Ribosomal RNA

11 Key excerpts on "Ribosomal RNA"

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  Introduction to Molecular Biology

  • S Bresler(Author)
  • 2012(Publication Date)
  • Academic Press

    (Publisher)

  The great stability of rRNA was shown in experiments of the following design. When a bacterial culture is grown in the presence of heavy isotopes and then transferred to light medium, isotopically labeled rRNA is transmitted to progeny cells without alteration, and can be detected in its original form even in the fourth and fifth generations. The isotopic composition of the inherited RNA does not change in the least, although all of the new components synthesized by the growing cells contain light constituents. In all cells, regardless of their origin, the participation of ribosomes in protein synthesis is obligatory. Ribosomes have even been found in the nuclei of cells from higher organisms where they mediate the synthesis of specific nuclear proteins. As with other cellular organelles, ribosomes separate a particular chemical reaction in space from others taking place concurrently in the same milieu. For example, amino acids, the building blocks of protein, can take part in many cellular processes since they are present in the cytoplasm as soluble compounds. The reactions leading to protein synthesis must therefore be separated spatially from oxidative or degradative reactions. This explains why distinct organelles are necessary for protein synthesis. Generally speaking, they must also be accessible only to essential substances in the cytoplasm such as amino acids and the compounds which mediate energy transfer, adenosine triphosphate (ATP) and guanosine triphosphate (GTP). A second type of RNA, called template or messenger RNA, carries genetic infor-mation from the chromosomal DNA to the sites of protein synthesis, that is, to the ribosomes where it becomes bound. Such RNA molecules apparently act as a template which directs the assembly of polypeptide chains. Messenger RNA is rapidly meta-bolized in bacterial cells throughout exponential growth ; its synthesis requires 20 to 30 seconds and it is generally degraded in the course of a few minutes.

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  Protein Synthesis: Methods and Protocols

  • Bhupendra Pushkar(Author)
  • 2020(Publication Date)
  • Delve Publishing

    (Publisher)

  This chapter also provides knowledge about the function of a ribosome. 6.1. INTRODUCTION There have been often seen that there are many organelles which tend to work together to complete the cell activities while examining the animal as well as plant cell by using a microscope. This is one of the essential cell organelles which are ribosomes. These are in charge of the protein synthesis. The ribosome is considered to be a complex made of protein and RNA. The ribosome tends to add up to numerous million Daltons in size and it is assumed to have an important part in the course of decoding the genetic message which is reserved in the genome into protein. There is an essential chemical step of protein synthesis and that is peptidyl transfer. In this, the movement of the developing or nascent peptide takes place from one tRNA molecule to the amino acid along with another tRNA. While developing the polypeptide, the amino acids are included along with the arrangement of codons of an mRNA. Therefore, the ribosome has important sites for one mRNA and not less than two tRNAs. A ribosome is said to be made up of two subunits. These include the big and the little subunit which contains a couple of Ribosomal RNA (rRNA) molecules and a random number of ribosomal proteins. Several protein factors catalyze the distinct impressions of protein synthesis. It is important to consider the translation of the genetic code for the manufacturing of the protein which is useful and also, for the growth of the cells. Ribosomes are said to be the particles that are present in large numbers in all the living cells. It serves as the site where the protein synthesis takes place. Ribosomes can occur both as free particles in prokaryotic as well as eukaryotic and also, it acts as the particles which are attached to the membranes of the endoplasmic reticulum in eukaryotic cells. Ribosome Structure and Function 151 Ribosomes are the small particles which are remarkably abundant in cells.

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  Fundamental Molecular Biology

  • Lizabeth A. Allison(Author)
  • 2021(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Not drawn to scale. 3.2 RNA is involved in a wide range of cellular processes 49 Messenger RNA (mRNA): a copy of the DNA sequence that encodes a protein and binds to ribosomes in the cytoplasm. Transfer RNA (tRNA): small RNA that is “charged” with a specific amino acid , the building block of proteins. tRNA delivers to the ribosome the appropriate amino acid via specific base-pairing interactions of the tRNA with the mRNA. Small nuclear RNA (snRNA): plays a role in pre-mRNA splicing , a process that pre-pares the mRNA for translation. Small nucleolar RNA (snoRNA): plays a role in rRNA processing, to prepare the rRNA for function. MicroRNA (miRNA): involved in post-transcriptional gene regulation; each miRNA binds to a complementary sequence in a target mRNA, usually resulting in gene silenc-ing, by triggering degradation of mRNA or by blocking translation by the ribosome. PIWI-interacting RNAs (piRNAs): small RNAs present in germline cells that are 24–31 nucleotides in length. They associate with PIWI proteins to form piRNA-induced silencing complexes, which repress transposable elements via transcriptional or post-transcriptional mechanisms. Long noncoding RNA (lncRNA): a large and diverse class of RNA molecules that do not encode proteins; they play a role in several cellular functions, including the regula-tion of gene transcription. Contributing to the versatility of RNA function is the ability of RNA to form comple-mentary base pairs with other RNA molecules and with single-stranded DNA. The ability of RNA to make specific base pairs is a key to understanding its role in everything from post-transcriptional gene silencing to translation. RNA–protein interactions are also of cen-tral importance. Most of the RNA in a eukaryotic cell is associated with protein as part of RNA–protein complexes termed ribonucleoproteins (RNPs) . In addition, most, if not all, RNA-based catalytic reactions are thought to take place in conjunction with proteins.

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  Advanced Chemical Biology

  Chemical Dissection and Reprogramming of Biological Systems

  • Howard C. Hang, Matthew R. Pratt, Jennifer A. Prescher, Howard C. Hang, Matthew R. Pratt, Jennifer A. Prescher(Authors)
  • 2023(Publication Date)
  • Wiley-VCH

    (Publisher)

  As such, metal ion concentrations are important to the energetic landscapes by which RNA can fold into different con- formations. RNA tertiary structure is a key driver of RNA function and protein–RNA interactions. Take the ribosome for example, which includes intricately folded Ribosomal RNA constituting many of the secondary structural elements listed above [17]. Tertiary inter- actions within and between Ribosomal RNAs help to fold the ribosome into its functional form and stabilize protein-binding sites [18]. In particular, the A-minor motif is one of the most observed tertiary interactions found in the large subunit of the ribosome [19]. This interaction generally consists of the preferential inser- tion of an unpaired adenosine nucleoside into the C–G base pair of the minor groove of a neighboring RNA helix. A-minor interactions typically involve one or more hydrogen bonds between the smooth N1-C2-N3 minor groove edge of the inserting adenine with the 2 ′ -OHs of the receptor duplex. In the case of the ribo- somal large subunit, A-minor tertiary motifs stabilize the contacts between helices found in the 23S rRNA and 3 ′ -terminal adenines found in tRNA. Although proteins are important components of the ribosome, the active site of the ribosome, which houses its peptidyl transferase activity, is made almost completely of RNA, leading to the conclusion that the ribosome is a ribozyme [20–23]. The active sites within the ribosome are significantly different between prokaryotes and mammals. Many small molecule antibiotics have been developed, which bind to regions of the prokaryotic peptidyl transferase site [24], thereby providing a pow- erful illustration of how RNA biology is important to medicinal chemistry. 4.3 Synthesis of RNA 4.3.1 Chemical Synthesis The current chemical synthesis of RNA is generally similar to the phosphoramidite-based solid-phase syn- thesis of DNA described in Section 2.3.1.

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  Chemistry and Biology of Non-canonical Nucleic Acids

  • Naoki Sugimoto(Author)
  • 2021(Publication Date)
  • Wiley-VCH

    (Publisher)

  Figure 7.4 ). Ribosome can be separated into two subunits (50S large subunit and 30S small subunit in prokaryotes and 60S large subunit and 40S small subunit in eukaryotes). Most of the ribosomal mass and inner surface, which binds mRNA and tRNA, is represented by rRNAs. Especially, the active site of the ribosome for the polymerization of amino acids is surrounded by 16S or 18S rRNA, and the rRNA functions to catalyze the polymerization of amino acids.

  Figure 7.4

  Structure and composition of ribosome. Ribosome consists of large and small ribosomal subunits. Each subunit contains Ribosomal RNAs (rRNAs) and ribosomal proteins. Structures of the larger and small ribosomal subunits and its complex (mature ribosome) are those derived from Escherichia coli (PDB ID: 5MDZ). Ribosomal RNAs are shown in gray. Ribosomal proteins for the large and small subunits are shown by space-filling model. Structure of mRNA pathway on the surface of small subunit is derived from Thermus thermophilus ribosome (PDB ID: 4V4P). In the image, mRNA on the small subunit is emphasized dark. Front side of the structure is clipped at the place of mRNA pathway.

  7.3 General Process of Translation

  The process of translation reaction is generally divided to three steps, which are initiation, elongation, and termination.

  7.3.1 Translation Initiation

  Translation starts from interaction of the small ribosomal subunit and mRNA. The beachhead of the ribosome binding on the mRNA is different between eukaryote and prokaryote. In the case of eukaryotes, mRNAs have a 7-methylguanylate (m7G) cap structure (5′ cap) at its 5′ end (Figure 7.5a ). Several eukaryotic initiation factors (eIFs) in eIF4 group recognize 5′ cap structure and recruit small ribosomal subunit on the mRNA. In the case of prokaryote, the small ribosomal subunit recognizes a conserved ribosomal binding site (RBS), which is also known as Shine-Dalgarno sequence, on mRNA (Figure 7.5b ). The sequence of RBS is purine rich and has complementarity to 3′ end of prokaryote 16S rRNA that enables direct interaction through base pairing. In both prokaryotes and eukaryotes, when the small ribosomal subunit interacts with mRNA, initiator tRNA is already located on a peptidyl-tRNA binding site (P-site) of the small ribosomal subunit with the aid of the initiation factor proteins. The initiator tRNA is generally attaching methionine (in eukaryote) or formylmethionine (in prokaryote). The anticodon sequence of the initiator tRNA is CAU, which base pairs with AUG start codon. After the binding to the mRNA, the small ribosomal subunit finds initiation codon. In prokaryotes, the initiation codon is generally located close downstream of the RBS. In eukaryotes, the small ribosomal subunit moves according to mRNA until the initiation codon (Figure 7.5a

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  Ribozymes

  Principles, Methods, Applications

  • Sabine Müller, Benoît Masquida, Wade Winkler, Sabine Müller, Benoît Masquida, Wade Winkler(Authors)
  • 2021(Publication Date)
  • Wiley-VCH

    (Publisher)

  [20] .

  8.3 Translation Cycle

  Translation is the most energy‐consuming pathway in a growing E. coli cell. Approximately 50% of the energy in form of ATP and guanosine‐5′‐triphosphate (GTP ) is consumed during protein synthesis [21 , 22 ]. Due to the enormous energy costs, translation is a tightly regulated and monitored process as errors during protein synthesis would have devastating effects. Therefore, ribosomes interact not only with mRNAs or tRNAs but also with many different protein factors like elongation factors or rescuing factors, which ensure fast and accurate translation. The order in which ribosomes interact with these different factors is dictated by the four steps of translation. These steps are (i) initiation; (ii) elongation, which can be further subdivided into decoding, peptide bond formation, and translocation; (iii) termination; and (iv) recycling (Figure 8.2 ). It is worth noting that the last step, recycling, and the first step, initiation, are connected, as the dissociation of both subunits from each other allows them to participate in another round of initiation. Hence, translation should be imagined as a circular process, and the order of events is often described as the translation cycle. Each single step and the corresponding sub‐steps will be described in more detail in the following sections 8.3.1 –8.3.4 .

  Figure 8.1

  Structural overview of the bacterial ribosome. (a) View on the SSU from the solvent side. The 16S rRNA (yellow) and rProteins (green) of the SSU are shown. The major subdivision of the SSU is indicated: H, head; N, neck; B, body; P, platform; S, shoulder; F, foot; and SP, spur (also known as toe) [7] . (b) View on the LSU from the solvent side. The 23S rRNA (gray), 5S rRNA (magenta), and rProteins (blue) are indicated [8]

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  Cellular Organelles

  • Edward Bittar(Author)
  • 1995(Publication Date)
  • Elsevier Science

    (Publisher)

  Chapter 10 The Ribosome RICHARD BRIMACOMBE Introduction Components of the E. Coli Ribosome Function Initiation Elongation Termination Structure Electron Microscopy Neutron Scattering Protein-Protein Cross-Linking, and Amino Acid Sequences RNA Primary Sequences and Secondary Structure Intra-RNA and RNA-Protein Cross-Linking Foot-Printing Three-Dimensional Models of the Ribosomal RNA Structure-Function Correlation Location of Functionally Important Sites in the 3OS and 50S Subunits Site-Directed Cross-Linking with Functional Ligands Conclusions And Prospects Site-Directed Mutagenesis Crystallization of Ribosomal Proteins and Whole Ribosomal Subunits H , ,,, 254 255 256 256 256 259 259 259 260 261 261 262 263 263 264 264 267 269 270 270 Principles of Medical Biology, Volume 2 Cellular Organelles, pages 253-273 Copyright 9 1995 by JAI Press Inc. All rights of reproduction in any form reserved. ISBN:l-55938-803-X 253 254 RICHARD BRIMACOMBE INTRODUCTION The flow of genetic information from DNA to RNA to protein is a universal process in all cellular organisms, and the final stage in this process-namely, the translation of a messenger RNA sequence into a protein molecule~takes place on the ribosome. Each consecutive triplet sequence of three bases on the mRNA corresponds to a single amino acid according to the genetic code, and the amino acids to be incorporated into the protein chain are brought to the ribosome in the form of covalent aminoacyl-tRNA complexes. A molecule of tRNA consists of about 80 nucleotides, which are folded into a rather rigid L- shape (Kim et al., 1973). The amino acid is attached to the short arm of the L, whereas at the end of the long arm of the L there is a triplet anti-codon sequence, which is able to bind to a coding triplet on the mRNA by Watson-Crick base-pairing.

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  Looking at Ribozymes

  Biology of Catalytic RNA

  • Fabrice Leclerc, Benoît Masquida(Authors)
  • 2024(Publication Date)
  • Wiley-ISTE

    (Publisher)

  1 Fundamentals of RNA and Ribozyme Structure This chapter is intended to familiarize the reader with the structure of RNAs. Understanding the structural basis of RNAs is a prerequisite for the study of ribozymes and RNA-mediated catalysis. This section shows how nucleotide stereochemistry guides the structuring of helices and consequently the addition of functional motifs that give this polymer its folding and interaction properties, as well as its catalytic properties. It is important to understand that all biological mechanisms rely on the interaction capabilities of structured molecules. The structure of biomolecules is therefore a fundamental aspect for the understanding of biology. The figures in this book are therefore often developed from experimental structures obtained by radio-crystallography or electron microscopy. Visualizing a biological mechanism through the molecular structures involved allows a better understanding of the actions of the different partners and the domains that compose them. It is then possible to deduce the mechanisms of chemical reactions and also to establish evolutionary relationships between homologous molecules of different organisms that perpetuate these mechanisms while adapting to different selection pressures resulting from distinct ecological constraints. For a color version of all the figures in this chapter, see www.iste.co.uk/masquida/ribozymes. zip. 2 Looking at Ribozymes 1.1. Sequences and secondary structures RNA (ribonucleic acid) is one of the three main biological polymers with DNA (deoxyribonucleic acid) and proteins. RNA adopts complex structures thanks to the physicochemical properties of the four main nucleotides from which it is assembled. The nucleotides are composed of a ribose-phosphate part and an aromatic part, the nucleobase, attached to the ribose. The base is composed of one or two fused aromatic rings containing imines and ethylenic carbons decorated by exocyclic amines and/or carbonyl groups.

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  Advanced Chemical Biology

  Chemical Dissection and Reprogramming of Biological Systems

  • Howard C. Hang, Matthew R. Pratt, Jennifer A. Prescher, Howard C. Hang, Matthew R. Pratt, Jennifer A. Prescher(Authors)
  • 2023(Publication Date)
  • Wiley-VCH

    (Publisher)

  4 RNA Function, Synthesis, and Probing Andreas Pintado‐Urbanc

  1 ,2

  and Matthew D. Simon

  1 ,2

  1 Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave, New Haven, CT, 06511, USA 2 Institute of Biomolecular Design and Discovery, Yale University, 600 West Campus Dr, West Haven, CT, 06516, USA

  4.1 Introduction

  How did life begin? There is ample evidence to support the hypothesis that life began with an RNA world [1] . RNA has the capacity to both encode information in its primary sequence and to perform complex functions (plausibly including self‐replication). This is because of its ability to fold into intricate three‐dimensional structures. Relics of the RNA world can be found throughout the pantheon of biomolecules, notably through the prevalence of ribonucleotides in cofactors, such as adenosine triphosphate (ATP ), nicotinamide adenine dinucleotide (

  NAD+

  ), and acetyl‐CoA. In modern life, RNA is at the heart of the central dogma of molecular biology, enabling the sequential flow of genetic information (DNA →  RNA →  protein). Additionally, RNA carries out a broad range of biological functions beyond coding for proteins. As will be explored in Chapters 4 and 5 , the chemical biology of RNA is central to the study and manipulation of biology, especially regulated gene expression. In this chapter, we will explore the chemical properties and principles of RNA molecules. Chapter 5 will extend this exploration to the regulatory roles of RNA in gene expression.

  The chemistry and biology of RNA are often closely aligned with that of DNA, the fundamental principles of which are described in Chapter 3 . As nucleotide chemistries are frequently portable, RNA chemical synthesis (Section 4.4.1 ) and sequencing strategies (Section 4.5

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  Exploring Integrated Science

  • Belal E. Baaquie, Frederick H. Willeboordse(Authors)
  • 2009(Publication Date)
  • CRC Press

    (Publisher)

  In the same way, in order for RNA to be able to catalyze a large range of different reactions it needs to be able to assume many different shapes. Catalytic RNA molecules are often referred to as ribozymes by combination of the words ribo nucleic acid and enzyme . Although RNA as such is single stranded, the fact that it is made up of nu-cleotides that allow for complementary base pairing means that an RNA sequence can have some of its sections pair up with others of its sections thus creating intri-cate three-dimensional structures. Furthermore, it turns out that some short struc-tural elements are used quite frequently, as illustrated in Figure 16.5. 5’ 3’ single strand 5’ 3’ 3’ 5’ double strand 5’ 3’ 5’ 3’ single nucleotide bulge three nucleotide bulge 5’ 3’ 5’ 3’ 5’ 3’ hairpin loop 5’ 3’ 5’ 3’ 3’ 5’ three stem junction 5’ 3’ 5’ 3’ 3’ 5’ 3’ 5’ four stem junction base pair unpaired nucleotide Figure 16.5: Some common elementary RNA secondary structures. In modern cells ribozymes are quite rare with the exception of the ribosome, essential for life on earth, that contains relatively large Ribosomal RNA molecules generally abbreviated as rRNA . In ribosomes, the messenger RNA is translated into proteins according to the genetic code that matches sequences of three nucleotides to certain amino acids by stringing these amino acids together with covalent bonds. 16: RNA 345 Although ribosomes also contain about 35% proteins besides rRNA (three rRNA molecules in prokaryotes and four rRNA molecules in eukaryotes), the cat-alytic activity needed for joining amino acids into a protein is carried out by the rRNA. In bacteria, only one type of RNA polymerase is used, but in eukaryotes there are three types: RNA polymerase I is responsible for three of the four rRNA molecules by transcribing a precursor rRNA that is then modified into the three types of rRNA while RNA polymerase III directly transcribes the fourth rRNA molecule.

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  Conformational Proteomics Of Macromolecular Architecture: Approaching The Structure Of Large Molecular Assemblies And Their Mechanisms Of Action (With Cd-rom)

  Approaching the Structure of Large Molecular Assemblies and Their Mechanisms of Action(With CD-ROM)

  • R Holland Cheng, Lena Hammar(Authors)
  • 2004(Publication Date)
  • World Scientific

    (Publisher)

  CONCLUDING REMARKS Ribosomal crystallography, initiated two decades ago, yielded exciting structural and clinical information. We found that both the decoding cen- ter and the peptidyl transferase centers are formed of RNA. Proteins seem to serve ancillary functions such as stabilizing required conforma- 280 Ada Yonath tion, binding of non-ribosomal factors, assisting the directionality of the translocation and gating of the ribosomal tunnel. The ribosome is an accurate and intricate machine, and as such it has ample of mobile regions. These include the head and the shoulder of the small subunit, the features lining the mRNA path; the peptidyl trans- ferase; the intersubunit bridges; the exit tunnel that control the release of nascent chains; the L1 stalk that provides the door for exiting tRNA. The studies presented here show that the peptidyl transferase center tolerates various binding modes, but precise positioning appears to be crucial for the biosynthesis of protein chains. This precise positioning is determined by the tRNA helical stem, rather than by its 3' end, and the ribosome provides the structural frame for it. Once properly positioned, the peptide bond can be formed spontaneously. Ribosomal components appear not participate directly in the catalytic event. They may, however, be of major importance for cell vitality, as they may increase the effi- ciency or enhance the rate of the reaction.. Ribosomes are a major target for antibiotics. The therapeutic use of antibiotics has been severely hampered by the emergence of drug resis- tance in many pathogenic bacteria. With the increased popularity of anti- biotics to treat bacterial infections, pathogenic strains have acquired anti- biotic resistance, thus became ineffective. Resistance posed extremely serious medical problems that have prompted extensive effort in the de- sign of modified or new antibacterial agents.

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