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Nucleic Acid HybridizationRNA, MessengerBase SequenceDNARNABiochemistryRNA, Small InterferingRNA, ViralRNA EditingRNA SplicingRNA, RibosomalGene Transfer TechniquesRNA, BacterialRNA, TransferMolecular Sequence DataDNA-Directed RNA PolymerasesRNA InterferenceRNA VirusesGene Transfer, HorizontalEmbryo TransferAmino Acid SequenceRNA, Transfer, TyrRNA, Double-StrandedKineticsRNA, CatalyticRNA FoldingRNA Polymerase IIModels, MolecularBinding SitesNucleic Acid ConformationRNA, FungalEscherichia coliRNA StabilityRNA, AntisenseRNA HelicasesRNA Processing, Post-TranscriptionalTransfer (Psychology)MutationFluorescence Resonance Energy TransferProtein BindingRNA PrecursorsRNA, Small NuclearRNA, UntranslatedProtein ConformationRNA CapsTyrosineSequence Analysis, RNABiochemical PhenomenaAdoptive TransferGenetic VectorsCell LineRNA, PlantPlasmidsElectron TransportMutagenesis, Site-DirectedRNA, ProtozoanPatient TransferPhospholipid Transfer ProteinsRNA, NeoplasmCatalysisSubstrate SpecificityRNA Ligase (ATP)Bacterial ProteinsProtein Structure, TertiaryRecombinant ProteinsOxidation-ReductionTransfer FactorMagnetic Resonance SpectroscopyDEAD-box RNA HelicasesConjugation, GeneticStructure-Activity RelationshipRNA Polymerase IIITime FactorsSequence Homology, Amino AcidThermodynamicsModels, BiologicalCholesterol Ester Transfer ProteinsHydrogen-Ion ConcentrationNuclear Transfer TechniquesModels, ChemicalCarrier ProteinsRNA Polymerase IRNA, NuclearCrystallography, X-RayTransfectionRNA, GuideRNA, Ribosomal, 28SCattleDNA PrimersTranscription, GeneticTendon TransferElectrophoresis, Polyacrylamide GelTemperaturePhylogenyGenetic TherapyRNA-Binding ProteinsProtein BiosynthesisRNA, Ribosomal, 18SRNA, Ribosomal, 16SCells, Cultured
TyrosineResiduesProteinsMolecular BiologyHydride transferMutationsPolymerStructuralGeneEnzymeRegulationCellsBacteriaTranscriptionTargetPositiveViewTRNAMRNACellular BiochemistryResidueGenomicGenesElectron transferEnzymesAmino acidsSequencesProteinRecognitionInitiationNuclearReactionMolecularEukaryotesSubunitStrandProton transferCatalyticCatalysisEnzymeSpecificComplexScience
Tyrosine3
Residues5
  • During Hg2+ transfer to the catalytic active site from the C terminus cysteine residues, a trigonal planar intermediate is formed stabilized by hydrogen bonding of a water molecule to the thiolates. (wikipedia.org)
  • Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila . (nature.com)
  • Aside from serving as protein residues,glucosamine also take involvement in the transfer of neurotransmitters and biosynthesis. (easy4learning.com)
  • Mutations of Tyr residues on OCLN showed the role of Tyr phosphorylation in regulating OCLN. (biomedcentral.com)
  • Using recombinant variants of ppFhCL3 we demonstrated the critical importance of a pair of propeptide residues (Tyr 46 Lys 47 ) for the interaction with the propeptide binding loop (PBL) of the mature enzyme and other residues (Leu 66 and Glu 68 ) that allow the propeptide to block the active site. (biomedcentral.com)
Proteins5
  • The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
  • Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
  • More recently, the application of RNA-seq technologies has enabled the elucidation of the biological partners and targets of several ProQ/FinO family proteins. (nature.com)
  • Insight into how these proteins recognize their cognate RNAs initiated with FinO. (nature.com)
  • It occurs in proteins that are part of signal transduction processes and functions as a receiver of phosphate groups that are transferred by way of protein kinase s. (explained.today)
Molecular Biology1
  • Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine and the Massey Cancer Center, Richmond, VA, USA. (sphingolipidclub.com)
Hydride transfer1
  • A Single Mutation Traps a Half-Sites Reactive Enzyme in Midstream, Explaining Asymmetry in Hydride Transfer. (ucsf.edu)
Mutations2
  • Considered together, these data indicate that impairing the primer strand transfer pathway required for proofreading increases the probability of common mutations by Pol ϵ, elucidating the association of homologous mutations in human DNA polymerase ϵ with cancer. (bvsalud.org)
  • A new mutation has been reported, making a total of 15 different mutations that can cause premature stop codons in the alpha-L-iduronidase gene (IDUA), and the biochemistry of these mutations has been investigated. (medscape.com)
Polymer1
  • Subsequently the latter was subdivided into solid state and molecular chemistry, while the formed spawned fields like polymer chemistry, biochemistry, or metal-organic chemistry. (degruyter.com)
Structural2
  • Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3' ssRNA tail. (nature.com)
  • A key finding from the original identification of Tdp2 was that the protein was more active in processing 5′ phosphotyrosyl-linked oligonucleotides, and that siRNA knockdown of Tdp2 in mammalian cells resulted in sensitivity to etoposide, a drug targeting topoisomerase II, but not camptothecin, a drug that targets topoisomerase I. Recent work has greatly enhanced our understanding of the biochemistry and structural biology of Tdp2. (prolekarniky.cz)
Gene1
  • These data indicated that GA was able to: (1) reduce the levels of reactive oxygen species, (2) down-regulate the expression of MITF, TYR, TRP-1, and TRP-2 gene levels in a timedependent manner, and (3) significantly reduce protein expression of the TRP-2 gene. (slideheaven.com)
Enzyme2
  • Unlike most undergraduate Biochemistry exams, MCAT Biochemistry is far more likely to ask reasoning questions than to ask for the intermediate or enzyme in a pathway that you are expected to review. (mcat-prep.com)
  • The conversion of Phe to Tyr is catalyzed by the enzyme phenylalanine hydroxylase , a monooxygenase. (explained.today)
Regulation1
  • Tyr-857 has therefore been assigned a role in positive regulation of kinase activity. (pdgfrsignaling.com)
Cells1
  • First, temporally and spatially restricted tissue or cell patterns cause difficulties in dissecting target tissues or cells to collect enough RNA. (biomedcentral.com)
Bacteria1
  • The Mtb genome (size 4.4 Mb, GC content 65.5 %) is relatively clonal compared to most other bacteria, with no horizontal transfer, and low mutation and recombination rates [ 3 ]. (biomedcentral.com)
Transcription1
  • Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. (mdpi.com)
Target1
  • sRNAs usually work by pairing with target mRNAs, often with the assistance of protein partners called RNA chaperones. (nature.com)
Positive1
  • DENV is an enveloped virus with a positive stranded RNA genome of approximately 11 kb in length that encodes a single polypeptide. (biomedcentral.com)
View1
  • Download the Gold Standard MCAT Biochemistry Review Summary PDF or scroll down and click on an image below to view the summaries. (mcat-prep.com)
TRNA5
  • [1] Schimmel PR, S?ll D. Aminoacyl-tRNA synthetases: general features and recognition of transfer RNAs. (org.ua)
  • Interaction of eukaryotic tyrosyl-tRNA-synthetase with high molecular weight RNA]. (org.ua)
  • [16] Bedouelle H. Recognition of tRNA(Tyr) by tyrosyl-tRNA synthetase. (org.ua)
  • The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. (wikidoc.org)
  • Recent examples indicate tissue-specific and transfer RNA (tRNA)-dependent effects of some genetic variations arguing against neutrality of synonymous SNVs for protein biogenesis. (biomedcentral.com)
MRNA2
  • Messenger RNA (mRNA)-template for the synthesis of proteins by ribosomes . (wikidoc.org)
  • Transfer RNAs (tRNAs) convert the nucleotide chemistry (mRNA) into a peptide alphabet (protein). (biomedcentral.com)
Cellular Biochemistry2
  • 1988), "Expression and Characterization of the Extracytoplasmic Portion of the Mouse Platelet Derived Growth Factor Receptor," Journal of Cellular Biochemistry, 12:110. (everypatent.com)
  • 1988), "Structural and Functional Model of the Platelet Derived Growth Factor Receptor Extracellular Domain," Journal of Cellular Biochemistry, 12:98. (everypatent.com)
Residue3
  • The water molecule is held in place by hydrogen bonding from the hydroxyl group of a nearby tyrosine residue (Tyr-194). (wikipedia.org)
  • The prediction model takes a matrix of sequence- and evolutionary profile-derived features and simulates the RNA-interacting state of every amino acid residue in a given sequence. (biomedcentral.com)
  • The positioning of the Tyr residue is critical for activity. (ward-lab.ch)
Genomic2
  • To this respect, post-genomic era studies including transcriptomics, metabolomics and proteomics provide a wide and unbiased view of plant physiology and biochemistry under adverse environmental conditions that, along with high-throughput phenotyping, could contribute to the characterization of plant genotypes exhibiting physiological and/or genetic traits that are correlated to abiotic stress tolerance. (frontiersin.org)
  • BACKGROUND & AIMS: RNase H2 is a holoenzyme, composed of 3 subunits (ribonuclease H2 subunits A, B, and C), that cleaves RNA:DNA hybrids and removes mis-incorporated ribonucleotides from genomic DNA through ribonucleotide excision repair. (bvsalud.org)
Genes6
  • To determine the relative order of the trp ,pyr,cys genes and the distances between them, the Hfr and Fminus strains were mated long enough to allow the transfer of the nic gene, after which Trp + recombinants were selected. (brainmass.com)
  • We name non-coding RNA (ncRNA) genes according to their RNA type, please see our recent review ( https://www.embopress.org/doi/full/10.15252/embj.2019103777 ) for a full description. (bioscience.org)
  • In cells , RNAP is needed for constructing RNA chains from DNA genes , a process called transcription . (wikidoc.org)
  • RNAP will preferentially release its RNA transcript at specific DNA sequences encoded at the end of genes known as terminators . (wikidoc.org)
  • Non-coding RNA or "RNA genes"-a broad class of genes that encode RNA that is not translated into protein. (wikidoc.org)
  • However, since the late 1990s, many new RNA genes have been found, and thus RNA genes may play a much more significant role than previously thought. (wikidoc.org)
Electron transfer3
  • 1. Introduction The molybdenum cofactor (Mo-co) is found in a variety of enzymes called hydroxylases or oxotransferases, most of which catalyze a net transfer of an oxygen atom to or from a substrate in a two electron transfer reaction [1^4]. (studyres.com)
  • Its ability to catalyze electron transfer from donors (NADH, NADPH) to acceptors (oxygen, ferricyanide, cytochrome c, gCYTB5-III) were studied in spectrophotometric rate assays. (trentu.ca)
  • We achieved this goal by engineering more favorable electrostatic interactions between a functional oxidase model designed in sperm whale myoglobin and its native redox partner, cyt b5, resulting in a 400-fold electron transfer (ET) rate enhancement. (ward-lab.ch)
Enzymes5
  • The kinome is made up of a large number of functionally diverse enzymes, with the classification indicating very little about the extent of the conserved kinetic mechanisms associated with phosphoryl transfer. (biomedcentral.com)
  • The International Union of Pure and Applied Chemistry and the International Union of Biochemistry (IUPAC/IUB) commission on the classification and nomenclature of enzymes placed the enzymes that transfer high energy phosphate bonds from nucleotides into two divisions: the transferases (kinases) and the ligases (synthetases) [ 1 ]. (biomedcentral.com)
  • Furthermore, during research carried out on the effect of deuteration at the C8 position of ATP on the activity of a number of kinase and synthetase enzymes, it became evident that the C8 proton of ATP plays a direct mechanistic role in initiating phosphoryl transfer, and probably also in the regulation of catalysis via the regulation of the rate of reaction [ 4 ]. (biomedcentral.com)
  • RNA polymerase enzymes are essential to life and are found in all organisms and many viruses . (wikidoc.org)
  • Introducing two His and one Tyr residues into myoglobin resulted in enzymes that reduce O2 to H2O with more than 1000 turnovers (red line, see scheme) and minimal release of reactive oxygen species. (ward-lab.ch)
Amino acids1
  • These mechanisms and the associated proton transfer cascades achieve the proton transfer via different family-specific conserved sets of amino acids. (biomedcentral.com)
Sequences1
  • However, none of these methods addresses the crucial issue of specific interactions i.e. the same protein interacts with some RNA sequences and not others. (biomedcentral.com)
Protein9
  • Sequence of amino acid in a protein helps in the generation of RNA probe. (brainmass.com)
  • This means no separate symbols for protein-coding or non-coding RNA isoforms of a protein-coding locus or alternative transcripts from a non-coding RNA locus. (bioscience.org)
  • Protein N α -acetylation (Nt-acetylation) is an irreversible protein modification where the acetyl moiety is transferred to the N α amino group of a protein or polypeptide by N-terminal acetyltransferases (NATs). (hindawi.com)
  • Regulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA-protein interactions. (biomedcentral.com)
  • Interaction preferences of protein subsequences and dinucleotides can be inferred from protein-RNA complex structures, enabling a training-based prediction approach. (biomedcentral.com)
  • We analyzed basic statistics of amino acid-dinucleotide contacts in protein-RNA complexes and found their pairing preferences could be identified. (biomedcentral.com)
  • Protein-RNA interactions are involved in various regulatory and constitutional cellular functions. (biomedcentral.com)
  • Yet, protein-RNA interactions are far less understood than protein-DNA and protein-protein interactions, partly because fewer structures are available and also likely because these interactions are more complex than the others. (biomedcentral.com)
  • We start with a statistical analysis of protein-RNA contacts and identify patterns of contact preferences that contrast or resemble protein-DNA contacts. (biomedcentral.com)
Recognition1
  • Knowledge of exact interaction partners and the mechanism of recognition are essential for an understanding and ability to control RNA-level regulatory processes. (biomedcentral.com)
Initiation1
  • A number of conserved mechanisms within the prescribed kinase fold families have been identified directly utilizing the C8-H of ATP in the initiation of phosphoryl transfer. (biomedcentral.com)
Nuclear1
  • After receiving his PhD at the University of Zurich in 1965, where he synthesized, and characterized Tetrahydropterins by nuclear magnetic resonance, he studied for one year Quantum Biochemistry as a postdoctoral fellow with Professor Pullman at the Institut de Biologie Physico-Chimique in Paris, France. (uc.edu)
Reaction2
  • We can tell from this that Glu must be the C-terminal amino acid, since the sequence must be either A) Ser-Tyr-X-X-X-X- Trp -Glu or b) Ser-X-X-X- Trp -X-Tyr-Glu D) Reaction of the original polypeptide with CNBr produced two tetrapeptides. (brainmass.com)
  • It has been reported that motions of these loops facilitate substrate access and product release, and loops 6 and 7 located at the substrate entrance of the binding pocket promote proton transfer reaction at the catalytic site motions. (biomedcentral.com)
Molecular2
  • The 2006 Nobel Prize in Chemistry was awarded to Roger Kornberg for creating detailed molecular images of RNA polymerase during various stages of the transcription process. (wikidoc.org)
  • 1. State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, People's Republic of China. (thno.org)
Eukaryotes1
  • Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. (mdpi.com)
Subunit1
  • RNA Polymerase binding involves the α subunit recognizing the upstream element (-40 to -70 base pairs) in DNA, as well as the σ factor recognizing the -10 to -35 region. (wikidoc.org)
Strand3
  • Considered together, these data indicate that impairing the primer strand transfer pathway required for proofreading increases the probability of common mutations by Pol ϵ, elucidating the association of homologous mutations in human DNA polymerase ϵ with cancer. (bvsalud.org)
  • Each RNAP is transcribing an RNA strand which can be seen branching off of the DNA. (wikidoc.org)
  • It then produces an RNA chain which is complementary to the template DNA strand. (wikidoc.org)
Proton transfer1
  • Associated with the "push" mechanism and "pull" mechanisms are a series of proton transfer cascades, initiated from C8-H, via the tri-phosphate backbone, culminating in the formation of the pentavalent transition state between the γ-phosphate of the ATP and the substrate nucleophile. (biomedcentral.com)
Catalytic2
  • During Hg2+ transfer to the catalytic active site from the C terminus cysteine residues, a trigonal planar intermediate is formed stabilized by hydrogen bonding of a water molecule to the thiolates. (wikipedia.org)
  • This classification relays little information on the catalytic mechanisms employed in nucleotide binding and phosphoryl transfer. (biomedcentral.com)
Catalysis1
  • The critical question that needed to be answered was to what extent the functionality required for the catalysis of phosphoryl transfer is conserved within the 25 families or 12 fold-groups. (biomedcentral.com)
Enzyme2
  • Portions of the enzyme were made transparent so as to make the path of RNA and DNA more clear. (wikidoc.org)
  • RNA polymerase ( RNAP or RNApol ) is an enzyme that makes an RNA copy of a DNA or RNA template. (wikidoc.org)
Specific1
  • Phosphoryl transfer within kinases is therefore a specific event mediated and regulated via the coordination of the adenyl moiety of ATP and the C8-H of the adenyl moiety. (biomedcentral.com)
Complex1
  • After binding to the DNA, the RNA polymerase switches from a closed complex to an open complex. (wikidoc.org)
Science1
  • Proteomics of BPs reaches a point where the information gained over the last decade, and the one that has to be acquired, should be transferred into transfusion science. (medscape.com)