 1656 in Paris, a Mr. Jaquin extracted from the scales of the fish Alburnus alburnus so-called pearl essence, in the cosmetics industry, crystalline guanine is used as an additive to various products, where it provides a pearly iridescent effect. It is also used in paints and simulated pearls and plastics
8.
Adenine
–
It also has functions in protein synthesis and as a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA, the image on the right shows pure adenine, as an independent molecule. When connected into DNA, a covalent bond is formed between deoxyribose sugar and the bottom left nitrogen, so removing the hydrogen, the remaining structure is called an adenine residue, as part of a larger molecule. Adenosine is adenine reacted with ribose as used in RNA and ATP, deoxyadenosine adenine attached to deoxyribose, adenine forms several tautomers, compounds that can be rapidly interconverted and are often considered equivalent. However, in isolated conditions, i. e. in an inert gas matrix and in the gas phase, purine metabolism involves the formation of adenine and guanine. Adenine is one of the two purine nucleobases used in forming nucleotides of the nucleic acids, in DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. In RNA, which is used for synthesis, adenine binds to uracil. Adenine forms adenosine, a nucleoside, when attached to ribose and it forms adenosine triphosphate, a nucleoside triphosphate, when three phosphate groups are added to adenosine. Adenosine triphosphate is used in cellular metabolism as one of the methods of transferring chemical energy between chemical reactions. In older literature, adenine was sometimes called Vitamin B4 and it is no longer considered a true vitamin or part of the Vitamin B complex. However, two B vitamins, niacin and riboflavin, bind with adenine to form the essential cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide, hermann Emil Fischer was one of the early scientists to study adenine. It was named in 1885 by Albrecht Kossel, in reference to the pancreas from which Kossels sample had been extracted. On August 8,2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting building blocks of DNA and RNA may have been formed extraterrestrially in outer space
9.
Uracil
–
Uracil /ˈjʊərəsɪl/ is one of the four nucleobases in the nucleic acid of RNA that are represented by the letters A, G, C and U. The others are adenine, cytosine, and guanine, in RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine, Uracil is a demethylated form of thymine. Uracil is a common and naturally occurring pyrimidine derivative, the name uracil was coined in 1885 by the German chemist Robert Behrend, who was attempting to synthesize derivatives of uric acid. Originally discovered in 1900 by Alberto Ascoli, it was isolated by hydrolysis of yeast nuclein, it was found in bovine thymus and spleen, herring sperm. It is a planar, unsaturated compound that has the ability to absorb light, based on 12C/13C isotopic ratios of organic compounds found in the Murchison meteorite, it is believed that uracil, xanthine and related molecules can also be formed extraterrestrially. In 2012, an analysis of data from the Cassini mission orbiting in the Saturn system showed that Titans surface composition may include uracil, in RNA, uracil base-pairs with adenine and replaces thymine during DNA transcription. In DNA, the substitution of thymine for uracil may have increased DNA stability. Uracil pairs with adenine through hydrogen bonding, when base pairing with adenine, uracil acts as both a hydrogen bond acceptor and a hydrogen bond donor. In RNA, uracil binds with a sugar to form the ribonucleoside uridine. When a phosphate attaches to uridine, uridine 5-monophosphate is produced, Uracil undergoes amide-imidic acid tautomeric shifts because any nuclear instability the molecule may have from the lack of formal aromaticity is compensated by the cyclic-amidic stability. The amide tautomer is referred to as the structure, while the imidic acid tautomer is referred to as the lactim structure. These tautomeric forms are predominant at pH7, the lactam structure is the most common form of uracil. Uracil also recycles itself to form nucleotides by undergoing a series of phosphoribosyltransferase reactions, degradation of uracil produces the substrates aspartate, carbon dioxide, and ammonia. C4H4N2O2 → H3NCH2CH2COO− + NH4+ + CO2 Oxidative degradation of uracil produces urea and maleic acid in the presence of H2O2 and Fe2+ or in the presence of diatomic oxygen, the first site of ionization of uracil is not known. The negative charge is placed on the anion and produces a pKa of less than or equal to 12. The basic pKa = -3.4, while the acidic pKa =9.389, in the gas phase, uracil has 4 sites that are more acidic than water. Uracil is rarely found in DNA, and this may have been a change to increase genetic stability
10.
Genome
–
In modern molecular biology and genetics, a genome is the genetic material of an organism. The genome includes both the genes, the noncoding DNA and the material of the mitochondria and chloroplasts. The term genome was created in 1920 by Hans Winkler, professor of botany at the University of Hamburg, the Oxford Dictionary suggests the name is a blend of the words gene and chromosome. However, see omics for a thorough discussion. A few related -ome words already existed—such as biome, rhizome, Some organisms have multiple copies of chromosomes, diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism the gamete has half the number of chromosomes of the somatic cell, the halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis. Additionally, the genome can comprise non-chromosomal genetic elements such as viruses, plasmids, even in species that exist in only one sex, what is described as a genome sequence may be a composite read from the chromosomes of various individuals. Colloquially, the genetic makeup is sometimes used to signify the genome of a particular individual or organism. Both the number of pairs and the number of genes vary widely from one species to another. The only exception in humans is found in red blood cells which become enucleated during development. In 1976, Walter Fiers at the University of Ghent was the first to establish the complete sequence of a viral RNA-genome. The next year Fred Sanger completed the first DNA-genome sequence, Phage Φ-X174, the first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made it easier and cheaper to do sequencing. The US National Institutes of Health maintains one of several databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the fish. In December 2013, scientists first sequenced the genome of a Neanderthal. The genome was extracted from the toe bone of a 130, new sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the genome of James D. Watson
11.
Thermostability
–
Thermostability is the quality of a substance to resist irreversible change in its chemical or physical structure, often by resisting decomposition or polymerisation, at a high relative temperature. Thermostable materials may be used industrially as fire retardants, Thermostability also commonly refers to a protein resistant to change in its protein structure due to applied heat. Most life-forms on Earth live at temperatures of less than 50 °C, above this, thermal energy may cause the unfolding of the protein structure, where the activity of the protein is abolished and a condition understandably deleterious to continuing life-functions. The denaturing of proteins in albumen from a clear, nearly colourless liquid to an opaque white, certain thermophilic life-forms exist which can withstand temperatures above this, and have corresponding adaptations to preserve protein function at these temperatures. These can include altered bulk properties of the cell to stabilize all proteins, examining homologous proteins present in these thermophiles and other organisms reveal only slight differences in the protein structure. One notable difference is the presence of hydrogen bonds in the thermophiles proteins—meaning that the protein structure is more resistant to unfolding. The presence of types of salt has been observed to alter thermostability in the proteins. Other factors of protein thermostability are compactness of protein structure, oligomerization, thermostable enzymes such as Taq polymerase and Pfu DNA polymerase are used in polymerase chain reactions where temperatures of 94 °C or over are used to melt apart DNA strands. Protein engineering can be used to enhance the thermostability of proteins, a number of site-directed and random mutagenesis techniques, in addition to directed evolution, have been used to increase the thermostability of target proteins. Comparative methods have used to increase the stability of mesophilic proteins based on comparison to thermophilic homologs. Additionally, analysis of the protein unfolding by molecular dynamics can be used to understand the process of unfolding, rational protein engineering for increasing protein thermostability includes mutations which truncate loops, increase salt bridges or hydrogen bonds, introduced disulfide bonds. In addition, ligand binding can increase the stability of the protein, certain poisonous fungi contain thermostable toxins, such as amatoxin found in the death cap and autumn skullcap mushrooms and patulin from molds. Therefore, applying heat to these will not remove the toxicity and is of concern for food safety. Thermophiles Thermus thermophilus Thermus aquaticus Pyrococcus furiosus Thermostability of Proteins
12.
Ribosomal RNA
–
Ribosomal ribonucleic acid is the RNA component of the ribosome, and is essential for protein synthesis in all living organisms. It constitutes the predominant material within the ribosome, which is approximately 60% rRNA and 40% protein by weight, ribosomes contain two major rRNAs and 50 or more proteins. The ribosomal RNAs form two subunits, the large subunit and small subunit, the LSU rRNA acts as a ribozyme, catalyzing peptide bond formation. RRNA sequences are used for working out evolutionary relationships among organisms. The ribosomal RNAs complex with proteins to form two subunits, the large subunit and small subunit. During translation, mRNA is sandwiched between the small and large subunits, and the ribosome catalyzes the formation of a bond between the two amino acids that are contained in the rRNA. A ribosome also has three binding sites called A, P, and E, the A site in the ribosome binds to an aminoacyl-tRNA. This reaction is catalyzed by peptidyl transferase, the tRNA that was holding onto the last amino acid is moved to the E site, and what used to be the aminoacyl-tRNA is the peptidyl-tRNA. A single mRNA can be translated simultaneously by multiple ribosomes, the sedimentation rate of each subunit is affected by its shape, as well as by its mass. Thent units can be added as these represent the number of units in the linear rRNA polymers. In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA, the large 50S ribosomal subunit contains two rRNA species. Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are organized as a co-transcribed operon. There may be one or more copies of the operon dispersed in the genome, archaea contains either a single rDNA operon or multiple copies of the operon. The 3 end of the 16S ribosomal RNA binds to a sequence on the 5 end of mRNA called the Shine-Dalgarno sequence, in contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats, in humans approximately 300–400 repeats are present in five clusters. Because of their structure and transcription behaviour, rRNA gene clusters are commonly called ribosomal DNA. The 18S rRNA in most eukaryotes is in the small subunit. Mammalian cells have 2 mitochondrial rRNA molecules and 4 types of cytoplasmic rRNA, the 28S,5. 8S, and 18S rRNAs are encoded by a single transcription unit separated by 2 internally transcribed spacers. The 45S rDNA is organized into 5 clusters on chromosomes 13,14,15,21 and these are transcribed by RNA polymerase I
13.
Transfer RNA
–
A transfer RNA is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length, that serves as the physical link between the mRNA and the amino acid sequence of proteins. It does this by carrying an amino acid to the protein synthetic machinery of a cell as directed by a sequence in a messenger RNA. As such, tRNAs are a component of translation, the biological synthesis of new proteins in accordance with the genetic code. The mRNA encodes a protein as a series of contiguous codons, one end of the tRNA matches the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three base pairs with a codon in mRNA during protein biosynthesis, on the other end of the tRNA is a covalent attachment to the amino acid that corresponds to the anticodon sequence. Each type of molecule can be attached to only one type of amino acid. Because the genetic code contains multiple codons that specify the amino acid. The covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl tRNA synthetases, a large number of the individual nucleotides in a tRNA molecule may be chemically modified, often by methylation or deamidation. These unusual bases sometimes affect the interaction with ribosomes and sometimes occur in the anticodon to alter base-pairing properties. The structure of tRNA can be decomposed into its structure, its secondary structure. The cloverleaf structure becomes the 3D L-shaped structure through coaxial stacking of the helices, the lengths of each arm, as well as the loop diameter, in a tRNA molecule vary from species to species. The tRNA structure consists of the following, A 5-terminal phosphate group, the acceptor stem is a 7- to 9-base pair stem made by the base pairing of the 5-terminal nucleotide with the 3-terminal nucleotide. The acceptor stem may contain non-Watson-Crick base pairs, the CCA tail is a cytosine-cytosine-adenine sequence at the 3 end of the tRNA molecule. The amino acid loaded onto the tRNA by aminoacyl tRNA synthetases and this sequence is important for the recognition of tRNA by enzymes and critical in translation. In prokaryotes, the CCA sequence is transcribed in some tRNA sequences, in most prokaryotic tRNAs and eukaryotic tRNAs, the CCA sequence is added during processing and therefore does not appear in the tRNA gene. The D arm is a 4- to 6-bp stem ending in a loop that often contains dihydrouridine, the anticodon arm is a 5-bp stem whose loop contains the anticodon. The tRNA 5-to-3 primary structure contains the anticodon but in reverse order, the T arm is a 4- to 5- bp stem containing the sequence TΨC where Ψ is pseudouridine, a modified uridine. Bases that have modified, especially by methylation, occur in several positions throughout the tRNA
14.
Non-coding RNA
–
A non-coding RNA is an RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA, non-messenger RNA, or functional RNA, the DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. The number of ncRNAs encoded within the genome is unknown, however. But see Many of the newly identified ncRNAs have not been validated for their function and it is also likely that many ncRNAs are non functional, and are the product of spurious transcription. Nucleic acids were first discovered in 1868 by Friedrich Miescher and by 1939 RNA had been implicated in protein synthesis. Two decades later, Francis Crick predicted a functional RNA component which mediated translation, the first non-coding RNA to be characterised was an alanine tRNA found in bakers yeast, its structure was published in 1965. To produce a purified alanine tRNA sample, Robert W. Holley et al. used 140kg of commercial bakers yeast to give just 1g of purified tRNAAla for analysis, the 80 nucleotide tRNA was sequenced by first being digested with Pancreatic ribonuclease and then with takadiastase ribonuclease Tl. Chromatography and identification of the 5 and 3 ends then helped arrange the fragments to establish the RNA sequence, of the three structures originally proposed for this tRNA, the cloverleaf structure was independently proposed in several following publications. The cloverleaf secondary structure was finalised following X-ray crystallography analysis performed by two independent research groups in 1974, ribosomal RNA was next to be discovered, followed by URNA in the early 1980s. Since then, the discovery of new non-coding RNAs has continued with snoRNAs, Xist, CRISPR, recent notable additions include riboswitches and miRNA, the discovery of the RNAi mechanism associated with the latter earned Craig C. Mello and Andrew Fire the 2006 Nobel Prize in Physiology or Medicine, noncoding RNAs belong to several groups and are involved in many cellular processes. These range from ncRNAs of central importance that are conserved across all or most cellular life through to more transient ncRNAs specific to one or a few related species. Many of the conserved, essential and abundant ncRNAs are involved in translation, ribonucleoprotein particles called ribosomes are the factories where translation takes place in the cell. The ribosome consists of more than 60% ribosomal RNA, these are made up of 3 ncRNAs in prokaryotes and 4 ncRNAs in eukaryotes, ribosomal RNAs catalyse the translation of nucleotide sequences to protein. Another set of ncRNAs, Transfer RNAs, form an adaptor molecule between mRNA and protein, the H/ACA box and C/D box snoRNAs are ncRNAs found in archaea and eukaryotes. RNase MRP is restricted to eukaryotes, both groups of ncRNA are involved in the maturation of rRNA. The snoRNAs guide covalent modifications of rRNA, tRNA and snRNAs, the ubiquitous ncRNA, RNase P, is an evolutionary relative of RNase MRP. RNase P matures tRNA sequences by generating mature 5-ends of tRNAs through cleaving the 5-leader elements of precursor-tRNAs, another ubiquitous RNP called SRP recognizes and transports specific nascent proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes
15.
Base pair
–
A base pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the blocks of the DNA double helix. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs allow the DNA helix to maintain a regular helical structure that is dependent on its nucleotide sequence. The complementary nature of this structure provides a backup copy of all genetic information encoded within double-stranded DNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes, intramolecular base pairs can occur within single-stranded nucleic acids. The size of a gene or an organisms entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of base pairs is equal to the number of nucleotides in one of the strands. The haploid human genome is estimated to be about 3.2 billion bases long and to contain 20, a kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC. Hydrogen bonding is the interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen donors and acceptors allows only the right pairs to form stably. Purine-pyrimidine base pairing of AT or GC or UA results in proper duplex structure, the only other purine-pyrimidine pairings would be AC and GT and UG, these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two bonds, does occur fairly often in RNA. Higher GC content results in higher melting temperatures, it is, therefore, on the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must also be taken into account when designing primers for PCR reactions, the following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5 end to the 3 end, thus and this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine, most intercalators are large polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine, an unnatural base pair is a designed subunit of DNA which is created in a laboratory and does not occur in nature
16.
Polymerase chain reaction
–
It is an easy, cheap, and reliable way to repeatedly replicate a focused segment of DNA, a concept which is applicable to numerous fields in modern biology and related sciences. Developed in 1983 by Kary Mullis, PCR is now a common and often indispensable technique used in clinical, in 1993, Mullis was awarded the Nobel Prize in Chemistry along with Michael Smith for his work on PCR. Primers containing sequences complementary to the region, along with a DNA polymerase, after which the method is named, enable selective. As PCR progresses, the DNA generated is used as a template for replication. The simplicity of the principle underlying PCR means it can be extensively modified to perform a wide array of genetic manipulations. PCR is not generally considered to be a recombinant DNA method, as it does not involve cutting and pasting DNA, almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase, an enzyme originally isolated from the thermophilic bacterium Thermus aquaticus. In the first step, the two strands of the DNA double helix are physically separated at a temperature in a process called DNA melting. In the second step, the temperature is lowered and the two DNA strands become templates for DNA polymerase to amplify the target DNA. The selectivity of PCR results from the use of primers that are complementary to the DNA region targeted for amplification under specific thermal cycling conditions, PCR amplifies a specific region of a DNA strand. Most PCR methods amplify DNA fragments of between 0.1 and 10 kilo base pairs, although some techniques allow for amplification of fragments up to 40 kbp in size. The amount of amplified product is determined by the available substrates in the reaction, the thermal cycler heats and cools the reaction tubes to achieve the temperatures required at each step of the reaction. Many modern thermal cyclers make use of the Peltier effect, which permits both heating and cooling of the holding the PCR tubes simply by reversing the electric current. Thin-walled reaction tubes permit favorable thermal conductivity to allow for rapid thermal equilibration, most thermal cyclers have heated lids to prevent condensation at the top of the reaction tube. Older thermal cyclers lacking a heated lid require a layer of oil on top of the mixture or a ball of wax inside the tube. Typically, PCR consists of a series of 20–40 repeated temperature changes, called cycles, the cycling is often preceded by a single temperature step at a very high temperature, and followed by one hold at the end for final product extension or brief storage. The individual steps common to most PCR methods are as follows, Initialization and it consists of heating the reaction chamber to a temperature of 94–96 °C, or 98 °C if extremely thermostable polymerases are used, which is then held for 1–10 minutes. Denaturation, This step is the first regular cycling event and consists of heating the reaction chamber to 94–98 °C for 20–30 seconds and this causes DNA melting, or denaturation, of the double-stranded DNA template by breaking the hydrogen bonds between complementary bases, yielding two single-stranded DNA molecules. Annealing, In the next step, the temperature is lowered to 50–65 °C for 20–40 seconds
17.
Primer (molecular biology)
–
A primer is a short strand of RNA or DNA that serves as a starting point for DNA synthesis. It is required for DNA replication because the enzymes that catalyze this process, DNA polymerases, the polymerase starts replication at the 3-end of the primer, and copies the opposite strand. In vivo DNA replication utilizes short strands of RNA called RNA primers to initiate DNA synthesis on both the leading and lagging strands — DNA primers are not seen in vivo in humans and these RNA primers can be made de novo. On the other hand, many of the in vitro laboratory techniques that involve DNA polymerase in biochemistry and molecular biology, in experiments, it is often important to use a primer with a similar Tm to the template strand it will be hybridizing to. These primers are usually short, chemically synthesized oligonucleotides, with a length of about twenty bases and they are hybridized to a target DNA, which is then copied by the polymerase. The lagging strand of DNA is that strand of the DNA double helix that is orientated in a 5 to 3 manner, therefore, its complement must be synthesized in a 3→5 manner. Because DNA polymerase III cannot synthesize in the 3→5 direction, the strand is synthesized in short segments known as Okazaki fragments. Along the lagging strands template, primase builds RNA primers in short bursts, DNA polymerases are then able to use the free 3-OH groups on the RNA primers to synthesize DNA in the 5→3 direction. The RNA fragments are removed by DNA polymerase I for prokaryotes or DNA polymerase δ for eukaryotes. DNA ligase then joins the deoxyribonucleotides together, completing the synthesis of the lagging strand and this mechanism is a potential explanation of how the HIV virus can transform its genome into double-stranded DNA from the RNA-DNA formed after reverse transcription of its RNA. DNA sequencing is used to determine the nucleotides in a DNA strand, the Sanger chain termination method of sequencing uses a primer to start the chain reaction. In PCR, primers are used to determine the DNA fragment to be amplified by the PCR process, the length of primers is usually not more than 30 nucleotides, and they need to match the beginning and the end of the DNA fragment to be amplified. They direct replication towards each other – the extension of one primer by polymerase then becomes the template for the other, leading to an exponential increase in the target segment. It is worth noting that primers are not always for DNA synthesis, pairs of primers should have similar melting temperatures since annealing in a PCR occurs for both simultaneously. Primer sequences need to be chosen to select for a region of DNA. A commonly used method is BLAST search whereby all the regions to which a primer may bind can be seen. Both the nucleotide sequence as well as the primer itself can be BLAST searched, the free NCBI tool Primer-BLAST integrates primer design and BLAST search into one application, as do commercial software products such as ePrime and Beacon Designer. Computer simulations of theoretical PCR results may be performed to assist in primer design, many online tools are freely available for primer design, some of which focus on specific applications of PCR
18.
Nucleic acid double helix
–
In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA. The double helical structure of a nucleic acid complex arises as a consequence of its secondary structure, the term entered popular culture with the publication in 1968 of The Double Helix, A Personal Account of the Discovery of the Structure of DNA, by James Watson. The DNA double helix polymer of nucleic acid, held together by nucleotides which base pair together, in B-DNA, the most common double helical structure found in nature, the double helix is right-handed with about 10–10.5 base pairs per turn. This translates into about 20-21 nucleotides per turn, the double helix structure of DNA contains a major groove and minor groove. In B-DNA the major groove is wider than the minor groove, given the difference in widths of the major groove and minor groove, many proteins which bind to B-DNA do so through the wider major groove. The prior model was triple-stranded DNA, Crick, Wilkins, and Watson each received one third of the 1962 Nobel Prize in Physiology or Medicine for their contributions to the discovery. Hybridization is the process of base pairs binding to form a double helix. Melting is the process by which the interactions between the strands of the helix are broken, separating the two nucleic acid strands. These bonds are weak, easily separated by gentle heating, enzymes, melting occurs preferentially at certain points in the nucleic acid. T and A rich regions are more easily melted than C and G rich regions, some base steps are also susceptible to DNA melting, such as T A and T G. These mechanical features are reflected by the use of such as TATA at the start of many genes to assist RNA polymerase in melting the DNA for transcription. Strand separation by heating, as used in polymerase chain reaction, is simple. The intertwining of the DNA strands makes long segments difficult to separate, helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase. The geometry of a base, or base pair step can be characterized by 6 coordinates, shift, slide, rise, tilt, roll, and twist. These values precisely define the location and orientation in space of every base or base pair in an acid molecule relative to its predecessor along the axis of the helix. Together, they characterize the structure of the molecule. In regions of DNA or RNA where the structure is disrupted. Opening Shift, displacement along an axis in the plane perpendicular to the first
19.
Spectrophotometry
–
In chemistry, spectrophotometry is the quantitative measurement of the reflection or transmission properties of a material as a function of wavelength. Spectrophotometry uses photometers, known as spectrophotometers, that can measure a light intensity as a function of its color. A spectrophotometer is commonly used for the measurement of transmittance or reflectance of solutions, transparent or opaque solids, such as polished glass, or gases. However they can also be designed to measure the diffusivity on any of the listed light ranges that cover around 200 nm -2500 nm using different controls. Within these ranges of light, calibrations are needed on the machine using standards that vary in type depending on the wavelength of the photometric determination, an example of an experiment in which spectrophotometry is used is the determination of the equilibrium constant of a solution. A certain chemical reaction within a solution may occur in a forward, at some point, this chemical reaction will reach a point of balance called an equilibrium point. In order to determine the concentrations of reactants and products at this point. The amount of light passes through the solution is indicative of the concentration of certain chemicals that do not allow light to pass through. The use of spectrophotometers spans various scientific fields, such as physics, materials science, chemistry, biochemistry and they are widely used in many industries including semiconductors, laser and optical manufacturing, printing and forensic examination, as well in laboratories for the study of chemical substances. By 1940 several spectrophotometers were available on the market, but early models could not work in the ultraviolet, arnold O. Beckman developed an improved version at the National Technical Laboratories Company, later the Beckman Instrument Company and ultimately Beckman Coulter. Models A, B, and C were developed, then the model D, all the electronics were contained within the instrument case, and it had a new hydrogen lamp with ultraviolet continuum, and a better monochromator. This instrument was produced from 1941 until 1976 with essentially the same design, nobel chemistry laureate Bruce Merrifield said it was probably the most important instrument ever developed towards the advancement of bioscience. There are two classes of devices, single beam and double beam. A double beam spectrophotometer compares the intensity between two light paths, one path containing a reference sample and the other the test sample. A single-beam spectrophotometer measures the light intensity of the beam before. Although comparison measurements from double-beam instruments are easier and more stable, single-beam instruments can have a dynamic range and are optically simpler. Additionally, some specialized instruments, such as spectrophotometers built onto microscopes or telescopes, are single-beam instruments due to practicality, historically, spectrophotometers use a monochromator containing a diffraction grating to produce the analytical spectrum. The grating can either be movable or fixed, if a single detector, such as a photomultiplier tube or photodiode is used, the grating can be scanned stepwise so that the detector can measure the light intensity at each wavelength
20.
Wavelength
–
In physics, the wavelength of a sinusoidal wave is the spatial period of the wave—the distance over which the waves shape repeats, and thus the inverse of the spatial frequency. Wavelength is commonly designated by the Greek letter lambda, the concept can also be applied to periodic waves of non-sinusoidal shape. The term wavelength is also applied to modulated waves. Wavelength depends on the medium that a wave travels through, examples of wave-like phenomena are sound waves, light, water waves and periodic electrical signals in a conductor. A sound wave is a variation in air pressure, while in light and other electromagnetic radiation the strength of the electric, water waves are variations in the height of a body of water. In a crystal lattice vibration, atomic positions vary, wavelength is a measure of the distance between repetitions of a shape feature such as peaks, valleys, or zero-crossings, not a measure of how far any given particle moves. For example, in waves over deep water a particle near the waters surface moves in a circle of the same diameter as the wave height. The range of wavelengths or frequencies for wave phenomena is called a spectrum, the name originated with the visible light spectrum but now can be applied to the entire electromagnetic spectrum as well as to a sound spectrum or vibration spectrum. In linear media, any pattern can be described in terms of the independent propagation of sinusoidal components. The wavelength λ of a sinusoidal waveform traveling at constant speed v is given by λ = v f, in a dispersive medium, the phase speed itself depends upon the frequency of the wave, making the relationship between wavelength and frequency nonlinear. In the case of electromagnetic radiation—such as light—in free space, the speed is the speed of light. Thus the wavelength of a 100 MHz electromagnetic wave is about, the wavelength of visible light ranges from deep red, roughly 700 nm, to violet, roughly 400 nm. For sound waves in air, the speed of sound is 343 m/s, the wavelengths of sound frequencies audible to the human ear are thus between approximately 17 m and 17 mm, respectively. Note that the wavelengths in audible sound are much longer than those in visible light, a standing wave is an undulatory motion that stays in one place. A sinusoidal standing wave includes stationary points of no motion, called nodes, the upper figure shows three standing waves in a box. The walls of the box are considered to require the wave to have nodes at the walls of the box determining which wavelengths are allowed, the stationary wave can be viewed as the sum of two traveling sinusoidal waves of oppositely directed velocities. Consequently, wavelength, period, and wave velocity are related just as for a traveling wave, for example, the speed of light can be determined from observation of standing waves in a metal box containing an ideal vacuum. In that case, the k, the magnitude of k, is still in the same relationship with wavelength as shown above
21.
Flow cytometry
–
It allows simultaneous multiparametric analysis of the physical and chemical characteristics of up to thousands of particles per second. Flow cytometry is used in the diagnosis of health disorders, especially blood cancers. A common variation is to physically sort particles based on their properties, the first impedance-based flow cytometry device, using the Coulter principle, was disclosed in U. S. Patent 2,656,508, issued in 1953, to Wallace H. Coulter, mack Fulwyler was the inventor of the forerunner to todays flow cytometers - particularly the cell sorter. Fulwyler developed this in 1965 with his publication in Science, at that time, absorption methods were still widely favored by other scientists over fluorescence methods. The first label-free high-frequency impedance flow cytometer based on a patented microfluidic lab-on-chip, the original name of the fluorescence-based flow cytometry technology was pulse cytophotometry, based on the first patent application on fluorescence-based flow cytometry. Modern flow cytometers are able to analyze several thousand particles every second, in real time, a flow cytometer is similar to a microscope, except that, instead of producing an image of the cell, flow cytometry offers high-throughput automated quantification of set parameters. To analyze solid tissues, a single-cell suspension must first be prepared, the process of collecting data from samples using the flow cytometer is termed acquisition. Acquisition is mediated by a physically connected to the flow cytometer. Early flow cytometers were, in general, experimental devices, due to these developments, a considerable market for instrumentation, analysis software, as well as the reagents used in acquisition such as fluorescently labeled antibodies has developed. Modern instruments usually have multiple lasers and fluorescence detectors, the current record for a commercial instrument is ten lasers and 30 fluorescence detectors. Increasing the number of lasers and detectors allows for multiple antibody labeling, certain instruments can even take digital images of individual cells, allowing for the analysis of fluorescent signal location within or on the surface of cells. The data generated by flow-cytometers can be plotted in a dimension, to produce a histogram. The regions on these plots can be separated, based on fluorescence intensity, by creating a series of subset extractions. Specific gating protocols exist for diagnostic and clinical purposes especially in relation to hematology, the plots are often made on logarithmic scales. Because different fluorescent dyes emission spectra overlap, signals at the detectors have to be compensated electronically as well as computationally, once the data is collected, there is no need to stay connected to the flow cytometer and analysis is most often performed on a separate computer. This is especially necessary in core facilities where usage of these machines is in high demand, recent progress on automated population identification using computational methods has offered an alternative to traditional gating strategies. Automated identification systems could potentially help findings of rare and hidden populations, representative automated methods include FLOCK in Immunology Database and Analysis Portal, SamSPECTRAL and flowClust in Bioconductor, and FLAME in GenePattern
22.
Sequencing
–
In genetics and biochemistry, sequencing means to determine the primary structure of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the structure of the sequenced molecule. DNA sequencing is the process of determining the order of a given DNA fragment. So far, most DNA sequencing has been performed using the chain termination developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates, however, new sequencing technologies such as pyrosequencing are gaining an increasing share of the sequencing market. More genome data are now being produced by pyrosequencing than Sanger DNA sequencing, pyrosequencing has enabled rapid genome sequencing. Bacterial genomes can be sequenced in a run with several times coverage with this technique. This technique was used to sequence the genome of James Watson recently. The sequence of DNA encodes the information for living things to survive. Determining the sequence is useful in fundamental research into why and how organisms live. Because of the key importance DNA has to living things, knowledge of DNA sequences is useful in any area of biological research. For example, in medicine it can be used to identify, diagnose, similarly, research into pathogens may lead to treatments for contagious diseases. Biotechnology is a discipline, with the potential for many useful products. The Carlson curve is a term coined by The Economist to describe the biotechnological equivalent of Moores law, Carlson accurately predicted the doubling time of DNA sequencing technologies would be at least as fast as Moores law. In chain terminator sequencing, extension is initiated at a site on the template DNA by using a short oligonucleotide primer complementary to the template at that region. The oligonucleotide primer is extended using a DNA polymerase, an enzyme that replicates DNA, included with the primer and DNA polymerase are the four deoxynucleotide bases, along with a low concentration of a chain terminating nucleotide. The fragments are then size-separated by electrophoresis in a polyacrylamide gel, or more commonly now. An alternative to the labelling of the primer is to label the terminators instead, the major advantage of this approach is the complete sequencing set can be performed in a single reaction, rather than the four needed with the labeled-primer approach
23.
Chromosome
–
A chromosome is a DNA molecule with part or all of the genetic material of an organism. Prokaryotes usually have one single circular chromosome, whereas most eukaryotes are diploid, chromosomes in eukaryotes are composed of chromatin fiber. Chromatin fiber is made of nucleosomes, a nucleosome is a histone octamer with part of a longer DNA strand attached to and wrapped around it. Chromatin fiber, together with associated proteins is known as chromatin, chromatin is present in most cells, with a few exceptions, for example, red blood cells. Occurring only in the nucleus of cells, chromatin contains the vast majority of DNA, except for a small amount inherited maternally. Chromosomes are normally visible under a microscope only when the cell is undergoing the metaphase of cell division. Before this happens every chromosome is copied once, and the copy is joined to the original by a centromere resulting in an X-shaped structure, the original chromosome and the copy are now called sister chromatids. During metaphase, when a chromosome is in its most condensed state, in this highly condensed form chromosomes are easiest to distinguish and study. In prokaryotic cells, chromatin occurs free-floating in cytoplasm, as these cells lack organelles, the main information-carrying macromolecule is a single piece of coiled double-helix DNA, containing many genes, regulatory elements and other noncoding DNA. The DNA-bound macromolecules are proteins that serve to package the DNA, chromosomes vary widely between different organisms. Some species such as certain bacteria also contain plasmids or other extrachromosomal DNA and these are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. Chromosomal recombination during meiosis and subsequent sexual reproduction plays a significant role in genetic diversity. In prokaryotes and viruses, the DNA is often densely packed and organized, in the case of archaea, by homologs to eukaryotic histones, small circular genomes called plasmids are often found in bacteria and also in mitochondria and chloroplasts, reflecting their bacterial origins. Some use the term chromosome in a sense, to refer to the individualized portions of chromatin in cells. However, others use the concept in a sense, to refer to the individualized portions of chromatin during cell division. The word chromosome comes from the Greek χρῶμα and σῶμα, describing their strong staining by particular dyes, schleiden, Virchow and Bütschli were among the first scientists who recognized the structures now so familiar to everyone as chromosomes. The term was coined by von Waldeyer-Hartz, referring to the term chromatin, in a series of experiments beginning in the mid-1880s, Theodor Boveri gave the definitive demonstration that chromosomes are the vectors of heredity. His two principles were the continuity of chromosomes and the individuality of chromosomes and it is the second of these principles that was so original
24.
Gene
–
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
25.
Gene-centered view of evolution
–
Proponents of the gene-centered viewpoint argue that it permits understanding of diverse phenomena such as altruism and intragenomic conflict that are otherwise difficult to explain. The gene-centered view of evolution is a synthesis of the theory of evolution by natural selection, the particulate inheritance theory, and it states that those alleles whose phenotypic effects successfully promote their own propagation will be favorably selected relative to their competitor alleles within the population. The gene-centered view of evolution is a model for the evolution of characteristics such as selfishness. It would imply that all evolutionary novelty requires changes in nucleic acids, J. B. S. Haldane, and Sewall Wright, paved the way to the formulation of the selfish-gene theory. For cases where environment can influence heredity, see epigenetics, the view of the gene as the unit of selection was developed mainly in the works of Richard Dawkins, W. D. Hamilton, Colin Pittendrigh and George C. Williams. It was mainly popularized by Dawkins in his book The Selfish Gene, according to Williams 1966 book Adaptation and Natural Selection, he essence of the genetical theory of natural selection is a statistical bias in the relative rates of survival of alternatives. The effectiveness of such bias in producing adaptation is contingent on the maintenance of certain quantitative relationships among the operative factors, one necessary condition is that the selected entity must have a high degree of permanence and a low rate of endogenous change, relative to the degree of bias. Williams argued that he natural selection of phenotypes cannot in itself produce cumulative change, each phenotype is the unique product of the interaction between genome and environment. It does not matter how fit and fertile a phenotype is, it eventually be destroyed. Since 1954, it has known that DNA is the main physical substrate to genetic information. So, a sequence of DNA can have a high permanence. In normal sexual reproduction, a genome is the unique combination of fathers and mothers chromosomes produced at the moment of fertilization. It is generally destroyed with its organism, because meiosis and recombination destroy genotypes as surely as death, only half of it is transmitted to each descendant due to independent segregation. The gene as an informational entity persists for a significant span of time through a lineage of many physical copies. In his book River out of Eden, Dawkins coins the phrase Gods utility function to explain his view on genes as units of selection and he uses this phrase as a synonym of the meaning of life or the purpose of life. Finally, Dawkins argues that it is a mistake to assume that an ecosystem or a species as a whole exists for a purpose, Genes are usually packed together inside a genome, which is itself contained inside an organism. They build vehicles to promote their interests of jumping into the next generation of vehicles. As Dawkins puts it, organisms are the machines of genes
26.
DNA repair
–
DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule, other lesions induce potentially harmful mutations in the cells genome, which affect the survival of its daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is active as it responds to damage in the DNA structure. When normal repair processes fail, and when cellular apoptosis does not occur, irreparable DNA damage may occur, including double-strand breaks and this can eventually lead to malignant tumors, or cancer as per the two hit hypothesis. The rate of DNA repair is dependent on many factors, including the type, the age of the cell. Many genes that were shown to influence life span have turned out to be involved in DNA damage repair. The 2015 Nobel Prize in Chemistry was awarded to Tomas Lindahl, Paul Modrich, there are two types, nucleotide excision repair and base excision repair. DNA damage, due to environmental factors and normal metabolic processes inside the cell, the vast majority of DNA damage affects the primary structure of the double helix, that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level, DNA is, however, supercoiled and wound around packaging proteins called histones, and both superstructures are vulnerable to the effects of DNA damage. Daughter cells that inherit these wrong bases carry mutations from which the original DNA sequence is unrecoverable, monoadduct damage cause by change in single nitrogenous base of DNA Diadduct damage Damage caused by exogenous agents comes in many forms. Some examples are, UV-B light causes crosslinking between adjacent cytosine and thymine bases creating pyrimidine dimers and this is called direct DNA damage. UV-A light creates mostly free radicals, the damage caused by free radicals is called indirect DNA damage. Ionizing radiation such as that created by decay or in cosmic rays causes breaks in DNA strands. Intermediate-level ionizing radiation may induce irreparable DNA damage leading to pre-mature aging, thermal disruption at elevated temperature increases the rate of depurination and single-strand breaks. For example, hydrolytic depurination is seen in the thermophilic bacteria, the rate of depurination is too high in these species to be repaired by normal repair machinery, hence a possibility of an adaptive response cannot be ruled out. UV damage, alkylation/methylation, X-ray damage and oxidative damage are examples of induced damage, spontaneous damage can include the loss of a base, deamination, sugar ring puckering and tautomeric shift
27.
Actinobacteria
–
The Actinobacteria are a phylum of Gram-positive bacteria. They can be terrestrial or aquatic and they are of great economic importance to humans because agriculture and forests depend on their contributions to soil systems. In soil, they behave much like fungi, helping to decompose the organic matter of dead organisms so the molecules can be taken up anew by plants. In this role the colonies often grow extensive mycelia, like a fungus would, some soil actinobacteria live symbiotically with the plants whose roots pervade the soil, fixing nitrogen for the plants in exchange for access to some of the plants saccharides. Beyond the great interest in Actinobacteria for their role, much is yet to be learned about them. Although currently understood primarily as soil bacteria, they might be abundant in fresh waters. Actinobacteria is one of the dominant bacterial phyla and contains one of the largest of bacterial genera, Streptomyces and other actinobacteria are major contributors to biological buffering of soils. They are also the source of many antibiotics, most Actinobacteria of medical or economic significance are in subclass Actinobacteridae, and belong to the order Actinomycetales. While many of these cause disease in humans, Streptomyces is notable as a source of antibiotics, of those Actinobacteria not in the Actinomycetales, Gardnerella is one of the most researched. Classification of Gardnerella is controversial, and MeSH catalogues it as both a Gram-positive and Gram-negative organism, actinobacteria-derived antibiotics that are important in medicine include aminoglycosides, anthracyclines, chloramphenicol, macrolide, tetracyclines, etc. Actinobacteria have high guanine and cytosine content in their DNA, the G+C content of Actinobacteria can be as high as 70%, though some may have a low G+C content. Analysis of glutamine synthetase sequence has been suggested for phylogenetic analysis of the Actinobacteria, the phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature, Zhi, Li & Stackebrandt 2009 Order Solirubrobacterales Reddy & Garcia-Pichel 2009 Family Conexibacteraceae Stackebrandt 2005 emend. Zhi, Li & Stackebrandt 2009 Family Patulibacteraceae Takahashi et al.2006 emend, Zhi, Li & Stackebrandt 2009 Family Solirubrobacteraceae Stackebrandt 2005 emend. Zhi et al.2009 Class Coriobacteriia Konig 2013 emend, Gupta et al.2013 Order Coriobacteriales Stackebrandt et al.1997 emend. Gupta et al.2013 Family Atopobiaceae Gupta et al.2013 Family Coriobacteriaceae Stackebrandt, Zhi, Li & Stackebrandt 2009 Order Eggerthellales Gupta et al.2013 Family Eggerthellaceae Gupta et al.2013 Class Acidimicrobiia Norris 2013 Order Acidimicrobiales Stackebrandt et al.1997 emend. Zhi et al.2009 Family Acidimicrobiaceae Stackebrandt et al.1997 emend, Zhi et al.2009 Order Catenulisporales Donadio et al.2012 Family Actinospicaceae Cavaletti et al.2006 emend. Zhi et al.2009 Family Catenulisporaceae Busti et al.2006 emend, Zhi et al.2009 Order Streptomycetales Kampfer 2012 Family Streptomycetaceae Waksman & Henrici 1943 emend
28.
Bacterium
–
Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
29.
Yeast
–
Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The yeast lineage originated hundreds of millions of years ago, and 1,500 species are currently identified and they are estimated to constitute 1% of all described fungal species. Yeast sizes vary greatly, depending on species and environment, typically measuring 3–4 µm in diameter, most yeasts reproduce asexually by mitosis, and many do so by the asymmetric division process known as budding. Yeasts, with their growth habit, can be contrasted with molds. Fungal species that can take both forms are called dimorphic fungi and it is also a centrally important model organism in modern cell biology research, and is one of the most thoroughly researched eukaryotic microorganisms. Researchers have used it to information about the biology of the eukaryotic cell. Other species of yeasts, such as Candida albicans, are opportunistic pathogens, yeasts have recently been used to generate electricity in microbial fuel cells, and produce ethanol for the biofuel industry. Yeasts do not form a taxonomic or phylogenetic grouping. The budding yeasts are classified in the order Saccharomycetales, within the phylum Ascomycota, the word yeast comes from Old English gist, gyst, and from the Indo-European root yes-, meaning boil, foam, or bubble. Yeast microbes are probably one of the earliest domesticated organisms, archaeologists digging in Egyptian ruins found early grinding stones and baking chambers for yeast-raised bread, as well as drawings of 4, 000-year-old bakeries and breweries. In 1680, Dutch naturalist Anton van Leeuwenhoek first microscopically observed yeast, but at the time did not consider them to be living organisms, researchers were doubtful whether yeasts were algae or fungi, but in 1837 Theodor Schwann recognized them as fungi. In 1857, French microbiologist Louis Pasteur proved in the paper Mémoire sur la fermentation alcoolique that alcoholic fermentation was conducted by living yeasts and not by a chemical catalyst. Pasteur showed that by bubbling oxygen into the yeast broth, cell growth could be increased, by the late 18th century, two yeast strains used in brewing had been identified, Saccharomyces cerevisiae and S. carlsbergensis. S. cerevisiae has been sold commercially by the Dutch for bread-making since 1780, while, around 1800, in 1825, a method was developed to remove the liquid so the yeast could be prepared as solid blocks. The industrial production of yeast blocks was enhanced by the introduction of the press in 1867. In 1872, Baron Max de Springer developed a process to create granulated yeast. Yeasts are chemoorganotrophs, as they use organic compounds as a source of energy, carbon is obtained mostly from hexose sugars, such as glucose and fructose, or disaccharides such as sucrose and maltose. Some species can metabolize pentose sugars such as ribose, alcohols, Yeast species either require oxygen for aerobic cellular respiration or are anaerobic, but also have aerobic methods of energy production
30.
Saccharomyces cerevisiae
–
Saccharomyces cerevisiae is a species of yeast. It has been instrumental to winemaking, baking, and brewing since ancient times and it is believed to have been originally isolated from the skin of grapes. It is one of the most intensively studied model organisms in molecular and cell biology. It is the microorganism behind the most common type of fermentation, S. cerevisiae cells are round to ovoid, 5–10 μm in diameter. It reproduces by a process known as budding. Many proteins important in biology were first discovered by studying their homologs in yeast, these proteins include cell cycle proteins, signaling proteins. S. cerevisiae is currently the only yeast cell known to have Berkeley bodies present, antibodies against S. cerevisiae are found in 60–70% of patients with Crohns disease and 10–15% of patients with ulcerative colitis. Saccharomyces derives from Latinized Greek and means sugar-mold or sugar-fungus, saccharo being the combining form sugar, cerevisiae comes from Latin and means of beer. Refinements in microbiology following the work of Louis Pasteur led to more advanced methods of culturing pure strains, in 1879, Great Britain introduced specialized growing vats for the production of S. The company created yeast that would rise twice as fast, cutting down on baking time, lesaffre would later create instant yeast in the 1970s, which has gained considerable use and market share at the expense of both fresh and dry yeast in their various applications. In nature, yeast cells are primarily on ripe fruits such as grapes. Since S. cerevisiae is not airborne, it requires a vector to move, queens of social wasps overwintering as adults can harbor yeast cells from autumn to spring and transmit them to their progeny. The intestine of Polistes dominula, a wasp, hosts S. cerevisiae strains as well as S. cerevisiae × S. paradoxus hybrids. The optimum temperature for growth of S. cerevisiae is 30–35 °C, two forms of yeast cells can survive and grow, haploid and diploid. The haploid cells undergo a simple lifecycle of mitosis and growth and this is the asexual form of the fungus. The diploid cells undergo a simple lifecycle of mitosis and growth. The rate at which the cell cycle progresses often differs substantially between haploid and diploid cells. Under conditions of stress, diploid cells can undergo sporulation, entering meiosis and producing four haploid spores and this is the sexual form of the fungus
31.
Model organism
–
Model organisms are in vivo models and are widely used to research human disease when human experimentation would be unfeasible or unethical. This strategy is made possible by the descent of all living organisms. Studying model organisms can be informative, but care must be taken when extrapolating from one organism to another, in researching human disease, model organisms allow for better understanding the disease process without the added risk of harming an actual human. The species chosen will usually meet a determined taxonomic equivalency to humans, although biological activity in a model organism does not ensure an effect in humans, many drugs, treatments and cures for human diseases are developed in part with the guidance of animal models. There are three types of disease models, homologous, isomorphic and predictive. Homologous animals have the same causes, symptoms and treatment options as would humans who have the same disease, isomorphic animals share the same symptoms and treatments. Predictive models are similar to a human disease in only a couple of aspects. The use of animals in research dates back to ancient Greece, with Aristotle, research using animal models has been central to most of the achievements of modern medicine. It has contributed most of the knowledge in fields such as human physiology and biochemistry. For example, the results have included the near-eradication of polio and the development of organ transplantation, from 1910 to 1927, Thomas Hunt Morgans work with the fruit fly Drosophila melanogaster identified chromosomes as the vector of inheritance for genes. Drosophila became one of the first, and for some time the most widely used, model organisms, D. melanogaster remains one of the most widely used eukaryotic model organisms. The mouse has since been used extensively as an organism and is associated with many important biological discoveries of the 20th. In the late 19th century, Emil von Behring isolated the diphtheria toxin and he went on to develop an antitoxin against diphtheria in animals and then in humans, which resulted in the modern methods of immunization and largely ended diphtheria as a threatening disease. The diphtheria antitoxin is famously commemorated in the Iditarod race, which is modeled after the delivery of antitoxin in the 1925 serum run to Nome. The success of animal studies in producing the diphtheria antitoxin has also attributed as a cause for the decline of the early 20th-century opposition to animal research in the United States. This led to the 1922 discovery of insulin and its use in treating diabetes, modern general anaesthetics, such as halothane and related compounds, were also developed through studies on model organisms, and are necessary for modern, complex surgical operations. In the 1940s, Jonas Salk used rhesus monkey studies to isolate the most virulent forms of the polio virus, the vaccine, which was made publicly available in 1955, reduced the incidence of polio 15-fold in the United States over the following five years. It has been estimated that developing and producing the vaccines required the use of 100,000 rhesus monkeys, models are those organisms with a wealth of biological data that make them attractive to study as examples for other species and/or natural phenomena that are more difficult to study directly
32.
Arabidopsis thaliana
–
Arabidopsis thaliana is a small flowering plant native to Eurasia. A. thaliana is considered a weed, it is found by roadsides, a winter annual with a relatively short life cycle, A. thaliana is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, A. thaliana has a small genome of approximately 135 megabase pairs. It was the first plant to have its genome sequenced, and is a tool for understanding the molecular biology of many plant traits, including flower development. Arabidopsis thaliana is a plant, usually growing to 20–25 cm tall. The leaves form a rosette at the base of the plant, leaves are covered with small, unicellular hairs. The flowers are 3 mm in diameter, arranged in a corymb, the fruit is a siliqua 5–20 mm long, containing 20–30 seeds. Roots are simple in structure, with a primary root that grows vertically downward. These roots form interactions with rhizosphere bacteria such as Bacillus megaterium, a. thaliana can complete its entire lifecycle in six weeks. The central stem produces flowers grows after about three weeks, and the flowers naturally self-pollinate. In the lab, A. thaliana may be grown in Petri plates, pots, or hydroponics, the plant was first described in 1577 in the Harz Mountains by Johannes Thal, a physician from Nordhausen, Thüringen, Germany, who called it Pilosella siliquosa. In 1753, Carl Linnaeus renamed the plant Arabis thaliana in honor of Thal, in 1842, the German botanist Gustav Heynhold erected the new genus Arabidopsis and placed the plant in that genus. The genus name, Arabidopsis, comes from Greek, meaning resembling Arabis, thousands of natural inbred accessions of A. thaliana have been collected from throughout its natural and introduced range. These accessions exhibit considerable genetic and phenotypic variation which can be used to study the adaptation of species to different environments. A. thaliana is native to Europe, Asia, and northwestern Africa and it also appears to be native in tropical afroalpine ecosystems. It has been introduced and naturalized worldwide, a. thaliana readily grows and often pioneers rocky, sandy and calcareous soils. It is generally considered a weed, due to its distribution in agricultural fields, roadside, railway lines, waste ground. Like most Brassicaceae species, A. thaliana is edible by humans as a salad or cooked, the first mutant in A. thaliana was documented in 1873 by Alexander Braun, describing a double flower phenotype
33.
Genetic code
–
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
34.
Plasmodium falciparum
–
Plasmodium falciparum is a protozoan parasite, one of the species of Plasmodium that cause malaria in humans. It is transmitted by the female Anopheles mosquito and this species causes the diseases most dangerous form, malignant or falciparum malaria. It has the highest complication rates and mortality, around the world, malaria is the most significant parasitic disease of humans and claims the lives of more children worldwide than any other infectious disease. The 2015 World Health Organization report found 214 million cases of malaria worldwide and this resulted in an estimated 438,000 deaths. Rates of infection decreased from 2000 to 2015 by 37%, in sub-Saharan Africa, over 75% of cases were due to P. falciparum, whereas in most other malarial countries, other, less virulent plasmodial species predominate. Almost every malarial death is caused by P. falciparum, of the six malarial parasites, P. falciparum causes the most-often fatal and medically severe form of disease. Roughly 50% of all malarial infections are caused by P. falciparum, Malaria is caused by an infection with protozoa of the genus Plasmodium. The name malaria, from the Italian mala aria, meaning bad air and this species name comes from the Latin falx, meaning sickle and parere meaning to give birth. The parasite was first seen by Laveran on November 6,1880, at a hospital in Constantine, Algeria. Patrick Manson hypothesised that mosquitoes could transmit malaria and this hypothesis was experimentally confirmed independently by Giovanni Battista Grassi and Ronald Ross in 1898. Grassi proposed an exerythrocytic stage in the lifecycle, later confirmed by Shortt, Garnham, Covell and Shute, since 1900, the area of the world exposed to malaria has been halved, yet two billion more people are presently exposed. Morbidity, as well as mortality, is substantial, Infection rates in children in endemic areas are on the order of 50%. Chronic infection has been shown to reduce school scores by up to 15%, reduction in the incidence of malaria coincides with increased economic output. RTO, S is a vaccine for this form of malaria, however no vaccines are known for any of the five or more other species that cause human malaria. In 1640, Huan del Vego first employed the tincture of the bark for treating malaria. Thompson introduced this Jesuits bark to England and its first recorded use there was by John Metford of Northampton in 1656. Morton presented the first detailed description of the picture of malaria. Gize studied the extraction of quinine from the cinchona bark and Pelletier and Caventou in France extracted pure quinine alkaloids
35.
Newcastle University
–
Newcastle University is a public research university located in Newcastle upon Tyne in the North-East of England. The university can trace its origins to a School of Medicine and Surgery, established in 1834 and these two colleges came to form one division of the federal University of Durham, with the Durham Colleges forming the other. The Newcastle colleges merged to form Kings College in 1937, in 1963, following an Act of Parliament, Kings College became the University of Newcastle upon Tyne. Newcastle University is a red brick university and is a member of the Russell Group, the university has one of the largest EU research portfolios in the UK. Newcastle attracts over 20,000 students from more than 120 different countries, in June 1851, following a dispute among the teaching staff, the School split into two rival institutions. The majority formed the Newcastle College of Medicine, and the others established themselves as the Newcastle upon Tyne College of Medicine, by 1852, the majority college was formally linked to the University of Durham. It awarded its first Licence in Medicine in 1856, and its teaching certificates were recognised by the University of London for graduation in medicine, the two colleges amalgamated in 1857 and renamed the University of Durham College of Medicine in 1870. Attempts to realise a place for the teaching of sciences in the city were met with the foundation of the College of Physical Science in 1871. By 1908, the Newcastle Division was teaching a range of subjects in the Faculties of Medicine, Arts, and Science. As the successor of Kings College, Durham, the university at its founding in 1963, in the Letters Patent authorising the transfer, the arms are blazoned Azure, a Cross of St Cuthbert Argent and in chief of the last a lion passant guardant Gules. While a Latin motto, mens agitat molem appears in the Students Union building, the university occupies a campus site close to Haymarket in central Newcastle upon Tyne. It is located to the northwest of the city centre between the spaces of Leazes Park and the Town Moor. The Armstrong building is the oldest building on the campus and is the site of the original Armstrong College. The building was constructed in three stages, the north east wing was completed first at a cost of £18,000, the south-east wing, which includes the Jubilee Tower, and south-west wings were opened in 1894. The Jubilee Tower was built with funds raised from an Exhibition to mark Queen Victorias Jubilee in 1887. The north-west front, forming the entrance, was completed in 1906. Much of the construction work was financed by Sir Isaac Lowthian Bell. In 1906 it was opened by King Edward VII, the building contains the Kings Hall, which serves as the universitys chief hall for ceremonial purposes where Congregation ceremonies are held
36.
PubMed Identifier
–
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
. PMID 16449200.