Genome
In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA; the genome includes both the genes and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of the genome is called genomics; the term genome was created in 1920 by Hans Winkler, professor of botany at the University of Hamburg, Germany. The Oxford Dictionary suggests the name is a blend of the words chromosome. However, see omics for a more thorough discussion. A few related -ome words existed, such as biome and rhizome, forming a vocabulary into which genome fits systematically. A genome sequence is the complete list of the nucleotides that make up all the chromosomes of an individual or a species. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity. In 1976, Walter Fiers at the University of Ghent was the first to establish the complete nucleotide sequence of a viral RNA-genome.
The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs. The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s; 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 genome sequencing cheaper and easier, the number of complete genome sequences is growing rapidly; the US National Institutes of Health maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the puffer fish, the bacteria E. coli.
In December 2013, scientists first sequenced the entire genome of a Neanderthal, an extinct species of humans. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave. New sequencing technologies, such as massive parallel sequencing have 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 full genome of James D. Watson, one of the co-discoverers of the structure of DNA. Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than aids in navigating around the genome; the Human Genome Project was organized to sequence the human genome. A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris. Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity.
The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service, to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA. LAND at the New York Genome Center, an example both of the economies of scale and of citizen science. Viral genomes can be composed of either RNA or DNA; the genomes of RNA viruses can be either single-stranded or double-stranded RNA, may contain one or more separate RNA molecules. DNA viruses can have either double-stranded genomes. Most DNA virus genomes are composed of a single, linear molecule of DNA, but some are made up of a circular DNA molecule. Prokaryotes and eukaryotes have DNA genomes. Archaea have a single circular chromosome. Most bacteria have a single circular chromosome. If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, if the cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and partially replicated chromosomes.
Most prokaryotes have little repetitive DNA in their genomes. However, some symbiotic bacteria have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins; some bacteria have auxiliary genetic material part of their genome, carried in plasmids. For this, the word genome should not be used as a synonym of chromosome. Eukaryotic genomes are composed of one or more linear DNA chromosomes; the number of chromosomes varies from Jack jumper ants and an asexual nemotode, which each have only one pair, to a fern species that has 720 pairs. A typical human cell has two copies of each of 22 autosomes, one inherited from each parent, plus two sex chromosomes, making it diploid. Gametes, such as ova, sperm and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to the chromosomes in the nucleus, organelles such as the chloroplasts and mitochondria have their own DNA. Mitochondria are sometimes said to have their own genome referred to as the "mitochondrial genome".
The DNA found within the chloroplast may be referred to as the "plastome". Like the bacteria they originated from and chloroplasts have a circular chromosome
Transcriptome
The transcriptome is the set of all RNA molecules in one cell or a population of cells. It is sometimes used to refer to all RNAs, or just mRNA, depending on the particular experiment, it differs from the exome in that it includes only those RNA molecules found in a specified cell population, includes the amount or concentration of each RNA molecule in addition to the molecular identities. The term can be applied to the total set of transcripts in a given organism, or to the specific subset of transcripts present in a particular cell type. Unlike the genome, fixed for a given cell line, the transcriptome can vary with external environmental conditions; because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are being expressed at any given time, with the exception of mRNA degradation phenomena such as transcriptional attenuation. The study of transcriptomics, examines the expression level of RNAs in a given cell population focusing on mRNA, but sometimes including others such as tRNAs, sRNAs.
Transcriptomics techniques include DNA microarrays and next-generation sequencing technologies called RNA-Seq. Transcription can be studied at the level of individual cells by single-cell transcriptomics. There are two general methods of inferring transcriptome sequences. One approach maps sequence reads onto a reference genome, either of the organism itself or of a related species; the other approach, de novo transcriptome assembly, uses software to infer transcripts directly from short sequence reads. A number of organism-specific transcriptome databases have been constructed and annotated to aid in the identification of genes that are differentially expressed in distinct cell populations. RNA-seq is emerging as the method of choice for measuring transcriptomes of organisms, though the older technique of DNA microarrays is still used. RNA-seq measures the transcription of a specific gene by converting long RNAs into a library of cDNA fragments; the cDNA fragments are sequenced using high-throughput sequencing technology and aligned to a reference genome or transcriptome, used to create an expression profile of the genes.
The transcriptomes of stem cells and cancer cells are of particular interest to researchers who seek to understand the processes of cellular differentiation and carcinogenesis. Analysis of the transcriptomes of human oocytes and embryos is used to understand the molecular mechanisms and signaling pathways controlling early embryonic development, could theoretically be a powerful tool in making proper embryo selection in in vitro fertilisation. Transcriptomics is an emerging and continually growing field in biomarker discovery for use in assessing the safety of drugs or chemical risk assessment. Transcriptomes may be used to infer phylogenetic relationships among individuals; the transcriptome can be seen as a subset of the proteome, that is, the entire set of proteins expressed by a genome. However, the analysis of relative mRNA expression levels can be complicated by the fact that small changes in mRNA expression can produce large changes in the total amount of the corresponding protein present in the cell.
One analysis method, known as gene set enrichment analysis, identifies coregulated gene networks rather than individual genes that are up- or down-regulated in different cell populations. Although microarray studies can reveal the relative amounts of different mRNAs in the cell, levels of mRNA are not directly proportional to the expression level of the proteins they code for; the number of protein molecules synthesized using a given mRNA molecule as a template is dependent on translation-initiation features of the mRNA sequence. The complete protein complement of a cell or organism is known as the proteome. Transcriptomics technologies Serial analysis of gene expression List of omics topics in biology Metabolome Gene expression Weighted gene co-expression network analysis Functional genomics ^ Wang Z, Gerstein M, Snyder M.. RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev. Genetics 10: 57-63. ^ Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP..
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545-50. ^ "Antisense Transcription in the Mammalian Transcriptome" by the RIKEN Genome Exploration Research Group and Genome Science Group and the FANTOM Consortium: S. Katayama et al. in Science, Vol 309, Issue 5740, 1564–1566, 2 September 2005. ^ Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B, Kinzler KW. Characterization of the yeast transcriptome. Cell. 1997 Jan 24. ^ Laule O, Hirsch-Hoffmann M, Hruz T, Gruissem W, P Zimmermann. Web-based analysis of the mouse transcriptome using Genevestigator. BMC Bioinformatics 7:311 ^ Assou, S.. "Dynamic changes in gene expression during human early embryo development: From fundamental aspects to clinical applications". Human Reproduction Update. 17: 272–290. Doi:10.1093/humupd/dmq036. PMC 3189516. PMID 20716614. ^ Ogorodnikov, A. "Processing and transcriptome expansion at the mRNA 3′ end in health and disease: finding the right end".
Eur J Physiol. 468: 993–1012. Doi:10.1007/s00424-016-
International Standard Serial Number
An International Standard Serial Number is an eight-digit serial number used to uniquely identify a serial publication, such as a magazine. The ISSN is helpful in distinguishing between serials with the same title. ISSN are used in ordering, interlibrary loans, other practices in connection with serial literature; the ISSN system was first drafted as an International Organization for Standardization international standard in 1971 and published as ISO 3297 in 1975. ISO subcommittee TC 46/SC 9 is responsible for maintaining the standard; when a serial with the same content is published in more than one media type, a different ISSN is assigned to each media type. For example, many serials are published both in electronic media; the ISSN system refers to these types as electronic ISSN, respectively. Conversely, as defined in ISO 3297:2007, every serial in the ISSN system is assigned a linking ISSN the same as the ISSN assigned to the serial in its first published medium, which links together all ISSNs assigned to the serial in every medium.
The format of the ISSN is an eight digit code, divided by a hyphen into two four-digit numbers. As an integer number, it can be represented by the first seven digits; the last code digit, which may be 0-9 or an X, is a check digit. Formally, the general form of the ISSN code can be expressed as follows: NNNN-NNNC where N is in the set, a digit character, C is in; the ISSN of the journal Hearing Research, for example, is 0378-5955, where the final 5 is the check digit, C=5. To calculate the check digit, the following algorithm may be used: Calculate the sum of the first seven digits of the ISSN multiplied by its position in the number, counting from the right—that is, 8, 7, 6, 5, 4, 3, 2, respectively: 0 ⋅ 8 + 3 ⋅ 7 + 7 ⋅ 6 + 8 ⋅ 5 + 5 ⋅ 4 + 9 ⋅ 3 + 5 ⋅ 2 = 0 + 21 + 42 + 40 + 20 + 27 + 10 = 160 The modulus 11 of this sum is calculated. For calculations, an upper case X in the check digit position indicates a check digit of 10. To confirm the check digit, calculate the sum of all eight digits of the ISSN multiplied by its position in the number, counting from the right.
The modulus 11 of the sum must be 0. There is an online ISSN checker. ISSN codes are assigned by a network of ISSN National Centres located at national libraries and coordinated by the ISSN International Centre based in Paris; the International Centre is an intergovernmental organization created in 1974 through an agreement between UNESCO and the French government. The International Centre maintains a database of all ISSNs assigned worldwide, the ISDS Register otherwise known as the ISSN Register. At the end of 2016, the ISSN Register contained records for 1,943,572 items. ISSN and ISBN codes are similar in concept. An ISBN might be assigned for particular issues of a serial, in addition to the ISSN code for the serial as a whole. An ISSN, unlike the ISBN code, is an anonymous identifier associated with a serial title, containing no information as to the publisher or its location. For this reason a new ISSN is assigned to a serial each time it undergoes a major title change. Since the ISSN applies to an entire serial a new identifier, the Serial Item and Contribution Identifier, was built on top of it to allow references to specific volumes, articles, or other identifiable components.
Separate ISSNs are needed for serials in different media. Thus, the print and electronic media versions of a serial need separate ISSNs. A CD-ROM version and a web version of a serial require different ISSNs since two different media are involved. However, the same ISSN can be used for different file formats of the same online serial; this "media-oriented identification" of serials made sense in the 1970s. In the 1990s and onward, with personal computers, better screens, the Web, it makes sense to consider only content, independent of media; this "content-oriented identification" of serials was a repressed demand during a decade, but no ISSN update or initiative occurred. A natural extension for ISSN, the unique-identification of the articles in the serials, was the main demand application. An alternative serials' contents model arrived with the indecs Content Model and its application, the digital object identifier, as ISSN-independent initiative, consolidated in the 2000s. Only in 2007, ISSN-L was defined in the
Peptide mass fingerprinting
Peptide mass fingerprinting is an analytical technique for protein identification in which the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be measured with a mass spectrometer such as MALDI-TOF or ESI-TOF. The method was developed in 1993 by several groups independently; the peptide masses are compared to either a database containing known protein sequences or the genome. This is achieved by using computer programs that translate the known genome of the organism into proteins theoretically cut the proteins into peptides, calculate the absolute masses of the peptides from each protein, they compare the masses of the peptides of the unknown protein to the theoretical peptide masses of each protein encoded in the genome. The results are statistically analyzed to find the best match; the advantage of this method is. Time-consuming de novo peptide sequencing is unnecessary. A disadvantage is. Additionally most PMF algorithms assume; the presence of a mixture can complicate the analysis and compromise the results.
Typical for the PMF based protein identification is the requirement for an isolated protein. Mixtures exceeding a number of 2-3 proteins require the additional use of MS/MS based protein identification to achieve sufficient specificity of identification. Therefore, the typical PMF samples are isolated proteins from two-dimensional gel electrophoresis or isolated SDS-PAGE bands. Additional analyses by MS/MS can either be direct, e.g. MALDI-TOF/TOF analysis or downstream nanoLC-ESI-MS/MS analysis of gel spot eluates. Due to the long, tedious process of analyzing proteins, peptide mass fingerprinting was developed. Edman degradation was used in protein analysis, it required an hour to analyze one amino acid residue. SDS-PAGE was used to separate proteins in complex mixtures, which employed methods of electroblotting and staining. Bands would be extracted from the gel and sequenced, automatically. A recurring problem in the process was that interfering proteins would purify with the protein of interest.
The sequences of these interfering proteins were compiled into what came to known as the Dayhoff database. Having the sequences of these known protein contaminants in databases decreased instrument time and expenses involved in protein analysis. Protein samples can be derived from SDS-PAGE or reversed phase HPLC, are subject to some chemical modifications. Disulfide bridges in proteins are reduced and cysteine amino acids are carbamidomethylated chemically or acrylamidated during the gel electrophoresis; the proteins are cut into several fragments using proteolytic enzymes such as trypsin, chymotrypsin or Glu-C. A typical sample:protease ratio is 50:1; the proteolysis is carried out overnight and the resulting peptides are extracted with acetonitrile and dried under vacuum. The peptides are dissolved in a small amount of distilled water or further concentrated and purified and are ready for mass spectrometric analysis; the digested protein can be analyzed with different types of mass spectrometers such as ESI-TOF or MALDI-TOF.
MALDI-TOF is the preferred instrument because it allows a high sample throughput and several proteins can be analyzed in a single experiment, if complemented by MS/MS analysis. LC/ESI-MS and CE/ESI-MS are great techniques for peptide mass fingerprinting. A small fraction of the peptide is pipetted onto a MALDI target and a chemical called a matrix is added to the peptide mix. Common matrices are Sinapinic acid, Alpha-Cyano-4-hydroxycinnamic acid, 2,3-Dihydroxybenzoic acid; the matrix molecules are required for the desorption of the peptide molecules. Matrix and peptide molecules are ready to be analyzed. There is one predominantly MALDI-MS sample preparation technique, namely dried droplet technique; the target is inserted into the vacuum chamber of the mass spectrometer and the desorption and ionisation of the polypeptide fragments is initiated by a pulsed laser beam which transfers high amounts of energy into the matrix molecules. The energy transfer is sufficient to promote the ionisation and transition of matrix molecules and peptides from the solid phase into the gas phase.
The ions are accelerated in the electric field of the mass spectrometer and fly towards an ion detector where their arrival is detected as an electric signal. Their mass-to-charge ratio is proportional to their time of flight in the drift tube and can be calculated accordingly. Coupling ESI with capillary LC can separate peptides from protein digests, while obtaining their molecular masses at the same time. Capillary electrophoresis coupled with ESI-MS is another technique; the mass spectrometric analysis produces a list of molecular weights of the fragments, called a peak list. The peptide masses are compared to protein databases such as Swissprot, which contain protein sequence information. Software performs in silico digests on proteins in the database with the same enzyme used in the chemical cleavage reaction; the mass of these peptide fragments is calculated and compared to the peak list of measured peptide masses. The results are statistically analyzed and possible matches are returned in a results table.
Protein mass spectrometry Shotgun proteomics Top-down proteomics Bottom-up proteomics
Mass spectrometry
Mass spectrometry is an analytical technique that ionizes chemical species and sorts the ions based on their mass-to-charge ratio. In simpler terms, a mass spectrum measures the masses within a sample. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a plot of the ion signal as a function of the mass-to-charge ratio; these spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, to elucidate the chemical structures of molecules and other chemical compounds. In a typical MS procedure, a sample, which may be solid, liquid, or gas, is ionized, for example by bombarding it with electrons; this may cause some of the sample's molecules to break into charged fragments. These ions are separated according to their mass-to-charge ratio by accelerating them and subjecting them to an electric or magnetic field: ions of the same mass-to-charge ratio will undergo the same amount of deflection.
The ions are detected by a mechanism capable of detecting charged particles, such as an electron multiplier. Results are displayed as spectra of the relative abundance of detected ions as a function of the mass-to-charge ratio; the atoms or molecules in the sample can be identified by correlating known masses to the identified masses or through a characteristic fragmentation pattern. In 1886, Eugen Goldstein observed rays in gas discharges under low pressure that traveled away from the anode and through channels in a perforated cathode, opposite to the direction of negatively charged cathode rays. Goldstein called these positively charged anode rays "Kanalstrahlen". Wilhelm Wien found that strong electric or magnetic fields deflected the canal rays and, in 1899, constructed a device with perpendicular electric and magnetic fields that separated the positive rays according to their charge-to-mass ratio. Wien found. English scientist J. J. Thomson improved on the work of Wien by reducing the pressure to create the mass spectrograph.
The word spectrograph had become part of the international scientific vocabulary by 1884. Early spectrometry devices that measured the mass-to-charge ratio of ions were called mass spectrographs which consisted of instruments that recorded a spectrum of mass values on a photographic plate. A mass spectroscope is similar to a mass spectrograph except that the beam of ions is directed onto a phosphor screen. A mass spectroscope configuration was used in early instruments when it was desired that the effects of adjustments be observed. Once the instrument was properly adjusted, a photographic plate was exposed; the term mass spectroscope continued to be used though the direct illumination of a phosphor screen was replaced by indirect measurements with an oscilloscope. The use of the term mass spectroscopy is now discouraged due to the possibility of confusion with light spectroscopy. Mass spectrometry is abbreviated as mass-spec or as MS. Modern techniques of mass spectrometry were devised by Arthur Jeffrey Dempster and F.
W. Aston in 1918 and 1919 respectively. Sector mass spectrometers known as calutrons were developed by Ernest O. Lawrence and used for separating the isotopes of uranium during the Manhattan Project. Calutron mass spectrometers were used for uranium enrichment at the Oak Ridge, Tennessee Y-12 plant established during World War II. In 1989, half of the Nobel Prize in Physics was awarded to Hans Dehmelt and Wolfgang Paul for the development of the ion trap technique in the 1950s and 1960s. In 2002, the Nobel Prize in Chemistry was awarded to John Bennett Fenn for the development of electrospray ionization and Koichi Tanaka for the development of soft laser desorption and their application to the ionization of biological macromolecules proteins. A mass spectrometer consists of three components: an ion source, a mass analyzer, a detector; the ionizer converts a portion of the sample into ions. There is a wide variety of ionization techniques, depending on the phase of the sample and the efficiency of various ionization mechanisms for the unknown species.
An extraction system removes ions from the sample, which are targeted through the mass analyzer and into the detector. The differences in masses of the fragments allows the mass analyzer to sort the ions by their mass-to-charge ratio; the detector measures the value of an indicator quantity and thus provides data for calculating the abundances of each ion present. Some detectors give spatial information, e.g. a multichannel plate. The following example describes the operation of a spectrometer mass analyzer, of the sector type. Consider a sample of sodium chloride. In the ion source, the sample is ionized into sodium and chloride ions. Sodium atoms and ions are monoisotopic, with a mass of about 23 u. Chloride atoms and ions come in two isotopes with masses of 35 u and 37 u; the analyzer part of the spectrometer contains electric and magnetic fields, which exert forces on ions traveling through these fields. The speed of a charged particle may be increased or decreased while passing through the electric field, its direction may be altered by the magnetic field.
The magnitude of the deflection of the moving ion's trajectory depends on its mass-to-charge ratio. L
Nature (journal)
Nature is a British multidisciplinary scientific journal, first published on 4 November 1869. It is one of the most recognizable scientific journals in the world, was ranked the world's most cited scientific journal by the Science Edition of the 2010 Journal Citation Reports and is ascribed an impact factor of 40.137, making it one of the world's top academic journals. It is one of the few remaining academic journals that publishes original research across a wide range of scientific fields. Research scientists are the primary audience for the journal, but summaries and accompanying articles are intended to make many of the most important papers understandable to scientists in other fields and the educated public. Towards the front of each issue are editorials and feature articles on issues of general interest to scientists, including current affairs, science funding, scientific ethics and research breakthroughs. There are sections on books and short science fiction stories; the remainder of the journal consists of research papers, which are dense and technical.
Because of strict limits on the length of papers the printed text is a summary of the work in question with many details relegated to accompanying supplementary material on the journal's website. There are many fields of research in which important new advances and original research are published as either articles or letters in Nature; the papers that have been published in this journal are internationally acclaimed for maintaining high research standards. Fewer than 8% of submitted papers are accepted for publication. In 2007 Nature received the Prince of Asturias Award for Humanity; the enormous progress in science and mathematics during the 19th century was recorded in journals written in German or French, as well as in English. Britain underwent enormous technological and industrial changes and advances in the latter half of the 19th century. In English the most respected scientific journals of this time were the refereed journals of the Royal Society, which had published many of the great works from Isaac Newton, Michael Faraday through to early works from Charles Darwin.
In addition, during this period, the number of popular science periodicals doubled from the 1850s to the 1860s. According to the editors of these popular science magazines, the publications were designed to serve as "organs of science", in essence, a means of connecting the public to the scientific world. Nature, first created in 1869, was not the first magazine of its kind in Britain. One journal to precede Nature was Recreative Science: A Record and Remembrancer of Intellectual Observation, created in 1859, began as a natural history magazine and progressed to include more physical observational science and technical subjects and less natural history; the journal's name changed from its original title to Intellectual Observer: A Review of Natural History, Microscopic Research, Recreative Science and later to the Student and Intellectual Observer of Science and Art. While Recreative Science had attempted to include more physical sciences such as astronomy and archaeology, the Intellectual Observer broadened itself further to include literature and art as well.
Similar to Recreative Science was the scientific journal Popular Science Review, created in 1862, which covered different fields of science by creating subsections titled "Scientific Summary" or "Quarterly Retrospect", with book reviews and commentary on the latest scientific works and publications. Two other journals produced in England prior to the development of Nature were the Quarterly Journal of Science and Scientific Opinion, established in 1864 and 1868, respectively; the journal most related to Nature in its editorship and format was The Reader, created in 1864. These similar journals all failed; the Popular Science Review survived longest, lasting 20 years and ending its publication in 1881. The Quarterly Journal, after undergoing a number of editorial changes, ceased publication in 1885; the Reader terminated in 1867, Scientific Opinion lasted a mere 2 years, until June 1870. Not long after the conclusion of The Reader, a former editor, Norman Lockyer, decided to create a new scientific journal titled Nature, taking its name from a line by William Wordsworth: "To the solid ground of nature trusts the Mind that builds for aye".
First owned and published by Alexander Macmillan, Nature was similar to its predecessors in its attempt to "provide cultivated readers with an accessible forum for reading about advances in scientific knowledge." Janet Browne has proposed that "far more than any other science journal of the period, Nature was conceived and raised to serve polemic purpose." Many of the early editions of Nature consisted of articles written by members of a group that called itself the X Club, a group of scientists known for having liberal and somewhat controversial scientific beliefs relative to the time period. Initiated by Thomas Henry Huxley, the group consisted of such important scientists as Joseph Dalton Hooker, Herbert Spencer, John Tyndall, along with another five scientists and mathematicians, it was in part its scientific liberality that made Nature a longer-lasti
Protein
Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, transporting molecules from one location to another. Proteins differ from one another in their sequence of amino acids, dictated by the nucleotide sequence of their genes, which results in protein folding into a specific three-dimensional structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are considered to be proteins and are called peptides, or sometimes oligopeptides; the individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, encoded in the genetic code.
In general, the genetic code specifies 20 standard amino acids. Shortly after or during synthesis, the residues in a protein are chemically modified by post-translational modification, which alters the physical and chemical properties, stability and the function of the proteins. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can work together to achieve a particular function, they associate to form stable protein complexes. Once formed, proteins only exist for a certain period and are degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan covers a wide range, they can exist for years with an average lifespan of 1 -- 2 days in mammalian cells. Abnormal or misfolded proteins are degraded more either due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in every process within cells.
Many proteins are enzymes that are vital to metabolism. Proteins have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for use in the metabolism. Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation and chromatography. Methods used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry. Most proteins consist of linear polymers built from series of up to 20 different L-α- amino acids. All proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, a variable side chain are bonded.
Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO–NH amide moiety into a fixed conformation. The side chains of the standard amino acids, detailed in the list of standard amino acids, have a great variety of chemical structures and properties; the amino acids in a polypeptide chain are linked by peptide bonds. Once linked in the protein chain, an individual amino acid is called a residue, the linked series of carbon and oxygen atoms are known as the main chain or protein backbone; the peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are coplanar. The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone; the end with a free amino group is known as the N-terminus or amino terminus, whereas the end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus.
The words protein and peptide are a little ambiguous and can overlap in meaning. Protein is used to refer to the complete biological molecule in a stable conformation, whereas peptide is reserved for a short amino acid oligomers lacking a stable three-dimensional structure. However, the boundary between the two is not well defined and lies near 20–30 residues. Polypeptide can refer to any single linear chain of amino acids regardless of length, but implies an absence of a defined conformation. Proteins can interact with many types of molecules, including with other proteins, with lipids, with carboyhydrates, with DNA, it has been estimated. Smaller bacteria, such as Mycoplasma or spirochetes contain fewer molecules, on the order of 50,000 to 1 million. By contrast, eukaryotic cells are larger and thus contain much more pro
