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.
Pyrophosphate
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In chemistry, a pyrophosphate is a phosphorus oxyanion. Compounds such as salts and esters are called pyrophosphates. The group is also called diphosphate or dipolyphosphate, although this should not be confused with phosphates, as a food additive, diphosphates are known as E450. A number of hydrogen pyrophosphates also exist, such as Na2H2P2O7, pyrophosphates were originally prepared by heating phosphates. They generally exhibit the highest solubilities among the phosphates, moreover, pyrophosphate is the first member of an entire series of polyphosphates. The term pyrophosphate is also the name of esters formed by the condensation of a phosphorylated biological compound with inorganic phosphate and this bond is also referred to as a high-energy phosphate bond. The synthesis of tetraethyl pyrophosphate was first described in 1854 by Philippe de Clermont at a meeting of the French Academy of Sciences, pyrophosphates are very important in biochemistry. The anion P2O74− is abbreviated PPi and is formed by the hydrolysis of ATP into AMP in cells, ATP → AMP + PPi For example, when a nucleotide is incorporated into a growing DNA or RNA strand by a polymerase, pyrophosphate is released. The pyrophosphate anion has the structure P2O74−, and is an anhydride of phosphate. This hydrolysis to inorganic phosphate effectively renders the cleavage of ATP to AMP and PPi irreversible, PPi occurs in synovial fluid, blood plasma, and urine at levels sufficient to block calcification and may be a natural inhibitor of hydroxyapatite formation in extracellular fluid. Cells may channel intracellular PPi into ECF, ANK is a nonenzymatic plasma-membrane PPi channel that supports extracellular PPi levels. Defective function of the membrane PPi channel ANK is associated with low extracellular PPi, ectonucleotide pyrophosphatase/phosphodiesterase may function to raise extracellular PPi. AMP + ATP →2 ADP2 ADP +2 Pi →2 ATP The plasma concentration of inorganic pyrophosphate has a range of 0. 58-3.78 µM. Various diphosphates are used as emulsifiers, stabilisers, acidity regulators, raising agents, sequestrants, schröder HC, Kurz L, Muller WE, Lorenz B. Pyrophosphates at the US National Library of Medicine Medical Subject Headings
3.
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
4.
Capping enzyme
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The addition of the cap occurs co-transcriptionally, after the growing RNA molecule contains as little as 25 nucleotides. The enzymatic reaction is catalyzed specifically by the phosphorylated carboxyl-terminal domain of RNA polymerase II, the 5 cap is therefore specific to RNAs synthesized by this polymerase rather than those synthesized by RNA polymerase I or RNA polymerase III. Three enzymes, RNA triphosphatase, guanylyltransferase, and methyltransferase are involved in the addition of the methylated 5 cap to the mRNA, capping is a three-step process that utilizes the enzymes RNA triphosphatase, guanylyltransferase, and methyltransferase. Through a series of three steps, the cap is added to the first nucleotides 5 hydroxyl group of the growing mRNA strand while transcription is still occurring, first, RNA5 triphosphatase hydrolyzes the 5 triphosphate group to make diphospate-RNA. Then, the addition of GMP by guanylyltransferase produces the guanosine cap, last, RNA methyltransferase transfers a methyl group to the guanosine cap to yield 7-methylguanosine cap that is attached to the 5 end of the transcript. When this complex of RNA polymerase II and the enzymes is achieved. 5 capping is essential for mRNA stability, enhancing mRNA processing, mRNA export, after successful capping, an additional phosphorylation event initiates the recruitment of machinery necessary for RNA splicing, a process by which introns are removed to produce a mature mRNA. The function of the 5 cap is essential to the expression of the RNA. The capping enzyme is part of the covalent nucleotidyl transferases superfamily, the NTase domain, conserved in capping enzymes, DNA and RNA ligases, is made up 5 motifs, I, III, IIIa, IV and V. Motif I or KxDG is the site where the covalent -N-GMP intermediate is formed. Both the NTase and OB domains undergo conformational changes that assist in the capping reaction, capping enzymes are found in the nucleus of eukaryotic cells. Depending on the organism, the enzyme is either a monofunctional or bifunctional polypeptide. The guanylyltransferases of Saccharomyces cerevisiae is encoded by the CEG1 gene and is composed of 459 amino acids, the RNA triphosphatase is a separate 549 amino acid polypeptide, encoded by the CET1 gene. The human capping enzyme is an example of a bifunctional polypeptide, the enzyme structure has three sub-domains referred to hinge, base and lid. The GTP binding site is located between the hinge and base domain, the lid domain determines the conformation of the active site cleft, which consists of the GTP binding site, phosphoamide linking lysine and surrounding residues. The guanylyltransferase domain is linked to the triphosphatase domain via a 25 amino acid flexible loop structure, splicing is dependent on the presence of the 7-methylguanosine cap. A defect in splicing can occur as a result of mutation in the guanylytransferase, however the severity of the effect is dependent on the guanlyltransferase mutation. Furthermore, the guanylyltransferase relieves transcriptional repression mediated by NELF, NELF together with DSIF prevents transcription elongation
5.
Five-prime cap
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In molecular biology, the five-prime cap is a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA. This process, known as mRNA capping, is regulated and vital in the creation of stable. Mitochondrial and chloroplast mRNA are not capped, in eukaryotes, the 5′ cap, found on the 5′ end of an mRNA molecule, consists of a guanine nucleotide connected to mRNA via an unusual 5′ to 5′ triphosphate linkage. This guanosine is methylated on the 7 position directly after capping in vivo by a methyltransferase and it is referred to as a 7-methylguanylate cap, abbreviated m7G. In multicellular eukaryotes and some viruses, further modifications exist, including the methylation of the 2′ hydroxy-groups of the first 2 ribose sugars of the 5′ end of the mRNA. Cap-1 has a methylated 2-hydroxy group on the first ribose sugar, the 5′ cap is chemically similar to the 3′ end of an RNA molecule. This provides significant resistance to 5′ exonucleases, small nuclear RNAs contain unique 5-caps. Sm-class snRNAs are found with 5-trimethylguanosine caps, while Lsm-class snRNAs are found with 5-monomethylphosphate caps, in bacteria, and potentially also in higher organisms, some RNAs are capped with NAD+, NADH, or 3-dephospho-coenzyme A. In all organisms, mRNA molecules can be decapped in a known as messenger RNA decapping. The starting point for capping with 7-methylguanylate is the unaltered 5′ end of an RNA molecule and this features a final nucleotide followed by three phosphate groups attached to the 5′ carbon. The capping process is initiated before the completion of transcription, as the nascent pre-mRNA is being synthesized, the mechanism of capping with NAD+, NADH, or 3-dephospho-coenzyme A is different. Both bacterial RNA polymerase and eukaryotic RNA polymerase II are able to carry out this ab initio capping mechanism, for capping with 7-methylguanylate, the capping enzyme complex binds to RNA polymerase II before transcription starts. As soon as the 5′ end of the new transcript emerges from RNA polymerase II, the enzymes for capping can only bind to RNA polymerase II, ensuring specificity to only these transcripts, which are almost entirely mRNA. Capping with NAD+, NADH, or 3-dephospho-coenzyme A is targeted by promoter sequence, the 5′ cap has four main functions, Regulation of nuclear export, Prevention of degradation by exonucleases, Promotion of translation, Promotion of 5′ proximal intron excision. Nuclear export of RNA is regulated by the cap binding complex, the CBC is then recognized by the nuclear pore complex and exported. Once in the cytoplasm after the round of translation, the CBC is replaced by the translation factors eIF4E. This complex is recognized by other translation initiation machinery including the ribosome. Capping with 7-methylguanylate prevents 5′ degradation in two ways, first, degradation of the mRNA by 5′ exonucleases is prevented by functionally looking like a 3′ end
6.
Messenger RNA
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Messenger RNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. As in DNA, mRNA genetic information is in the sequence of nucleotides, each codon encodes for a specific amino acid, except the stop codons, which terminate protein synthesis. It should not be confused with mitochondrial DNA, the brief existence of an mRNA molecule begins with transcription, and ultimately ends in degradation. During its life, a molecule may also be processed, edited. Eukaryotic mRNA molecules often require extensive processing and transport, while prokaryotic mRNA molecules do not, a molecule of eukaryotic mRNA and the proteins surrounding it are together called a messenger RNP. Transcription is when RNA is made from DNA, during transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed. This process is similar in eukaryotes and prokaryotes, the short-lived, unprocessed or partially processed product is termed precursor mRNA, or pre-mRNA, once completely processed, it is termed mature mRNA. Processing of mRNA differs greatly among eukaryotes, bacteria, and archea, non-eukaryotic mRNA is, in essence, mature upon transcription and requires no processing, except in rare cases. Eukaryotic pre-mRNA, however, requires extensive processing, a 5 cap is a modified guanine nucleotide that has been added to the front or 5 end of a eukaryotic messenger RNA shortly after the start of transcription. The 5 cap consists of a terminal 7-methylguanosine residue that is linked through a 5-5-triphosphate bond to the first transcribed nucleotide and its presence is critical for recognition by the ribosome and protection from RNases. Cap addition is coupled to transcription, and occurs co-transcriptionally, such that each influences the other, shortly after the start of transcription, the 5 end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the reactions that are required for mRNA capping. Synthesis proceeds as a biochemical reaction. In some instances, an mRNA will be edited, changing the composition of that mRNA. An example in humans is the apolipoprotein B mRNA, which is edited in some tissues, the editing creates an early stop codon, which, upon translation, produces a shorter protein. Polyadenylation is the covalent linkage of a moiety to a messenger RNA molecule. In eukaryotic organisms most messenger RNA molecules are polyadenylated at the 3 end, the poly tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is also important for transcription termination, export of the mRNA from the nucleus, MRNA can also be polyadenylated in prokaryotic organisms, where poly tails act to facilitate, rather than impede, exonucleolytic degradation
7.
Directionality (molecular biology)
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Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a DNA double helix, the run in opposite directions to permit base pairing between them, which is essential for replication or transcription of the encoded information. The relative positions of structures along a strand of nucleic acid, including genes, directionality is related to, but independent from sense. The other strand is not copied directly, but necessarily its sequence will be similar to that of the RNA, transcription initiation sites generally occur on both strands of an organisms DNA, and specify the location, direction, and circumstances under which transcription will occur. For example, in a typical gene a start codon is a DNA sequence within the sense strand, transcription begins at an upstream site, and as it proceeds through the region it copies the 3′-TAC-5′ from the template strand to produce 5′-AUG-3′ within a messenger RNA. The mRNA is scanned by the ribosome from the 5′ end, by convention, single strands of DNA and RNA sequences are written in a 5′-to-3′ direction except as needed to illustrate the pattern of base pairing. The 5′-end designates the end of the DNA or RNA strand that has the carbon in the sugar-ring of the deoxyribose or ribose at its terminus. A phosphate group attached to the 5′-end permits ligation of two nucleotides, i. e. the covalent binding of a 5′-phosphate to the 3′-hydroxyl group of another nucleotide, removal of the 5′-phosphate prevents ligation. To prevent unwanted nucleic acid ligation, molecular biologists commonly remove the 5′-phosphate with a phosphatase, the 5′-end of nascent messenger RNA is the site at which post-transcriptional capping occurs, a process which is vital to producing mature messenger RNA. Capping increases the stability of the messenger RNA while it undergoes translation and it consists of a methylated nucleotide attached to the messenger RNA in a rare 5′- to 5′-triphosphate linkage. The 5′-flanking region of a gene often denotes a region of DNA which is not transcribed into RNA, the 5′-flanking region contains the gene promoter, and may also contain enhancers or other protein binding sites. The 5′-untranslated region is a region of a gene which is transcribed into mRNA and this region of an mRNA may or may not be translated, but is usually involved in the regulation of translation. The 5′-untranslated region is the portion of the DNA starting from the cap site and this region may have sequences, such as the ribosome binding site and Kozak sequence, which determine the translation efficiency of the mRNA, or which may affect the stability of the mRNA. The 3′-end of a strand is so named due to it terminating at the group of the third carbon in the sugar-ring. The 3′-hydroxyl is necessary in the synthesis of new nucleic acid molecules as it is ligated to the 5′-phosphate of a separate nucleotide, molecular biologists can use nucleotides that lack a 3′-hydroxyl to interrupt the replication of DNA. This technique is known as the dideoxy chain-termination termination method or the Sanger method, the 3′-end of nascent messenger RNA is the site of post-transcriptional polyadenylation, which attaches a chain of 50 to 250 adenosine residues to produce mature messenger RNA. This chain helps in determining how long the messenger RNA lasts in the cell, the 3′-flanking region is a region of DNA that is not copied into the mature mRNA, but which is present adjacent to 3′-end of the gene. The 3′-flanking region often contains sequences that affect the formation of the 3′-end of the message and it may also contain enhancers or other sites to which proteins may bind
8.
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
9.
Lysine
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Lysine, encoded by the codons AAA and AAG, is an α-amino acid that is used in the biosynthesis of proteins. It contains a group, an α-carboxylic acid group. It is essential in humans, meaning the body cannot synthesize it, lysine is a base, as are arginine and histidine. The ε-amino group often participates in hydrogen bonding and as a base in catalysis. The ε-amino group is attached to the carbon from the α-carbon. O-Glycosylation of hydroxylysine residues in the endoplasmic reticulum or Golgi apparatus is used to mark certain proteins for secretion from the cell, deficiencies may cause blindness, as well as many other problems due to its ubiquitous presence in proteins. As an essential amino acid, lysine is not synthesized in animals, in plants and most bacteria, it is synthesized from aspartic acid, L-aspartate is first converted to L-aspartyl-4-phosphate by aspartokinase. ATP is needed as a source for this step. β-Aspartate semialdehyde dehydrogenase converts this into β-aspartyl-4-semialdehyde, energy from NADPH is used in this conversion. 4-hydroxy-tetrahydrodipicolinate synthase adds a pyruvate group to the β-aspartyl-4-semialdehyde, and a molecule is removed. This causes cyclization and gives rise to -4-hydroxy-2,3,4 and this product is reduced to 2,3,4, 5-tetrahydrodipicolinate by 4-hydroxy-tetrahydrodipicolinate reductase. This reaction consumes an NADPH molecule and releases a water molecule. Tetrahydrodipicolinate N-acetyltransferase opens this ring and gives rise to N-succinyl-L-2-amino-6-oxoheptanedionate, two water molecules and one acyl-CoA enzyme are used in this reaction. This reaction is catalyzed by the enzyme succinyl diaminopimelate aminotransferase, a glutamic acid molecule is used in this reaction and an oxoacid is produced as a byproduct. N-succinyl-LL-2, 6-diaminoheptanedionate is converted into LL-2, 6-diaminoheptanedionate by succinyl diaminopimelate desuccinylase, a water molecule is consumed in this reaction and a succinate is produced a byproduct. LL-2, 6-diaminoheptanedionate is converted by diaminopimelate epimerase into meso-2, 6-diamino-heptanedionate, finally, meso-2, 6-diamino-heptanedionate is converted into L-lysine by diaminopimelate decarboxylase. It is worth noting, however, that in fungi, euglenoids, lysine is metabolised in mammals to give acetyl-CoA, via an initial transamination with α-ketoglutarate. The bacterial degradation of lysine yields cadaverine by decarboxylation, allysine is a derivative of lysine, used in the production of elastin and collagen
10.
Covalent bond
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A covalent bond, also called a molecular bond, is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are known as shared pairs or bonding pairs, for many molecules, the sharing of electrons allows each atom to attain the equivalent of a full outer shell, corresponding to a stable electronic configuration. Covalent bonding includes many kinds of interactions, including σ-bonding, π-bonding, metal-to-metal bonding, agostic interactions, bent bonds, the term covalent bond dates from 1939. In the molecule H2, the atoms share the two electrons via covalent bonding. Covalency is greatest between atoms of similar electronegativities, thus, covalent bonding does not necessarily require that the two atoms be of the same elements, only that they be of comparable electronegativity. Covalent bonding that entails sharing of electrons more than two atoms is said to be delocalized. The term covalence in regard to bonding was first used in 1919 by Irving Langmuir in a Journal of the American Chemical Society article entitled The Arrangement of Electrons in Atoms and Molecules. Langmuir wrote that we shall denote by the term covalence the number of pairs of electrons that an atom shares with its neighbors. The idea of covalent bonding can be traced several years before 1919 to Gilbert N. Lewis and he introduced the Lewis notation or electron dot notation or Lewis dot structure, in which valence electrons are represented as dots around the atomic symbols. Pairs of electrons located between atoms represent covalent bonds, multiple pairs represent multiple bonds, such as double bonds and triple bonds. An alternative form of representation, not shown here, has bond-forming electron pairs represented as solid lines, Lewis proposed that an atom forms enough covalent bonds to form a full outer electron shell. In the diagram of methane shown here, the atom has a valence of four and is, therefore, surrounded by eight electrons, four from the carbon itself. Each hydrogen has a valence of one and is surrounded by two electrons – its own one electron plus one from the carbon, walter Heitler and Fritz London are credited with the first successful quantum mechanical explanation of a chemical bond in 1927. Their work was based on the valence bond model, which assumes that a bond is formed when there is good overlap between the atomic orbitals of participating atoms. Atomic orbitals have specific directional properties leading to different types of covalent bonds, sigma bonds are the strongest covalent bonds and are due to head-on overlapping of orbitals on two different atoms. A single bond is usually a σ bond, pi bonds are weaker and are due to lateral overlap between p orbitals. A double bond between two given atoms consists of one σ and one π bond, and a bond is one σ. Covalent bonds are also affected by the electronegativity of the atoms which determines the chemical polarity of the bond
11.
Transfer RNA
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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
12.
Histidine
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Histidine is an α-amino acid that is used in the biosynthesis of proteins. It contains a group, a carboxylic acid group. Initially thought essential only for infants, longer-term studies have shown it is essential for adults also, Histidine was first isolated by German physician Albrecht Kossel and Sven Hedin in 1896. It is also a precursor to histamine, an inflammatory agent in immune responses. The conjugate acid of the side chain in histidine has a pKa of approximately 6.0. This means that, at physiologically relevant pH values, relatively small shifts in pH will change its average charge, below a pH of 6, the imidazole ring is mostly protonated as described by the Henderson–Hasselbalch equation. When protonated, the ring bears two NH bonds and has a positive charge. The positive charge is distributed between both nitrogens and can be represented with two equally important resonance structures. As the pH increases past approximately 6, one of the protons is lost, the remaining proton of the now-neutral imidazole ring can reside on either nitrogen, giving rise to what are known as the N1-H or N3-H tautomers. When both imidazole ring nitrogens are protonated, their 15N chemical shifts are similar, NMR shows that the chemical shift of N1-H drops slightly, whereas the chemical shift of N3-H drops considerably. This indicates that the N1-H tautomer is preferred, it is presumed due to hydrogen bonding to the neighboring ammonium, as the pH rises above 9, the chemical shifts of N1 and N3 become approximately 185 and 170 ppm. An entirely deprotonated form of the ring, the imidazolate ion, would be formed only above a pH of 14. This change in chemical shifts can be explained by the presumably decreased hydrogen bonding of an amine over an ammonium ion, and this should act to decrease the N1-H tautomer preference. The imidazole ring of histidine is aromatic at all pH values and it contains six pi electrons, four from two double bonds and two from a nitrogen lone pair. It can form pi stacking interactions, but is complicated by the positive charge and it does not absorb at 280 nm in either state, but does in the lower UV range more than some amino acids. The imidazole sidechain of histidine is a coordinating ligand in metalloproteins and is a part of catalytic sites in certain enzymes. It has the ability to switch between protonated and unprotonated states, which allows histidine to participate in acid-base catalysis, in catalytic triads, the basic nitrogen of histidine is used to abstract a proton from serine, threonine, or cysteine to activate it as a nucleophile. In a histidine proton shuttle, histidine is used to quickly shuttle protons and it can do this by abstracting a proton with its basic nitrogen to make a positively charged intermediate and then use another molecule, a buffer, to extract the proton from its acidic nitrogen
13.
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
14.
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
15.
Fucose
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Fucose is a hexose deoxy sugar with the chemical formula C6H12O5. It is found on N-linked glycans on the mammalian, insect and plant cell surface, α linked core fucose is a suspected carbohydrate antigen for IgE-mediated allergy. Two structural features distinguish fucose from other six-carbon sugars present in mammals, the lack of a group on the carbon at the 6-position. In the fucose-containing glycan structures, fucosylated glycans, fucose can exist as a modification or serve as an attachment point for adding other sugars. In human N-linked glycans, fucose is most commonly linked α-1,6 to the reducing terminal β-N-acetylglucosamine, however, fucose at the non-reducing termini linked α-1,2 to galactose forms the H antigen, the substructure of the A and B blood group antigens. Fucose is released from fucose-containing polymers by an enzyme called α-fucosidase, l-Fucose is claimed to have application in cosmetics, pharmaceuticals, and dietary supplements. However, these claims are not supported by peer-reviewed scientific studies. Fucosylation of antibodies has been established to reduce binding to the Fc receptor of Natural Killer cells, fucitol Verotoxin-producing Escherichia coli Digitalose, the methyl ether of D-fucose
16.
Transferase
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A transferase is any one of a class of enzymes that enact the transfer of specific functional groups from one molecule to another. They are involved in hundreds of different biochemical pathways throughout biology, transferases are involved in myriad reactions in the cell. Transferases are also utilized during translation, in this case, an amino acid chain is the functional group transferred by a peptidyl transferase. Group would be the group transferred as a result of transferase activity. The donor is often a coenzyme, some of the most important discoveries relating to transferases occurred as early as the 1930s. Earliest discoveries of transferase activity occurred in other classifications of enzymes, including Beta-galactosidase, protease, prior to the realization that individual enzymes were capable of such a task, it was believed that two or more enzymes enacted functional group transfers. This observance was later verified by the discovery of its reaction mechanism by Braunstein and their analysis showed that this reversible reaction could be applied to other tissues. This assertion was validated by Rudolf Schoenheimers work with radioisotopes as tracers in 1937 and this in turn would pave the way for the possibility that similar transfers were a primary means of producing most amino acids via amino transfer. Another such example of early research and later reclassification involved the discovery of uridyl transferase. In 1953, the enzyme UDP-glucose pyrophosphorylase was shown to be a transferase, when it was found that it could reversibly produce UTP and G1P from UDP-glucose, another example of historical significance relating to transferase is the discovery of the mechanism of catecholamine breakdown by catechol-O-methyltransferase. This discovery was a part of the reason for Julius Axelrod’s 1970 Nobel Prize in Physiology or Medicine. Classification of transferases continues to this day, with new ones being discovered frequently, an example of this is Pipe, a sulfotransferase involved in the dorsal-ventral patterning of Drosophilia. Initially, the mechanism of Pipe was unknown, due to a lack of information on its substrate. Research into Pipes catalytic activity eliminated the likelihood of it being a heparan sulfate glycosaminoglycan, further research has shown that Pipe targets the ovarian structures for sulfation. Pipe is currently classified as a Drosophilia heparan sulfate 2-O-sulfotransferase, systematic names of transferases are constructed in the form of donor, acceptor grouptransferase. For example, a DNA methyltransferase is a transferase that catalyzes the transfer of a group to a DNA acceptor. In practice, many molecules are not referred to using this terminology due to more prevalent common names, in the EC system of classification, the accepted name for RNA Polymerase is DNA-directed RNA polymerase. Described primarily based on the type of biochemical group transferred, transferases can be divided into ten categories and these categories comprise over 450 different unique enzymes
17.
Phosphorus
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Phosphorus is a chemical element with symbol P and atomic number 15. As an element, phosphorus exists in two major forms—white phosphorus and red phosphorus—but because it is reactive, phosphorus is never found as a free element on Earth. At 0. 099%, phosphorus is the most abundant pnictogen in the Earths crust, with few exceptions, minerals containing phosphorus are in the maximally oxidised state as inorganic phosphate rocks. The glow of phosphorus itself originates from oxidation of the white phosphorus — a process now termed chemiluminescence, together with nitrogen, arsenic, antimony, and bismuth, phosphorus is classified as a pnictogen. Phosphates are a component of DNA, RNA, ATP, and the phospholipids, demonstrating the link between phosphorus and life, elemental phosphorus was first isolated from human urine, and bone ash was an important early phosphate source. Phosphate mines contain fossils, especially marine fossils, because phosphate is present in the deposits of animal remains. Low phosphate levels are an important limit to growth in aquatic systems. The vast majority of compounds produced are consumed as fertilisers. Phosphate is needed to replace the phosphorus that plants remove from the soil, other applications include the role of organophosphorus compounds in detergents, pesticides, and nerve agents. Phosphorus exists as several forms that exhibit different properties. The two most common allotropes are white phosphorus and red phosphorus, from the perspective of applications and chemical literature, the most important form of elemental phosphorus is white phosphorus, often abbreviated as WP. It is a soft and waxy solid consists of tetrahedral P4 molecules. This P4 tetrahedron is also present in liquid and gaseous phosphorus up to the temperature of 800 °C when it starts decomposing to P2 molecules, White phosphorus exists in two crystalline forms, α and β. At room temperature, the α-form is stable, which is common and it has cubic crystal structure and at 195.2 K, it transforms into β-form. These forms differ in terms of the orientations of the constituent P4 tetrahedra. White phosphorus is the least stable, the most reactive, the most volatile, the least dense, White phosphorus gradually changes to red phosphorus. This transformation is accelerated by light and heat, and samples of white phosphorus almost always some red phosphorus. For this reason, white phosphorus that is aged or otherwise impure is also called yellow phosphorus, when exposed to oxygen, white phosphorus glows in the dark with a very faint tinge of green and blue
18.
Kinase
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In biochemistry, a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the substrate gains a phosphate group and this transesterification produces a phosphorylated substrate and ADP. Conversely, it is referred to as dephosphorylation when the phosphorylated substrate donates a phosphate group and these two processes, phosphorylation and dephosphorylation, occur four times during glycolysis. Kinases are part of the family of phosphotransferases. Kinases are not to be confused with phosphorylases, which catalyze the addition of phosphate groups to an acceptor, nor with phosphatases. The phosphorylation state of a molecule, whether it be a protein, lipid, or carbohydrate, can affect its activity, reactivity, kinases mediate the transfer of a phosphate moiety from a high energy molecule to their substrate molecule, as seen in the figure below. Kinases are needed to stabilize this reaction because the phosphoanhydride bond contains a level of energy. Kinases properly orient their substrate and the group within their active sites. Additionally, they commonly use positively charged amino acid residues, which stabilize the transition state by interacting with the negatively charged phosphate groups. Alternatively, some kinases utilize bound metal cofactors in their sites to coordinate the phosphate groups. Kinases are used extensively to transmit signals and regulate processes in cells. Phosphorylation of molecules can enhance or inhibit their activity and modulate their ability to interact with other molecules, the addition and removal of phosphoryl groups provides the cell with a means of control because various kinases can respond to different conditions or signals. In 1956, Edmond H. Fischer and Edwin G. Krebs discovered that the interconversion between phosphorylase a and phosphorylase b was mediated by phosophorylation and dephosphorylation, the kinase that transferred a phosphoryl group to Phosphorylase b, converting it to Phosphorylase a, was named Phosphorylase Kinase. Years later, the first example of a kinase cascade was identified, at the same time, it was found that PKA inhibited glycogen synthase, which was the first example of a phosphorylation event that resulted in inhibition. In the same year, Tom Langan discovered that PKA phosphorylates histone H1, the 1970s included the discovery of calmodulin-dependent protein kinases and the finding that proteins can be phosphorylated on more than one amino acid residue. The 1990s may be described as the decade of protein kinase cascades, during this time, the MAPK/ERK pathway, the JAK kinases, and the PIP3-dependent kinase cascade were discovered. Kinases are classified into groups by the substrate they act upon, protein kinases, lipid kinases. Kinases can be found in a variety of species, from bacteria to mold to worms to mammals, more than five hundred different kinases have been identified in humans
19.
Alcohol
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In chemistry, an alcohol is any organic compound in which the hydroxyl functional group is bound to a saturated carbon atom. The term alcohol originally referred to the alcohol ethanol, the predominant alcohol in alcoholic beverages. The suffix -ol in non-systematic names also typically indicates that the substance includes a functional group and, so. But many substances, particularly sugars contain hydroxyl functional groups without using the suffix, an important class of alcohols, of which methanol and ethanol are the simplest members is the saturated straight chain alcohols, the general formula for which is CnH2n+1OH. The word alcohol is from the Arabic kohl, a used as an eyeliner. Al- is the Arabic definite article, equivalent to the in English, alcohol was originally used for the very fine powder produced by the sublimation of the natural mineral stibnite to form antimony trisulfide Sb 2S3, hence the essence or spirit of this substance. It was used as an antiseptic, eyeliner, and cosmetic, the meaning of alcohol was extended to distilled substances in general, and then narrowed to ethanol, when spirits as a synonym for hard liquor. Bartholomew Traheron, in his 1543 translation of John of Vigo, Vigo wrote, the barbarous auctours use alcohol, or alcofoll, for moost fine poudre. The 1657 Lexicon Chymicum, by William Johnson glosses the word as antimonium sive stibium, by extension, the word came to refer to any fluid obtained by distillation, including alcohol of wine, the distilled essence of wine. Libavius in Alchymia refers to vini alcohol vel vinum alcalisatum, Johnson glosses alcohol vini as quando omnis superfluitas vini a vino separatur, ita ut accensum ardeat donec totum consumatur, nihilque fæcum aut phlegmatis in fundo remaneat. The words meaning became restricted to spirit of wine in the 18th century and was extended to the class of substances so-called as alcohols in modern chemistry after 1850, the term ethanol was invented 1892, based on combining the word ethane with ol the last part of alcohol. In the IUPAC system, in naming simple alcohols, the name of the alkane chain loses the terminal e and adds ol, e. g. as in methanol and ethanol. When necessary, the position of the group is indicated by a number between the alkane name and the ol, propan-1-ol for CH 3CH 2CH 2OH, propan-2-ol for CH 3CHCH3. If a higher priority group is present, then the prefix hydroxy is used, in other less formal contexts, an alcohol is often called with the name of the corresponding alkyl group followed by the word alcohol, e. g. methyl alcohol, ethyl alcohol. Propyl alcohol may be n-propyl alcohol or isopropyl alcohol, depending on whether the group is bonded to the end or middle carbon on the straight propane chain. As described under systematic naming, if another group on the molecule takes priority, Alcohols are then classified into primary, secondary, and tertiary, based upon the number of carbon atoms connected to the carbon atom that bears the hydroxyl functional group. The primary alcohols have general formulas RCH2OH, the simplest primary alcohol is methanol, for which R=H, and the next is ethanol, for which R=CH3, the methyl group. Secondary alcohols are those of the form RRCHOH, the simplest of which is 2-propanol, for the tertiary alcohols the general form is RRRCOH
20.
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
21.
Glucokinase
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Glucokinase is an enzyme that facilitates phosphorylation of glucose to glucose-6-phosphate. Glucokinase occurs in cells in the liver and pancreas of humans, mutations of the gene for this enzyme can cause unusual forms of diabetes or hypoglycemia. Glucokinase is a hexokinase isozyme, related homologously to at least three other hexokinases, all of the hexokinases can mediate phosphorylation of glucose to glucose-6-phosphate, which is the first step of both glycogen synthesis and glycolysis. However, glucokinase is coded by a gene and its distinctive kinetic properties allow it to serve a different set of functions. Because of this reduced affinity, the activity of glucokinase, under physiological conditions. Alternative names for this enzyme are, human hexokinase IV, hexokinase D, the common name, glucokinase, is derived from its relative specificity for glucose under physiologic conditions.7.1.2. Nevertheless, glucokinase remains the name preferred in the contexts of medicine, another mammalian glucose kinase, ADP-specific glucokinase, was discovered in 2004. The gene is distinct and similar to that of primitive organisms and it is dependent on ADP rather than ATP, and the metabolic role and importance remain to be elucidated. The principal substrate of physiologic importance of glucokinase is glucose, the other necessary substrate, from which the phosphate is derived, is adenosine triphosphate, which is converted to adenosine diphosphate when the phosphate is removed. The reaction catalyzed by glucokinase is, ATP participates in the reaction in a form complexed to magnesium as a cofactor, furthermore, under certain conditions, glucokinase, like other hexokinases, can induce phosphorylation of other hexoses and similar molecules. Two important kinetic properties distinguish glucokinase from the other hexokinases, allowing it to function in a role as glucose sensor. Glucokinase has an affinity for glucose than the other hexokinases. Glucokinase changes conformation and/or function in parallel with rising glucose concentrations in the physiologically important range of 4–10 mmol/L and it is half-saturated at a glucose concentration of about 8 mmol/L. Glucokinase is not inhibited by its product, glucose-6-phosphate and this allows continued signal output amid significant amounts of its product These two features allow it to regulate a supply-driven metabolic pathway. That is, the rate of reaction is driven by the supply of glucose, another distinctive property of glucokinase is its moderate cooperativity with glucose, with a Hill coefficient of about 1.7. Glucokinase has only a binding site for glucose and is the only monomeric regulatory enzyme known to display substrate cooperativity. The nature of the cooperativity has been postulated to involve a transition between two different enzyme states with different rates of activity. If the dominant state depends upon glucose concentration, it would produce an apparent cooperativity similar to that observed, because of this cooperativity, the kinetic interaction of glucokinase with glucose does not follow classical Michaelis-Menten kinetics
22.
Fructokinase
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Fructokinase, also known as D-fructokinase or D-fructose kinase, is an enzyme of the liver, intestine, and kidney cortex. Fructokinase specifically catalyzes the transfer of a group from ATP to fructose as the initial step in its utilization. The main role of fructokinase is in carbohydrate metabolism, more specifically, the reaction equation is as follows, ATP + D-fructose = ADP + D-fructose 6-phosphate. This is notable because in most tissues this reaction is catalyzed by hexokinase, fructokinase has been characterized from various organisms such as pea seeds, avocado fruit, and maize kernels, and many more. Specifically, fructokinase may also regulate starch synthesis in conjunction with SS, sucrose synthase, there are also two divergent fructokinase genes that are differentially expressed and which also have different enzymatic properties such as those found in tomatoes. In tomatoes, fructokinase 1 mRNA is expressed at a constant level during fruit development, however, fructokinase 2 mRNA has a high expression level in young tomato fruit but then decreases during the later stages of fruit development. Frk 2 has an affinity for fructose than Frk 1 but Frk 2 activity is inhibited by high levels of fructose. In Sinorhizobium meliloti, a common bacterium, fructokinase is also used in the metabolism of mannitol and sorbitol. In human liver, purified fructokinase, when coupled with aldolase, has discovered to contribute to an alternative mechanism to produce oxalate from xylitol. In coupled sequence, fructokinase and aldolase produce glycolaldehyde, a precursor to oxalate, in rat liver cells, GTP is also a substrate of fructokinase. It can be used at a rate by fructokinase. In these isolated hepatocytes, in vivo, when the concentration of ATP falls to about 1 millimole in a time interval. Unlike phosphofructokinase, fructokinase is not inhibited by ATP, fructosuria or hepatic fructokinase deficiency is a rare but benign inherited metabolic disorder. This condition is caused by a deficiency of fructokinase in the liver, affected individuals usually display a large blood fructose concentration after the ingestion of fructose, sucrose or sorbitol. The disease is characterized by the detection of the abnormal excretion of fructose in the urine through a urinalysis. Fructokinase is needed for the synthesis of glycogen, the form of stored energy. The presence of fructose in the blood and urine may lead to a diagnosis of diabetes mellitus. Biochemical abnormalities that may lead to the diagnosis of fructosuria are hepatic fructokinase deficiency, levulosuria
23.
Galactokinase
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Galactokinase is an enzyme that facilitates the phosphorylation of α-D-galactose to galactose 1-phosphate at the expense of one molecule of ATP. Galactokinase catalyzes the second step of the Leloir pathway, a metabolic pathway found in most organisms for the catabolism of β-D-galactose to glucose 1-phosphate, first isolated from mammalian liver, galactokinase has been studied extensively in yeast, archaea, plants, and humans. Galactokinase is composed of two separated by a large cleft. The two regions are known as the N- and C-terminal domains, and the ring of ATP binds in a hydrophobic pocket located at their interface. Galactokinase does not belong to the kinase family, but rather to a class of ATP-dependent enzymes known as the GHMP superfamily. GHMP is an abbreviation referring to its members, galactokinase, homoserine kinase, mevalonate kinase. Members of the GHMP superfamily have great three-dimensional similarity despite only ten to 20% sequence identity and these enzymes contain three well-conserved motifs, the second of which is involved in nucleotide binding and has the sequence Pro-X-X-X-Gly-Leu-X-Ser-Ser-Ala. Interestingly, galactokinases across different species display a diversity of substrate specificities. E. coli galactokinase can also phosphorylate 2-deoxy-D-galactose, 2-amino-deoxy-D-galactose, 3-deoxy-D-galactose and D-fucose, the enzyme cannot tolerate any C-4 modifications, but changes at the C-2 position of D-galactose do not interfere with enzyme function. Both human and rat galactokinases are also able to successfully phosphorylate 2-deoxy-D-galactose, galactokinase from S. cerevisiae, on the other hand, is highly specific for D-galactose and cannot phosphorylate glucose, mannose, arabinose, fucose, lactose, galactitol, or 2-deoxy-D-galactose. Moreover, the properties of galactokinase also differ across species. The sugar specificity of galactokinases from different sources has been expanded through directed evolution. The corresponding broadly permissive sugar anomeric kinases serve as a cornerstone for in vitro, recently, the roles of active site residues in human galactokinase have become understood. Asp-186 abstracts a proton from C1-OH of α-D-galactose, and the alkoxide nucleophile attacks the γ-phosphorus of ATP. A phosphate group is transferred to the sugar, and Asp-186 may be deprotonated by water, nearby Arg-37 stabilizes Asp-186 in its anionic form and has also been proven to be essential to galactokinase function in point mutation experiments. Both the aspartic acid and arginine active site residues are conserved among galactokinases. The Leloir pathway catalyzes the conversion of galactose to glucose, galactose is found in dairy products, as well as in fruits and vegetables, and can be produced endogenously in the breakdown of glycoproteins and glycolipids. Three enzymes are required in the Leloir pathway, galactokinase, galactose-1-phosphate uridylyltransferase, galactokinase catalyzes the first committed step of galactose catabolism, forming galactose 1-phosphate
24.
Phosphofructokinase
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Phosphofructokinase is a kinase enzyme that phosphorylates fructose 6-phosphate in glycolysis. The enzyme-catalysed transfer of a group from ATP is an important reaction in a wide variety of biological processes. It is allosterically inhibited by ATP and allosterically activated by AMP, PFK exists as a homotetramer in bacteria and mammals and as an octomer in yeast. This protein may use the model of allosteric regulation. These conformations are thought to be successive stages of a pathway that requires subunit closure to bring the 2 molecules sufficiently close to react. Sufferers are usually able to lead an ordinary life by learning to adjust activity levels. The reverse reaction is catalyzed by the enzyme Fructose-1, 6-bisphosphatase
25.
Phosphofructokinase 1
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Phosphofructokinase-1 is one of the most important regulatory enzymes of glycolysis. It is an enzyme made of 4 subunits and controlled by many activators and inhibitors. PFK-1 catalyzes the important committed step of glycolysis, the conversion of fructose 6-phosphate and ATP to fructose 1, 6-bisphosphate, glycolysis is the foundation for respiration, both anaerobic and aerobic. PFK is able to regulate glycolysis through allosteric inhibition, and in this way, for example, a high ratio of ATP to ADP will inhibit PFK and glycolysis. The key difference between the regulation of PFK in eukaryotes and prokaryotes is that in eukaryotes PFK is activated by fructose 2, the purpose of fructose 2, 6-bisphosphate is to supersede ATP inhibition, thus allowing eukaryotes to have greater sensitivity to regulation by hormones like glucagon and insulin. Mammalian PFK1 is a 340kd tetramer composed of different combinations of three types of subunits, muscle, liver, and platelet, the composition of the PFK1 tetramer differs according to the tissue type it is present in. For example, mature muscle expresses only the M isozyme, therefore, the liver and kidneys express predominantly the L isoform. In erythrocytes, both M and L subunits randomly tetramerize to form M4, L4 and the three forms of the enzyme. As a result, the kinetic and regulatory properties of the various isoenzymes pools are dependent on subunit composition, tissue-specific changes in PFK activity and isoenzymic content contribute significantly to the diversities of glycolytic and gluconeogenic rates which have been observed for different tissues. PFK1 is an enzyme and has a structure similar to that of hemoglobin in so far as it is a dimer of a dimer. One half of each contains the ATP binding site whereas the other half the substrate binding site as well as a separate allosteric binding site. Each subunit of the tetramer is 319 amino acids and consists of two domain, one that binds the substrate ATP, and the other that binds fructose-6-phosphate, each domain is a b barrel, and has cylindrical b sheet surrounded by alpha helices. On the opposite side of the each subunit from each site is the allosteric site. ATP and AMP compete for this site, F6P binds with a high affinity to the R state but not the T state enzyme. For every molecule of F6P that binds to PFK1, the enzyme progressively shifts from T state to the R state, thus a graph plotting PFK1 activity against increasing F6P concentrations would adopt the sigmoidal curve shape traditionally associated with allosteric enzymes. PFK1 belongs to the family of phosphotransferases and it catalyzes the transfer of γ-phosphate from ATP to fructose-6-phosphate, the PFK1 active site comprises both the ATP-Mg2+ and the F6P binding sites. Some proposed residues involved with substrate binding in E. coli PFK1 include Asp127, in the T state, enzyme conformation shifts slightly such that the space previously taken up by the Arg162 is replaced with Glu161. This swap in positions between adjacent amino acid residues inhibits the ability of F6P to bind the enzyme, allosteric activators such as AMP and ADP bind to the allosteric site as to facilitate the formation of the R state by inducing structural changes in the enzyme
26.
PFKM
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6-phosphofructokinase, muscle type is an enzyme that in humans is encoded by the PFKM gene on chromosome 12. Three phosphofructokinase isozymes exist in humans, muscle, liver and platelet and these isozymes function as subunits of the mammalian tetramer phosphofructokinase, which catalyzes the phosphorylation of fructose-6-phosphate to fructose-1, 6-bisphosphate. Tetramer composition varies depending on tissue type and this gene encodes the muscle-type isozyme. Mutations in this gene have been associated with glycogen storage disease type VII, alternatively spliced transcript variants have been described. This gene is found on chromosome 12, the coding region in PFKM only shares a 68% similarity with that of the liver-type PFKL. This 85-kDa protein is one of two types that comprise the seven tetrameric PFK isozymes. The muscle isozyme is composed solely of PFKM, the liver PFK contains solely the second subunit type, PFKL, while the erythrocyte PFK includes five isozymes composed of different combinations of PFKM and PFKL. These subunits evolved from a common ancestor via gene duplication and mutation events. Generally, the N-terminal of the subunits carries out their catalytic activity while the C-terminal contains allosteric ligand binding sites, in particular, the binding site for the PFK inhibitor citrate is found in the PFKL C-terminal region. This gene encodes one of three subunits of PFK, which are expressed and combined to form the tetrameric PFK in a tissue-specific manner. As a PFK subunit, PFKL is involved in catalyzing the phosphorylation of fructose 6-phosphate to fructose 1 and this irreversible reaction serves as the major rate-limiting step of glycolysis. Though the PFKM subunit majorly incorporates into muscle and erythrocyte PFKs, PFKM also is expressed in the heart, brain, notably, mutations in PFKM have been shown to cause Tarui disease due to homozygosity for catalytically inactive M subunits. PFKM is confirmed to be involved in muscle PFK deficiency with early-onset hyperuricemia, interestingly, even though PFKM functions to drive glycolysis, its overexpression has been associated with type 2 diabetes and insulin resistance in skeletal muscle. PFKM has been shown to interact with ATP6V0A4, click on genes, proteins and metabolites below to link to respective articles
27.
PFKP
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Phosphofructokinase, platelet, also known as PFKP is an enzyme which in humans is encoded by the PFKP gene. The PFKP gene encodes the platelet isoform of phosphofructokinase, PFK catalyzes the irreversible conversion of fructose 6-phosphate to fructose 1, 6-bisphosphate and is a key regulatory enzyme in glycolysis. The PFKP gene, which maps to chromosome 10p, is expressed in fibroblasts. See also the muscle and liver isoforms of phosphofructokinase, which map to chromosomes 12q13 and 21q22, full tetrameric phosphofructokinase enzyme expressed in platelets can be composed of subunits P4, P3L, and P2L2. Click on genes, proteins and metabolites below to link to respective articles and this article incorporates text from the United States National Library of Medicine, which is in the public domain
28.
Phosphofructokinase 2
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Phosphofructokinase 2 or fructose bisphosphatase 2, is an enzyme responsible for regulating the rates of glycolysis and gluconeogenesis in the human body. It is a homodimer of 55 kDa subunits arranged in a head-to-head fashion, when Ser-32 of the bifunctional protein is phosphorylated, the negative charge causes the conformation change of the enzyme to favor the FBPase2 activity, otherwise, PFK2 activity is favored. The monomers of the protein are clearly divided into two functional domains. The kinase domain is located on the N-terminal and it consists of a central six-stranded β sheet, with five parallel strands and an antiparallel edge strand, surrounded by seven α helices. The domain contains nucleotide-binding fold at the C-terminal end of the first β-strand, on the other hand, the phosphatase domain is located on the C-terminal. It resembles the family of proteins that include phosphoglycerate mutases and acid phosphatases, the domain has a mixed α/ β structure, with a six-stranded central β sheet, plus an additional α-helical subdomain that covers the presumed active site of the molecule. Finally, N-terminal region modulates PFK2 and FBPase2 activities, and stabilizes the dimer form of the enzyme, when glucose level is low, glucagon is released into the bloodstream, triggering a cAMP signal cascade. In the liver Protein kinase A inactivates the PFK-2 domain of the enzyme via phosphorylation. The F-2, 6-BPase domain is activated which lowers fructose 2. Because F-2, 6-BP normally stimulates phosphofructokinase-1, the decrease in its concentration leads to the inhibition of glycolysis, so PFK2 domain is activated and the kinase catalyzes the formation of F-2, 6-BP. Thus, glycolysis is stimulated and gluconeogenesis is inhibited, the allosteric regulation of PFK2 is very similar to the regulation of PFK1. High levels of AMP or phosphate group signifies a low energy state, on the other hand, a high concentration of phosphoenolpyruvate and citrate signifies that there is a high level of biosynthetic precursor and hence inhibits PFK2. However, unlike PFK1, PFK2 is not affected by the ATP concentration, yet, the formation of fructose 2, 6-bisphosphate could theoretically occur by a variety of mechanisms, including the intermediary formation of Fructose-6-phosphate 2-pyrophosphate. The breakdown of the state and the release of F6P. Histidine increases the nucleophilicity of water, which attacks phosphohistidine, generating phosphate, the Pfkfb2 gene encoding PFK2/FBPase2 protein is linked to the predisposition to schizophrenia. Furthermore, the control of PFK2/FBPase2 activity was found to be linked to heart functioning and the control against hypoxia
29.
Riboflavin kinase
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Riboflavin is converted into catalytically active cofactors by the actions of riboflavin kinase, which converts it into FMN, and FAD synthetase, which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single protein that can carry out both catalyses, although exceptions occur in both cases. The bacterial FAD synthetase that is part of the enzyme has remote similarity to nucleotidyl transferases and, hence. This enzyme belongs to the family of transferases, to be specific, the systematic name of this enzyme class is ATP, riboflavin 5-phosphotransferase. This enzyme is also called flavokinase and this enzyme participates in riboflavin metabolism. The complete enzyme arrangement can be observed with X-ray crystallography and with NMR, the riboflavin kinase enzyme isolated from Thermoplasma acidophilum contains 220 amino acids. The structure of this enzyme has been determined X-ray crystallography at a resolution of 2.20 Å and its secondary structure contains 69 residues in alpha helix form, and 60 residues a beta sheet conformation. The enzyme contains a binding site at amino acids 131 and 133. As of late 2007,14 structures have been solved for this class of enzymes, with PDB accession codes 1N05, 1N06, 1N07, 1N08, 1NB0, 1NB9, 1P4M, 1Q9S, 2P3M, 2VBS, 2VBT, 3CTA, 2VBU, and 2VBV. This article incorporates text from the public domain Pfam and InterPro IPR015865
30.
Shikimate kinase
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Shikimate kinase is an enzyme that catalyzes the ATP-dependent phosphorylation of shikimate to form shikimate 3-phosphate. This reaction is the step of the shikimate pathway, which is used by plants and bacteria to synthesize the common precursor of aromatic amino acids. The systematic name of this class is ATP, shikimate 3-phosphotransferase. Other names in use include shikimate kinase, and shikimate kinase II. The aromatic amino acids are used in the synthesis of proteins and, in plants, fungi, chorismate and several other intermediates of the pathway serve as precursors for a number of other metabolites, such as folates, quinates, and quinones. The shikimate pathway is not found in humans and other animals, the reaction catalyzed by shikimate kinase is shown below, This reaction involves the transfer of a phosphate group from ATP to the 3-hydroxyl group of shikimate. Shikimate kinase thus has two substrates, shikimate and ATP, and two products, shikimate 3-phosphate and ADP, mAPK7, THNSL1, Morell H, Sprinson DB. Shikimate kinase isoenzymes in Salmonella typhimurium, hartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD. Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis
31.
Thymidine kinase
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Thymidine kinase is an enzyme, a phosphotransferase, 2-deoxythymidine kinase, ATP-thymidine 5-phosphotransferase, EC2.7.1.21. It can be found in most living cells and it is present in two forms in mammalian cells, TK1 and TK2. Certain viruses also have information for expression of viral thymidine kinases. Thymidine kinase catalyzes the reaction, Thd + ATP → TMP + ADP where Thd is thymidine, ATP is adenosine triphosphate, TMP is thymidine monophosphate and ADP is adenosine diphosphate. Thymidine kinases have a key function in the synthesis of DNA and therefore in cell division, Thymidine is present in the body fluids as a result of degradation of DNA from food and from dead cells. Thymidine kinase is required for the action of many antiviral drugs and it is used to select hybridoma cell lines in production of monoclonal antibodies. In clinical chemistry it is used as a marker in the diagnosis, control of treatment and follow-up of malignant disease. The incorporation of thymidine in DNA was demonstrated around 1950, somewhat later, it was shown that this incorporation was preceded by phosphorylation, and, around 1960, the enzyme responsible was purified and characterized. The major capsid protein of insect iridescent viruses also belongs to this family, the Prosite pattern recognizes only the cellular type of thymidine kinases. Mammals have two isoenzymes, that are very different, TK1 and TK2. The former was first found in tissue, the second was found to be more abundant in adult tissue. Soon it was shown that TK1 is present in the only in anticipation of cell division. The two isoenzymes have different reaction kinetics and are inhibited by different inhibitors, the viral thymidine kinases differ completely from the mammalian enzymes both structurally and biochemically and are inhibited by inhibitors that do not inhibit the mammalian enzymes. The genes of the two human isoenzymes were localized in the mid-1970s, the gene for TK1 was cloned and sequenced. The corresponding protein has a weight of about 25 kD. Normally, it occurs in tissue as a dimer with a weight of around 50 kD. It can be activated by ATP, after activation, is a tetramer with a molecular weight around 100 kD. This complex is stable and has a higher specific activity than any of the lower molecular weight forms
32.
NAD+ kinase
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NAD+ kinase is an enzyme that converts nicotinamide adenine dinucleotide into NADP+ through phosphorylating the NAD+ coenzyme. The structure of the NADK from the archaean Archaeoglobus fulgidus has been determined, in humans, the genes NADK and MNADK encode NAD+ kinases localized in cytosol and mitochondria, respectively. Similarly, yeast have both cytosolic and mitochondrial isoforms, and the yeast mitochondrial isoform accepts both NAD+ and NADH as substrates for phosphorylation, ATP + NAD+ ⇌ ADP + NADP+ NADK phosphorylates NAD+ at the 2’ position of the ribose ring that carries the adenine moiety. It is highly selective for its substrates, NAD and ATP, NADK also uses magnesium to coordinate the ATP in the active site. However, in studies with other divalent metal ions have shown that zinc and manganese are preferred over magnesium, while copper. A proposed mechanism involves the 2 alcohol oxygen acting as a nucleophile to attack the gamma-phosphoryl of ATP, NADK is highly regulated by the redox state of the cell. Whereas NAD is predominantly found in its oxidized state NAD+, the phosphorylated NADP is largely present in its reduced form, thus, NADK can modulate responses to oxidative stress by controlling NADP synthesis. Bacterial NADK is shown to be inhibited allosterically by both NADPH and NADH, NADK is also reportedly stimulated by calcium/calmodulin binding in certain cell types, such as neutrophils. NAD kinases in plants and sea urchin eggs have also found to bind calmodulin. Due to the role of NADPH in lipid and DNA biosynthesis. Furthermore, NADPH is required for the antioxidant activities of thioredoxin reductase, while the role of NADK in increasing the NADPH pool appears to offer protection against apoptosis, there are also cases where NADK activity appears to potentiate cell death. Genetic studies done in human cell lines indicate that knocking out NADK may protect from certain non-apoptotic stimuli. Oxidative phosphorylation Electron transport chain Metabolism ENZYME entry on EC2.7.1.23 BRENDA entry on EC2.7.1.23
33.
Mevalonate kinase
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Mevalonate kinase is an enzyme that in humans is encoded by the MVK gene. Mevalonate kinases are found in a variety of organisms from bacteria to mammals. This enzyme catalyzes the following reaction, mevalonate is a key intermediate, and mevalonate kinase a key early enzyme, in isoprenoid and sterol synthesis. Defects can be associated with hyperimmunoglobulinemia D with recurrent fever, Mevalonic aciduria Mevalonic acid mevalonate kinase at the US National Library of Medicine Medical Subject Headings
34.
Pyruvate kinase
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Pyruvate kinase is the enzyme that catalyzes the final step of glycolysis. It catalyzes the transfer of a group from phosphoenolpyruvate to adenosine diphosphate, yielding one molecule of pyruvate. There are four isozymes of pyruvate kinase in vertebrates, L, R, M1, R and L isozymes differ from M1 and M2 in that they are both exclusively allosterically and reversibly regulated. From a kinetic standpoint, the R and L isozymes of pyruvate kinase have two key conformation states, one with a high affinity and one with a low substrate affinity. The R-state, characterized by high affinity, serves as the activated form of pyruvate kinase and is stabilized by PEP and FBP. Gene expression varies between the different isozymes, M1 and M2 isozymes are regulated by the gene PKM and R and L isozymes are regulated by the gene PKLR. In terms of structure, there is both a tetrameric and dimeric form of pyruvate kinase, the tetrameric form is the pyruvate kinase structure in its R-state conformation, namely with high binding affinity to PEP. In contrast, the form is its structure in T-state conformation. Many Enterobacteriaceae, including E. coli, have two isoforms of pyruvate kinase, PykA and PykF, which are 37% identical in E. coli. They catalyze the reaction as in eukaryotes, namely the generation of ATP from ADP and PEP, the last step in glycolysis. PykF is allosterically regulated by fructose 1, 6-bisphosphate which reflects the position of PykF in cellular metabolism. PykF transcription in E. coli is regulated by the transcriptional regulator. PfkB was shown to be inhibited by MgATP at low concentrations of Fru-6P, there are two steps in the pyruvate kinase reaction in glycolysis. First, PEP transfers a phosphate group to ADP, producing ATP, secondly, a proton must be added to the enolate of pyruvate to produce the functional form of pyruvate that the cell requires. In yeast cells, the interaction of yeast pyruvate kinase with PEP and its allosteric effector Fructose 1, therefore, Mg2+ was isolated as an important component in the successful catalysis of PEP into pyruvate by pyruvate kinase. Furthermore, the metal ion Mn2+ was shown to have a similar, the binding of metal ions to the metal binding sites on pyruvate kinase enhance the rate of this glycolytic reaction. The glycolytic reaction catalyzed by pyruvate kinase is the step of glycolysis. It is one of the three rate-affecting steps of the catabolic reaction cascade, the rate-affecting steps are the slower steps of a reaction and thus determines the rate of the overall reaction
35.
Deoxycytidine kinase
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Deoxycytidine kinase is an enzyme which is encoded by the DCK gene in humans. DCK predominantly phosphorylates deoxycytidine and converts dC into deoxycytidine monophosphate, there has been recent biomedical research interest in investigating dCKs potential as a therapeutic target for different types of cancer. DCK is a homodimer where each subunit consists of multiple alpha helices surrounding a beta sheet core. Each subunit includes a nucleotide binding site, nucleoside acceptor binding site, nucleotide base sensing loop. DCK has several different protein conformations but its conformation depends on the nucleoside or nucleotide it binds to. DCK can bind to ADP, ATP, UDP or UTP but UDP/UTP binding changes the enzymes conformation by rearranging the nucleotide base sensing loop as compared to the dCKs conformation when bound to ATP. This change in conformation when a specific phosphoryl donor is bound in the binding site determines which nucleoside can bind in the nucleoside binding site. Below is a pathway that displays dCKs role in synthesizing nucleotides using the nucleoside salvage pathway. This has deemed the closed conformation as the active conformation since it catalyzes the phosphoryl transfer between phosphoryl donors and receiving nucleosides. One method of to regulate both catalytic activity and substrate specificity is a modification on Serine 74, a residue in the insert region on each of the individual dCK subunits. Although serine 74 is far from dCKs active site, phosphorylation of serine 74 on dCK causes a change in enzyme conformation, dCKs closed conformation allows dCK to transfer phosphoryl groups, but not bind or release nucleosides. The open and closed refer to the nucleoside binding site on dCK. dCK is a key enzyme in the nucleoside salvage pathway. More specifically, this pathway recycles preformed nucleosides from degrading DNA molecules to synthesize dNTPs for the cell, the nucleoside salvage pathway can act as a alternative path to produce nucleotides in case of de novo pathway downregulation. That is, the pathway is upregulated when the de novo pathway is downregulated or inhibited in order to compensate for the loss in nucleotide production. Both the de novo pathway and the salvage pathway are anabolic pathways that produce deoxyribonucleotide triphosphates or nucleotides. Deficiency of dCK is associated with resistance to antiviral and anticancer chemotherapeutic agents, conversely, increased deoxycytidine kinase activity is associated with increased activation of these agents to cytotoxic nucleoside triphosphate derivatives. DCK is clinically important because of its relationship to drug resistance, for example, gemcitabine is a FDA-approved pyrimidine nucleoside analogue and a dCK activity based prodrug that has been used to treat pancreatic, breast, bladder and non-small cell lung cancer. Mechanistically, dCK, which uptakes preformed nucleosides, adds the first phosphoryl group on dFdC to convert it into dFdCMP, cytidylate kinase or UMP-CMP kinase then adds the second phosphoryl group to form dFdCDP, which can inhibit ribonucleotide reductase
36.
Diacylglycerol kinase
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Diacylglycerol kinase is a family of enzymes that catalyzes the conversion of diacylglycerol to phosphatidic acid utilizing ATP as a source of the phosphate. In bacteria, DGK is very small membrane protein which seems to contain three transmembrane domains, the best conserved region is a stretch of 12 residues which are located in a cytoplasmic loop between the second and third transmembrane domains. Some Gram-positive bacteria also encode a soluble diacylglycerol kinase capable of reintroducing DAG into the phospholipid biosynthesis pathway, DAG accumulates in Gram-positive bacteria as a result of the transfer of glycerol-1-phosphate moieties from phosphatidylglycerol to lipotechoic acid. Currently, nine members of the DGK family have been cloned and identified.7.1.107
