transfer RNA

6 Key excerpts on "transfer RNA"

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  eBook - ePub

  Advanced Molecular Biology

  A Concise Reference

  • Richard Twyman(Author)
  • 2018(Publication Date)
  • Garland Science

    (Publisher)

  petidyltransferase domain, which provides the catalytic activity for peptide bond formation, and a GTPase domain, whose activities are required for translocation of the ribosome along the mRNA. The roles of these sites during protein synthesis are discussed in more detail below.

  transfer RNA. Before the genetic code (q.v.) was understood, Francis Crick proposed the adaptor hypothesis to explain how the nucleotide sequence in mRNA could be translated into protein. The model predicted the existence of an adaptor molecule which would recognize both the nucleic acid sequence of the message and the appropriate amino acid, bringing the two together at the ribosome.

  The adaptor molecule is transfer RNA (tRNA). The tRNAs are a relatively homogeneous family of RNA molecules, usually 75–100 nucleotides in length, which are extensively processed during their production (see RNA Processing). They possess a characteristic secondary and tertiary structure (Box 23.2 ), most importantly the acceptor stem (to which the amino acid binds) and the anti-codon loop (which carries the three nucleotide anticodon that forms complementary base pairs with codons in the mRNA). Bacterial cells contain up to 35 different tRNAs, and eukaryotic cells up to 50. This number is lower than the number of possible codons in the genetic code, but greater than the number of amino acids specified by the code. This indicates that individual tRNAs can recognize more than one codon (reflecting wobble pairing, q.v), but that different tRNAs may be charged with the same amino acids (these are isoaccepting tRNAs, q.v.).

  The tRNAs are charged (conjugated to their corresponding amino acids) by enzymes termed amino acyl tRNA synthetases. There is one enzyme for each amino acid, and therefore each synthetase recognizes all its cognate isoaccepting tRNAs. The charging mechanism and its regulation are considered in detail elsewhere (see

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  eBook - ePub

  Molecular Biology

  Structure and Dynamics of Genomes and Proteomes

  • Jordanka Zlatanova(Author)
  • 2023(Publication Date)
  • Garland Science

    (Publisher)

  Translation: The Players

  DOI: 10.1201/9781003132929-15

  Learning objectives

  Translation is the process by which messenger RNA chains are read to yield protein chains. Translation requires both RNA–RNA and RNA–amino acid recognition. The three major players in translation are the mRNA that carries the message, the tRNA (adaptor) molecules that carry the amino acid specified by the next codon in the mRNA, and the ribosome, the active platform on which the process occurs.

  tRNA molecules carry both an anticodon that matches the codon on the message and the amino acid that is specified by that codon. The charging of tRNAs with amino acids is catalyzed by a set of enzymes called aminoacyl-tRNA synthetases. In this two-step process, the amino acid is first activated by adenylation and then attached to the acceptor end of the corresponding tRNA. Various modes of proofreading ensure the fidelity of matching the amino acid with the appropriate tRNA.

  Functional ribosomes in all cells are composed of two subunits, designated by their sedimentation coefficients: 30S and 50S subunits give rise to 70S ribosomes in bacteria and archaea, while 40S and 60S subunits form 80S ribosomes in eukaryotes. Each ribosome contains several RNAs and many proteins, which form three tRNA-binding sites shared between the large and small subunit. During elongation, tRNA is transferred between these sites in a unidirectional manner. Ribosome biogenesis is a complicated multistep process that requires coordinated synthesis of several RNA molecules and the whole set of ribosomal proteins. Assembly of eukaryotic ribosomes requires additional RNA processing and auxiliary protein factors.

  Initiation of translation occurs via different mechanisms in bacteria and eukaryotes. Bacteria use a special sequence (known as the Shine–Dalgarno, SD, sequence) located near the 5′-terminus of the mRNA: SD base-pairs with a sequence in the 16S rRNA of the small ribosomal subunit. In eukaryotes, the ribosome attaches near the cap and hunts downstream for the first methionine codon. Finally, termination of translation involves both specific stop codons and termination factors that bind to the ribosome instead of tRNAs.

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  eBook - ePub

  Snyder and Champness Molecular Genetics of Bacteria

  • Tina M. Henkin, Joseph E. Peters(Authors)
  • 2020(Publication Date)
  • ASM Press

    (Publisher)

  genetic code .

  The actual translation from the language of nucleotide sequences to the language of amino acid sequences is performed by small RNAs called tRNAs and enzymes called aminoacyl-tRNA synthetases (aaRSs). The aaRS enzymes attach specific amino acids to their matching tRNAs. Each aminoacylated tRNA (aa-tRNA) specifically pairs with a codon in the mRNA as it moves through the ribosome, and the amino acid carried by the tRNA is added to the growing protein. The tRNA pairs with the codon in the mRNA through a 3-nucleotide sequence in the tRNA called the anticodon that is complementary to the codon in the mRNA. The base-pairing rules for codons and anticodons are basically the same as the base-pairing rules for DNA replication, and the pairing is antiparallel. The only major differences are that RNA has uracil (U) rather than thymine (T) and that the pairing between the last of the 3 bases in the codon and the first base in the anticodon is less stringent.

  This basic outline of gene expression leaves many important questions unanswered. How does mRNA synthesis begin and end at the correct places and on the correct strand in the DNA? Similarly, how does translation start and stop at the correct places on the mRNA? What actually happens to the tRNA and ribosomes during translation? What happens to the mRNA and proteins after they are made? The answers to these questions and many others are important for the interpretation of genetic experiments, so we will discuss the structure of RNA and proteins and the processes by which they are synthesized in more detail.

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  Textbook of Structural Biology

  • Anders Liljas, Lars Liljas;Miriam-Rose Ash;G?ran Lindblom;Poul Nissen;Morten Kjeldgaard(Authors)
  • 2016(Publication Date)
  • WSPC

    (Publisher)

  An important aspect of protein synthesis is that nucleic acid molecules have central roles, in contrast to most other processes in cells where proteins dominate. Central components are the mRNA, the tRNA and the ribosomal rRNA molecules. An mRNA molecule contains a copy of the gene sequence and binds to the ribosome. The tRNA molecules, the adapters suggested by Francis Crick, decode the gene sequence and link the amino acid into the growing peptide on the ribosome.

  Fig. 11.1 ▪ The universal genetic code. The trinucleotide codons are translated to the 20 amino acids, given here with their three and one letter codes.

  11.1.1The Genetic Code and the tRNAs

  The base triplets of the genetic code (Figure 11.1 ) that build up a messenger rRNA (mRNA) are called codons and correspond to the 20 different amino acids. In addition, there are normally three stop codons (UAA, UAG and UGA). The synthesis of a protein normally starts at an AUG codon, which is also the codon for methionine. Special systems have developed to differentiate between ordinary methionine codons and the start signal, the initiation codon. In some cases (methionine, tryptophan), there is only one triplet that codes for a certain amino acid, but sometimes there are as many as six (serine, leucine, arginine). The code is degenerate. There is no one-to-one relationship between codons and tRNA molecules. Mammalian mitochondria have a very limited set of tRNA molecules, but many species have around 40. This relates to the variable codon usage as well as to the capacity of some tRNAs to read several codons (tRNA wobble base-paring).

  The tRNA molecules are normally around 75 nucleotides long (Section 5.3.10.1 ). The secondary structure looks like a cloverleaf with a stem and three leaves (Figure 5.47 ). The stem has the unique sequence CCA at the 3′-end. It is the ribose of the 3′-terminal A that gets aminoacylated by specific enzymes, tRNA synthetases. This stem is therefore called the aminoacyl or acceptor stem. The three leaves or arms of the tRNA are called the D stem and loop, the anticodon stem and loop, and the T stem and loop, respectively. In addition, there is a variable loop (V-loop) that can be upto 21 nucleotides in length. Serine and leucine tRNAs generally have long V-loops as does tyrosine tRNA in bacteria and chloroplasts. The anticodon at the end of the middle loop can match a codon in the mRNA. The three-dimensional structure of the tRNA molecule has the shape of an “L” (Figure 5.47

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  eBook - ePub

  Molecular Biology

  • David P. Clark(Author)
  • 2009(Publication Date)
  • Academic Cell

    (Publisher)

  Figure 8.03 transfer RNA Recognizes CodonsSeveral tRNAs are seen bound to mRNA codons by their anticodons. Each tRNA carries a different amino acid at the end of the adaptor stem. This diagram is intended to show the principle of mRNA decoding. It does NOT illustrate the actual mechanism of protein synthesis. In real life, the codons are contiguous and there are no spacers in between and only two tRNAs are bound at any given time.

  The anticodon of tRNA recognizes the codon on mRNA by base pairing.

  Each transfer RNA carries one particular amino acid.

  transfer RNA Forms a Flat Cloverleaf Shape and a Folded “L” Shape

  transfer RNA molecules are about 80 nucleotides in length. About half the bases are paired to form double helical segments. A typical tRNA has four short base-paired stems and three loops (Fig. 8.04 ).This is shown best in the cloverleaf structure , intended to reveal details of base pairing, which shows the tRNA spread out flat in only two dimensions. (Such a diagram is sometimes called a secondary structure map). The tRNA cloverleaf is folded up further to give an L-shaped 3-D structure, in which the TΨC-loop (or T-loop) and the D-loop are pushed together. The anticodon and attached amino acid are located at the two ends of the L-structure. Different tRNA molecules vary considerably in sequence, but they all conform to this same overall structure. Variations in length (from 73 to 93 nucleotides) occur, due mostly to the variable loop.

  Figure 8.04

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  Single-Particle Cryo-Electron Microscopy

  The Path Toward Atomic Resolution/ Selected Papers of Joachim Frank with Commentaries

  • Joachim Frank(Author)
  • 2018(Publication Date)
  • WSPC

    (Publisher)

  The ribosome is a very large (2.4 MDa in eubacteria) ribonucleic-protein complex composed of two distinct subunits, the small subunit (30S) charged with the task of decoding the genetic message carried by the messenger RNA (mRNA), the large subunit (50S) to the catalysis of peptide bond formation. Instrumental for these fundamental processes is the interaction of the ribosome with transfer RNA (tRNA), a small L-shaped molecule that embodies in its various forms the association of each amino acid with a three-base “word” of the genetic code, the codon. Translation is based on the mutual recognition, by partial Watson–Crick pairing, between the codon on the mRNA and the anticodon of the tRNA carrying the corresponding amino acid. In facilitating tRNA selection, decoding, and the stepwise formation of the polypeptide, ribosomal RNA (rRNA) acts as both a structural framework and a catalyst.

  Despite the success in the elucidation of ribosomal structure by x-ray crystallography, the detailed mechanism by which translation of mRNA code into peptide proceeds is still only scantly understood. One of the obstacles we face is that although the process is complex and dynamic, x-ray crystallography represents the molecule in a static form—packed in a crystal, moreover, whose very stability depends on intermolecular contacts that are largely nonphysiological. Of crucial importance for the understanding of the multistep translation process is the knowledge of how the ribosome interacts with its ligands, notably (apart from the most crucial ligands mRNA and tRNAs) the various factors catalyzing initiation, elongation, termination, and recycling. To date, with the exception of ribosomal complexes containing eubacterial release (RF1 or RF2) (1 ) or recycling (RRF) (2 , 3 ) factors, there exists no x-ray structure of a factor–ribosome complex. The crystal structures of individual subunits complexed with initiation (4 –6 ) and recycling (7

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