1.
Yeast
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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
2.
Eukaryote
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A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota, the presence of a nucleus gives eukaryotes their name, which comes from the Greek εὖ and κάρυον. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular or multicellular, only eukaryotes form multicellular organisms consisting of many kinds of tissue made up of different cell types. Eukaryotes can reproduce asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two identical cells. In meiosis, DNA replication is followed by two rounds of division to produce four daughter cells each with half the number of chromosomes as the original parent cell. These act as sex cells resulting from genetic recombination during meiosis, the domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features, eukaryotes represent a tiny minority of all living things. However, due to their larger size, eukaryotes collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1. 6–2.1 billion years ago, in 1905 and 1910, the Russian biologist Konstantin Mereschkowsky argued three things about the origin of nucleated cells. Firstly, plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, secondly, the host had earlier in evolution formed by symbiosis between an amoeba-like host and a bacteria-like cell that formed the nucleus. Thirdly, plants inherited photosynthesis from cyanobacteria, the split between the prokaryotes and eukaryotes was introduced in the 1960s. The concept of the eukaryote has been attributed to the French biologist Edouard Chatton, the terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1938 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in one paragraph, and the idea was effectively ignored until Chattons statement was rediscovered by Stanier. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in cells in her paper. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA and this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts
3.
Hexokinase
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A hexokinase is an enzyme that phosphorylates hexoses, forming hexose phosphate. In most organisms, glucose is the most important substrate of hexokinases, scientists have discovered and demonstrated that Hexokinase posses the ability to transfer a inorganic phosphate group from ATP to a substrate. Hexokinases should not be confused with glucokinase, which is an isoform of hexokinase. While other hexokinases are capable of phosphorylating several hexoses, glucokinase acts with a 50-fold lower substrate affinity and its only hexose substrate is glucose. Genes that encode hexokinase have been discovered in every domain of life, and exist among a variety of species range from bacteria, yeast. They are categorized as actin fold proteins, sharing a common ATP binding site core that is surrounded by more variable sequences which determine substrate affinities, several hexokinase isoforms or isozymes that provide different functions can occur in a single species. Phosphorylation of a such as glucose often limits it to a number of intracellular metabolic processes. This is because phosphorylated hexoses are charged, and thus difficult to transport out of a cell. Most bacterial hexokinases are approximately 50 kD in size, multicellular organisms including plants and animals often have more than one hexokinase isoform. Most are about 100 kD in size and consist of two halves, which share much sequence homology and this suggests an evolutionary origin by duplication and fusion of a 50kD ancestral hexokinase similar to those of bacteria. There are four important mammalian hexokinase isozymes that vary in subcellular locations and kinetics with respect to different substrates and conditions, and physiological function. They are designated hexokinases I, II, III, and IV or hexokinases A, B, C, and D. Hexokinases I, II, Hexokinases I and II follow Michaelis-Menten kinetics at physiologic concentrations of substrates. All three are strongly inhibited by their product, glucose-6-phosphate, molecular weights are around 100 kD. Each consists of two similar 50kD halves, but only in hexokinase II do both halves have functional active sites, Hexokinase I/A is found in all mammalian tissues, and is considered a housekeeping enzyme, unaffected by most physiological, hormonal, and metabolic changes. Hexokinase II/B constitutes the principal regulated isoform in many types and is increased in many cancers. It is the hexokinase found in muscle and heart, Hexokinase II is also located at the mitochondria outer membrane so it can have direct access to ATP. Hexokinase III/C is substrate-inhibited by glucose at physiologic concentrations, little is known about the regulatory characteristics of this isoform. Mammalian hexokinase IV, also referred to as glucokinase, differs from other hexokinases in kinetics, the location of the phosphorylation on a subcellular level occurs when glucokinase translocates between the cytoplasm and nucleus of liver cells
4.
Phosphoglycerate kinase
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Phosphoglycerate kinase is an enzyme that catalyzes the reversible transfer of a phosphate group from 1, 3-bisphosphoglycerate to ADP producing 3-phosphoglycerate and ATP. Like all kinases it is a transferase, PGK is a major enzyme used in glycolysis, in the first ATP-generating step of the glycolytic pathway. In gluconeogenesis, the reaction catalyzed by PGK proceeds in the direction, generating ADP and 1. In humans, two isozymes of PGK have been so far identified, PGK1 and PGK2, PGK is present in all living organisms as one of the two ATP-generating enzymes in glycolysis. In the gluconeogenic pathway, PGK catalyzes the reverse reaction, under biochemical standard conditions, the glycolytic direction is favored. In the Calvin cycle in photosynthetic organisms, PGK catalyzes the phosphorylation of 3-PG, producing 1, 3-BPG and ADP, as part of the reactions that regenerate ribulose-1, 5-bisphosphate. PGK has been reported to exhibit thiol reductase activity on plasmin, leading to angiostatin formation, the enzyme was also shown to participate in DNA replication and repair in mammal cell nuclei. The human isozyme PGK2, which is expressed during spermatogenesis, was shown to be essential for sperm function in mice. Click on genes, proteins and metabolites below to link to respective articles, PGK is found in all living organisms and its sequence has been highly conserved throughout evolution. The enzyme exists as a 415-residue monomer containing two nearly equal-sized domains that correspond to the N- and C-termini of the protein, 3-phosphoglycerate binds to the N-terminal, while the nucleotide substrates, MgATP or MgADP, bind to the C-terminal domain of the enzyme. This extended two-domain structure is associated with large-scale hinge-bending conformational changes, the two domains of the protein are separated by a cleft and linked by two alpha-helices. At the core of each domain is a 6-stranded parallel beta-sheet surrounded by alpha helices, the two lobes are capable of folding independently, consistent with the presence of intermediates on the folding pathway with a single domain folded. Though the binding of either substrate triggers a change, only through the binding of both substrates does domain closure occur, leading to the transfer of the phosphate group. Magnesium ions are complexed to the phosphate groups the nucleotide substrates of PGK. It is known that in the absence of magnesium, no enzyme activity occurs and it is theorized that the ion may also encourage domain closure when PGK has bound both substrates. Without either substrate bound, PGK exists in an open conformation, then, in the case of the forward glycolytic reaction, the beta-phosphate of ADP initiates a nucleophilic attack on the 1-phosphate of 1, 3-BPG. The Lys219 on the enzyme guides the group to the substrate. In the glycolytic pathyway,1, 3-BPG is the donor and has a high phosphoryl-transfer potential
5.
Aminoacyl tRNA synthetase
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An aminoacyl tRNA synthetase is an enzyme that attaches the appropriate amino acid onto its tRNA. It does so by catalyzing the esterification of a specific amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. In humans, the 21 different types of aa-tRNA are made by the 21 different aminoacyl-tRNA synthetases and this is sometimes called charging or loading the tRNA with the amino acid. Once the tRNA is charged, a ribosome can transfer the amino acid from the tRNA onto a growing peptide, aminoacyl tRNA therefore plays an important role in DNA translation, the expression of genes to create proteins. The synthetase first binds ATP and the amino acid to form an aminoacyl-adenylate. The adenylate-aaRS complex then binds the appropriate tRNA molecules D arm, if the incorrect tRNA is added, the aminoacyl-tRNA bond is hydrolyzed. This can happen when two amino acids have different properties even if they have similar shapes—as is the case with Valine and Threonine, there are two classes of aminoacyl tRNA synthetase, Class I has two highly conserved sequence motifs. It aminoacylates at the 2-OH of a terminal adenosine nucleotide on tRNA, Class II has three highly conserved sequence motifs. It aminoacylates at the 3-OH of a terminal adenosine on tRNA, although phenylalanine-tRNA synthetase is class II, it aminoacylates at the 2-OH. The amino acids are attached to the group of the adenosine via the carboxyl group. Regardless of where the aminoacyl is initially attached to the nucleotide, both classes of aminoacyl-tRNA synthetases are multidomain proteins. In a typical scenario, an aaRS consists of a catalytic domain, in addition, some aaRSs have additional RNA binding domains and editing domains that cleave incorrectly paired aminoacyl-tRNA molecules. The catalytic domains of all the aaRSs of a class are found to be homologous to one another, whereas class I. The class I aaRSs have the ubiquitous Rossmann fold and have the parallel beta-strands architecture, the alpha helical anticodon binding domain of Arginyl, Glycyl and Cysteinyl-tRNA synthetases is known as the DALR domain after characteristic conserved amino acids. Most of the aaRSs of a given specificity are evolutionarily closer to one another than to aaRSs of another specificity, however, AsnRS and GlnRS group within AspRS and GluRS, respectively. Most of the aaRSs of a given specificity also belong to a single class, however, there are two distinct versions of the LysRS - one belonging to the class I family and the other belonging to the class II family. In addition, the phylogenies of aaRSs are often not consistent with accepted organismal phylogenies. That is, they violate the so-called canonical phylogenetic pattern shown by most other enzymes for the three domains of life - Archaea, Bacteria, and Eukarya, furthermore, the phylogenies inferred for aaRSs of different amino acids often do not agree with one another
6.
RNA
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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
