1.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
2.
Transposable element
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A transposable element is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cells genome size. Transposition often results in duplication of the TE, Barbara McClintocks discovery of these jumping genes earned her a Nobel Prize in 1983. Transposable elements make up a fraction of the genome and are responsible for much of the mass of DNA in a eukaryotic cell. It has been shown that TEs are important in genome function and evolution, in Oxytricha, which has a unique genetic system, these elements play a critical role in development. Transposons are also useful to researchers as a means to alter DNA inside a living organism. Barbara McClintock discovered the first TEs in maize at the Cold Spring Harbor Laboratory in New York, McClintock was experimenting with maize plants that had broken chromosomes. In the winter of 1944–1945, McClintock planted corn kernels that were self-pollinated and these kernels came from a long line of plants that had been self-pollinated, causing broken arms on the end of their ninth chromosomes. As the maize plants began to grow, McClintock noted unusual color patterns on the leaves, for example, one leaf had two albino patches of almost identical size, located side by side on the leaf. McClintock hypothesized that cell division certain cells lost genetic material. However, when comparing the chromosomes of the current generation of plants with the parent generation and this refuted the popular genetic theory of the time that genes were fixed in their position on a chromosome. McClintock found that genes could not only move, but they could also be turned on or off due to environmental conditions or during different stages of cell development. McClintock also showed that mutations could be reversed. She presented her report on her findings in 1951, and published an article on her discoveries in Genetics in November 1953 entitled Induction of Instability at Selected Loci in Maize. Her work would be dismissed and ignored until the late 1960s–1970s when it would be rediscovered after TEs were found in bacteria. She was awarded a Nobel Prize in Physiology or Medicine in 1983 for her discovery of TEs, approximately 90% of the maize genome is made up of TEs, as is 44% of the human genome. Transposable elements represent one of several types of genetic elements. TEs are assigned to one of two classes according to their mechanism of transposition, which can be described as either copy and paste or cut and paste. Class I TEs are copied in two stages, first, they are transcribed from DNA to RNA, and the RNA produced is then transcribed to DNA
3.
Genome
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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
4.
Tn3 transposon
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The Tn3 transposon is a 4957 base pair mobile genetic element, found in prokaryotes. It encodes three proteins, β-lactamase, an enzyme that confers resistance to β-lactam antibiotics, Tn3 transposase Tn3 resolvase Initially discovered as a repressor of transposase, resolvase also plays a role in facilitating Tn3 replication. The transposon is flanked by a pair of 38bp inverted repeats and this first stage is catalysed by transposase. The plasmid containing the transposon fuses with a host plasmid, in the process, the transposon and a short section of host DNA are replicated. The end product is a plasmid containing two copies of the transposon. Shapiro proposed the mechanism for this process, Four single-strand cleavages occur - one on each strand of the donor plasmid. The donor and target plasmids are ligated together, but there are two single-stranded regions, due to the positioning of the original cleavages, DNA replication makes the single-stranded regions double stranded, using the existing strand as a template. It is in this stage that the transposon is replicated, the diagrams on the right illustrate the way in which the positions of the cleavages lead to the replication of certain regions once the plasmids have fused. Res is 114 bp long and it consists of 3 sub-sites, namely sites I, each of these sites is of different lengths and they are unevenly spaced with 22bp separating sites I and II and only 5bp between sites II and III. The sites consist of 6bp inverted repeat motifs flanking a central sequence of variable length and these motifs act as binding sites for resolvase, so that each site binds a resolvase dimer but with varying affinity and probably a slightly different protein-DNA complex architecture. All three sub-sites are essential for recombination, at recombination, two directly repeated res sites with resolvase dimers bound to each sub-site, come together to form a large complex structure called the synaptosome. Resolvase bound to sites II and III initiates the assembly of this complex, again, it is the interaction between the resolvase dimers bound at accessory sites and resolvase at site I that causes the two dimers to synapse and form a tetramer. After the tetramer is formed it becomes activated and the top, the strand exchange ensues by as yet unknown mechanism with a resulting net rotation of 180°. The strand exchange is followed by the religation. Recombination between two directly repeated res sites separates, or resolves, the “cointegrate” into two molecules, each one now containing a copy of the Tn3 transposon. After resolution these two molecules remain linked as a simple two-noded catenane which can be separated in vivo by a type II topoisomerase. Wild type resolvase system absolutely requires a supercoiled substrate and that the sites are oriented in a direct repeat on the same DNA molecule. However, a number of “deregulated” or “hyperactive” mutants that have lost the requirement for the sites have been isolated
5.
Barbara McClintock
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Barbara McClintock was an American scientist and cytogeneticist who was awarded the 1983 Nobel Prize in Physiology or Medicine. McClintock received her PhD in botany from Cornell University in 1927, there she started her career as the leader in the development of maize cytogenetics, the focus of her research for the rest of her life. From the late 1920s, McClintock studied chromosomes and how they change during reproduction in maize and she developed the technique for visualizing maize chromosomes and used microscopic analysis to demonstrate many fundamental genetic ideas. One of those ideas was the notion of genetic recombination by crossing-over during meiosis—a mechanism by which exchange information. She produced the first genetic map for maize, linking regions of the chromosome to physical traits and she demonstrated the role of the telomere and centromere, regions of the chromosome that are important in the conservation of genetic information. She was recognized among the best in the field, awarded prestigious fellowships, during the 1940s and 1950s, McClintock discovered transposition and used it to demonstrate that genes are responsible for turning physical characteristics on and off. She developed theories to explain the suppression and expression of genetic information from one generation of plants to the next. Due to skepticism of her research and its implications, she stopped publishing her data in 1953, later, she made an extensive study of the cytogenetics and ethnobotany of maize races from South America. Barbara McClintock was born Eleanor McClintock on June 16,1902 in Hartford, Connecticut, Thomas McClintock was the child of British immigrants, and Sara Handy, born Grace, descended from an old American Mayflower family. Marjorie, the oldest child, was born in October 1898, Mignon, the youngest, Malcolm Rider, was born 18 months after Barbara. As a young girl, her parents determined that Eleanor, a feminine and delicate name, was not appropriate for her, McClintock was an independent child beginning at a very young age, a trait she later identified as her capacity to be alone. She was described as a solitary and independent child and she was close to her father, but had a difficult relationship with her mother, tension that began when she was young. The McClintock family moved to Brooklyn in 1908 and McClintock completed her education there at Erasmus Hall High School. She discovered her love of science and reaffirmed her solitary personality during high school and she wanted to continue her studies at Cornell Universitys College of Agriculture. Her mother resisted sending McClintock to college, for fear that she would be unmarriageable, McClintock was almost prevented from starting college, but her father intervened just before registration began, and she matriculated at Cornell in 1919. McClintock began her studies at Cornells College of Agriculture in 1919, there, she participated in student government and was invited to join a sorority, though she soon realized that she preferred not to join formal organizations. Instead, McClintock took up music, specifically jazz and she studied botany, receiving a BSc in 1923. Her interest in genetics began when she took her first course in that field in 1921, the course was based on a similar one offered at Harvard University, and was taught by C. B
6.
Maize
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Maize, also known as corn, is a large grain plant first domesticated by indigenous peoples in Mexico about 10,000 years ago. The six major types of corn are dent corn, flint corn, pod corn, popcorn, flour corn, the leafy stalk of the plant produces separate pollen and ovuliferous inflorescences or ears, which are fruits, yielding kernels or seeds. Maize kernels are used in cooking as a starch. Most historians believe maize was domesticated in the Tehuacan Valley of Mexico, recent research modified this view somewhat, scholars now indicate the adjacent Balsas River Valley of south-central Mexico as the center of domestication. The Olmec and Mayans cultivated maize in numerous varieties throughout Mesoamerica, cooked and its believed that beginning about 2500 BC, the crop spread through much of the Americas. The region developed a network based on surplus and varieties of maize crops. Nevertheless, recent data indicates that the spread of maize took place even earlier, according to Piperno, A large corpus of data indicates that it was dispersed into lower Central America by 7600 BP and had moved into the inter-Andean valleys of Colombia between 7000 and 6000 BP. Since then, even earlier dates have been published, the study also demonstrated that the oldest surviving maize types are those of the Mexican highlands. Later, maize spread from this region over the Americas along two major paths and this is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. Before they were domesticated, maize plants only grew small,25 millimetres long corn cobs, Maize is the most widely grown grain crop throughout the Americas, with 361 million metric tons grown in the United States in 2014. Approximately 40% of the crop—130 million tons—is used for corn ethanol, genetically modified maize made up 85% of the maize planted in the United States in 2009. After the arrival of Europeans in 1492, Spanish settlers consumed maize and explorers and traders carried it back to Europe, Spanish settlers far preferred wheat bread to maize, cassava, or potatoes. Maize flour could not be substituted for wheat for bread, since in Christian belief only wheat could undergo transubstantiation. At another level, Spaniards worried that by eating indigenous foods, which they did not consider nutritious, that not only would they weaken, despite these worries, Spaniards did consume maize and archeological evidence from Florida sites indicate they cultivated it as well. Maize spread to the rest of the world because of its ability to grow in diverse climates and it was cultivated in Spain just a few decades after Columbuss voyages and then spread to Italy, West Africa and elsewhere. The word maize derives from the Spanish form of the indigenous Taíno word for the plant and it is known by other names around the world. The word corn outside North America, Australia, and New Zealand refers to any cereal crop, in the United States, Canada, Australia, and New Zealand, corn primarily means maize, this usage started as a shortening of Indian corn. Indian corn primarily means maize, but can more specifically to multicolored flint corn used for decoration
7.
Chromosome
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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
8.
Pfam
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Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 31.0, was released in March 2017, the general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a method of curating information on known protein families to improve the efficiency of annotating genomes. The Pfam classification of families has been widely adopted by biologists because of its wide coverage of proteins. Early genome projects, such as human and fly used Pfam extensively for functional annotation of genomic data, the Pfam website allows users to submit protein or DNA sequences to search for matches to families in the database. If DNA is submitted, a translation is performed, then each frame is searched. Family is the class, which simply indicates that members are related. Domains are defined as a structural unit or reusable sequence unit that can be found in multiple protein contexts. Repeats are not usually stable in isolation, but rather are required to form tandem repeats in order to form a domain or extended structure. Motifs are usually shorter sequence units found outside of globular domains, the descriptions of Pfam families are managed by the general public using Wikipedia. As of release 29.0,76. 1% of protein sequences in UniprotKB matched to at least one Pfam domain, new families come from a range of sources, primarily the PDB and analysis of complete proteomes to find genes with no Pfam hit. For each family, a subset of sequences are aligned into a high-quality seed alignment. Sequences for the alignment are taken primarily from pfamseq with some supplementation from UniprotKB. This seed alignment is used to build a profile hidden Markov model using HMMER. This HMM is then searched against sequence databases, and all hits that reach a curated gathering threshold are classified as members of the protein family, the resulting collection of members is then aligned to the profile HMM to generate a full alignment. For each family, a curated gathering threshold is assigned that maximises the number of true matches to the family while excluding any false positive matches. False positives are estimated by observing overlaps between Pfam family hits that are not from the same clan and this threshold is used to assess whether a match to a family HMM should be included in the protein family. Upon each update of Pfam, gathering thresholds are reassessed to prevent overlaps between new and existing families, domains of Unknown Function represent a growing fraction of the Pfam database
9.
InterPro
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The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models which describe protein families, domains or sites, models are built from the amino acid sequences of known families or domains and they are subsequently used to search unknown sequences in order to classify them. Each of the databases of InterPro contribute towards a different niche, from very high-level. InterPros intention is to provide a one-stop-shop for protein classification, where all the signatures produced by the different member databases are placed into entries within the InterPro database. Signatures which represent equivalent domains, sites or families are put into the same entry, additional information such as a description, consistent names and Gene Ontology terms are associated with each entry, where possible. InterPro contains three main entities, proteins, signatures and entries, the proteins in UniProtKB are also the central protein entities in InterPro. Information regarding which signatures significantly match these proteins are calculated as the sequences are released by UniProtKB, only signatures deemed to be of sufficient quality are integrated into InterPro. InterPro also includes data for splice variants and the contained in the UniParc. The signatures from InterPro come from 11 member databases, which are listed below, cATH-Gene3D describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity, mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains. Functional annotation is provided to proteins from multiple resources, functional prediction and analysis of domain architectures is available from the Gene3D website. HAMAP stands for High-quality Automated and Manual Annotation of microbial Proteomes, HAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded proteins families or subfamilies. PANTHER is a collection of protein families that have been subdivided into functionally related subfamilies. Hidden Markov models are built for each family and subfamily for classifying additional protein sequences, Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. The primary PIRSF classification unit is the family, whose members are both homologous and homeomorphic. PRINTS is a compendium of protein fingerprints, a fingerprint is a group of conserved motifs used to characterise a protein family, its diagnostic power is refined by iterative scanning of UniProt. Usually the motifs do not overlap, but are separated along a sequence, ProDom domain database consists of an automatic compilation of homologous domains. Current versions of ProDom are built using a procedure based on recursive PSI-BLAST searches
. PMID 20215432.
