|
Phenylalanine—tRNA Ligase
In enzymology, a phenylalanine—tRNA ligase () is an enzyme that catalyzes the chemical reaction :ATP + L-phenylalanine + tRNAPhe \rightleftharpoons AMP + diphosphate + L-phenylalanyl-tRNAPhe The 3 substrates of this enzyme are ATP, L-phenylalanine, and tRNAPhe, whereas its 3 products are AMP, diphosphate, and L-phenylalanyl-tRNAPhe. This enzyme belongs to the family of ligases, to be specific those forming carbon-oxygen bonds in aminoacyl-tRNA and related compounds. The systematic name of this enzyme class is L-phenylalanine:tRNAPhe ligase (AMP-forming). Other names in common use include phenylalanyl-tRNA synthetase, phenylalanyl-transfer ribonucleate synthetase, phenylalanine-tRNA synthetase, phenylalanyl-transfer RNA synthetase, phenylalanyl-tRNA ligase, phenylalanyl-transfer RNA ligase, L-phenylalanyl-tRNA synthetase, and phenylalanine translase. This enzyme participates in phenylalanine, tyrosine and tryptophan biosynthesis and aminoacyl-tRNA biosynthesis. Phenylalanin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzymology
An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecules known as product (chemistry), products. Almost all metabolism, metabolic processes in the cell (biology), cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called ''enzymology'' and the field of pseudoenzyme, pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts include Ribozyme, catalytic RNA molecules, also called ribozymes. They are sometimes descr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mitochondrion
A mitochondrion () is an organelle found in the cell (biology), cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double lipid bilayer, membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used throughout the cell as a source of chemical energy. They were discovered by Albert von Kölliker in 1857 in the voluntary muscles of insects. The term ''mitochondrion'', meaning a thread-like granule, was coined by Carl Benda in 1898. The mitochondrion is popularly nicknamed the "powerhouse of the cell", a phrase popularized by Philip Siekevitz in a 1957 ''Scientific American'' article of the same name. Some cells in some multicellular organisms lack mitochondria (for example, mature mammalian red blood cells). The multicellular animal ''Henneguya zschokkei, Henneguya salminicola'' is known to have retained mitochondrion-related organelles despite a complete loss of their mitochondrial genome. A large number ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Domains
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins. Background The concept of the domain was first proposed in 1973 by Wetlaufer after ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, Nuclear magnetic resonance spectroscopy of proteins, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert Biocuration, biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organizations (PDBe, PDBj, RCSB PDB, and BMRB). The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tertiary Structure
Protein tertiary structure is the three-dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains and the backbone may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure. A number of these structures may bind to each other, forming a quaternary structure. History The science of the tertiary structure of proteins has progressed from one of hypothesis to one of detailed definition. Although Emil Fischer had suggested proteins were made of polypeptide chains and amino acid side chains, it was Dorothy Maud Wrinch who incorporated geometry into the prediction of protein structures. Wrinch demon ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha Helix
An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the Protein secondary structure, secondary structure of proteins. It is also the most extreme type of local structure, and it is the local structure that is most easily predicted from a sequence of amino acids. The alpha helix has a right-handed helix conformation in which every backbone amino, N−H group hydrogen bonds to the backbone carbonyl, C=O group of the amino acid that is four residue (biochemistry), residues earlier in the protein sequence. Other names The alpha helix is also commonly called a: * Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure) * 3.613-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen) Discovery ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Antiparallel (biochemistry)
In biochemistry, two biopolymers are antiparallel if they run parallel (geometry), parallel to each other but with opposite directionality (molecular biology), directionality (alignments). An example is the two complementarity (molecular biology), complementary strands of a DNA nucleic acid double helix, double helix, which antiparallel vectors, run in opposite directions alongside each other. Nucleic acids Nucleic acid molecules have a phosphoryl (5') end and a hydroxyl (3') end. This notation follows from IUPAC nomenclature of organic chemistry, organic chemistry nomenclature, and can be used to define the movement of enzymes such as DNA polymerases relative to the DNA strand in a non-arbitrary manner. G-quadruplexes G-quadruplexes, also known as G4 DNA are secondary structures found in nucleic acids that are rich in guanine. These structures are normally located at the telomeres (the ends of the Chromosome, chromosomes). The G-quadruplex can either be parallel or antiparallel ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNA Recognition Motif
RNA recognition motif, RNP-1 is a putative RNA-binding domain of about 90 amino acids that are known to bind single-stranded RNAs. It was found in many eukaryotic proteins. The largest group of single strand RNA-binding protein is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins ( hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF2, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation ( PABP, La, Hu). The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor appears to have two RRM-like domains with specialised features for protein recognition. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Motif
In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules. A structural motif does not have to be associated with a sequence motif; it can be represented by different and completely unrelated sequences in different proteins or RNA. In nucleic acids Depending upon the sequence and other conditions, nucleic acids can form a variety of structural motifs which is thought to have biological significance. ;Stem-loop: Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Domain
In molecular biology, a protein domain is a region of a protein's Peptide, polypeptide chain that is self-stabilizing and that Protein folding, folds independently from the rest. Each domain forms a compact folded Protein tertiary structure, three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or Disulfide bond, disulfide bridges. Domains often form functional units, such as the calcium-binding EF-hand, EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimera (protein), chimeric ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anticodon
Transfer ribonucleic acid (tRNA), formerly referred to as soluble ribonucleic acid (sRNA), is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes). In a cell, it provides the physical link between the genetic code in messenger RNA (mRNA) and the amino acid sequence of proteins, carrying the correct sequence of amino acids to be combined by the protein-synthesizing machinery, the ribosome. Each three-nucleotide codon in mRNA is complemented by a three-nucleotide anticodon in tRNA. As such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code. Overview The process of translation starts with the information stored in the nucleotide sequence of DNA. This is first transformed into mRNA, then tRNA specifies which three-nucleotide codon from the genetic code corresponds to which amino acid. Each mRNA codon is recognized by a particular type of tRNA, which docks to it along a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ferredoxin
Ferredoxins (from Latin ''ferrum'': iron + redox, often abbreviated "fd") are iron–sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.C. Wharton of the DuPont Co. and applied to the "iron protein" first purified in 1962 by Mortenson, Valentine, and Carnahan from the anaerobic organism, anaerobic bacterium ''Clostridium pasteurianum''. Another redox protein, isolated from spinach chloroplasts, was termed "chloroplast ferredoxin". The chloroplast ferredoxin is involved in both cyclic and non-cyclic photophosphorylation reactions of photosynthesis. In non-cyclic photophosphorylation, ferredoxin is the last electron acceptor thus reducing the enzyme NADP+ reductase. It accepts electrons produced from sunlight-Electron excitation, excited chlorophyll and transfers them to the enzyme ferredoxin: NADP+ oxidoreductase . Ferredoxins are small proteins containing iron and sulfur atoms organized as iron–sulfur clusters ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
