Chemistry
RNA
RNA, or ribonucleic acid, is a molecule essential for various biological processes, including protein synthesis and gene regulation. It is composed of nucleotides containing a ribose sugar, a phosphate group, and one of four nitrogenous bases: adenine, guanine, cytosine, or uracil. RNA is involved in translating genetic information from DNA into functional proteins within cells.
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7 Key excerpts on "RNA"
eBook - PDF- Bin Wang(Author)
- 2014(Publication Date)
- Jenny Stanford Publishing(Publisher)
Deemed as one of the most essential molecules in life, RNA participates in transferring genetic information to the translation machinery. Nucleic acids are made of nucleotides, which are a long chain of components consisting of nucleobases, sugars, and phosphate groups. With these components, both DNA and RNA fold to form a variety of helical structures in order to perform biological functions. RNA forms more diverse structures due to its flexibility and complexity. The diverse roles of RNA are determined by its folding fashion, which makes the proper structure. In this chapter, prior to elaboration on the description of structural probing aspects of RNA, it is vital to discuss some basic information about RNA. RNAs are composed of four nucleotides: adenosine (A), cystidine (C), guanosine (G), and uridine (U). In terms of chemistry, an –OH group (hydroxyl group) is at the 2 position of the ribose sugar in RNA. In contrast, there is thymine (T) instead of the uracil base and a lack of oxygen (deoxy) at the 2 position of the ribose sugar in DNA. Generally, RNA can be synthesized chemically (from 3 to 5 ) or enzymatically (from 5 to 3 ). In the enzymatic synthesis, usually a T7 promoter region is added at the 5 end of the DNA template. This enzymatic process known as transcription involves the role of nucleoside triphosphates in linking the hydroxyl group of one nucleotide to the phosphate of another. The 5 end of the resulting product will have one to three phosphates while the 3 end has a free hydroxyl group. Thus, RNA molecules can be labeled at either the 5 end following de-phosphorylation or the 3 end by the ligation reaction. Major subtypes of RNAs are categorized as ribosomal RNA (rRNA), messenger RNA (mRNA) and transfer RNA (tRNA). There are many RNA-nanotechnological applications characterized by dif-ferent subtypes such as small interfering RNA (siRNA), RNA aptamer,
eBook - PDFAdvanced 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)
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) often share reagents and follow the same guiding principles as in DNA chemical synthesis and sequencing. Unlike DNA, which is generally found as a double helix in cells, RNA assumes diverse con- formations with distinct chemical, biophysical, and functional properties. A single difference in the sugar molecule of the nucleotide building blocks of these two biopolymers – a 2 ′ -hydroxyl on the ribose ring of RNA – has substantial consequences on their respective conformations, stabilities, and reactivities. As we will explore in this chapter, these differences are reflected in the biological roles and functionalities of RNA. Consider a molecule of tRNA, the first high-resolution structures of which were solved to 3 Å in 1974 [2, 3]. The role of tRNA in protein synthesis is twofold: it both “reads” the triplet codon in an mRNA through a three-base anticodon interaction and delivers the correct amino acid to the growing peptide chain. The codon–anticodon interactions found between the tRNA and mRNA can mostly be understood using the conventional base-pairing rules previ- ously described for DNA (A with U/T and G with C), but even in codon–anticodon recognition, there are examples of non-Watson–Crick pairing (i.e. wob- ble pairs, see Section 4.2.2) and noncanonical bases (see Section 5.4.1).
eBook - ePubAdvanced 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‐Urbanc1 ,2and Matthew D. Simon1 ,21 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, USA4.1 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
eBook - PDF- S Bresler(Author)
- 2012(Publication Date)
- Academic Press(Publisher)
Chapter V RNA Function 1. Introduction Ribonucleic acid (RNA) is the second component of living tissue which performs a cybernetic function, in this case by providing and supporting a flow of information in the cell. Its role is perhaps even more complicated than that of deoxyribonucleic acid (DNA). While DNA stores the information necessary for the growth and repro-duction of each cell, different types of RNA participate directly in this process, supplying working components of the protein-synthesizing machinery. Accordingly, the quantity of DNA in the cell is invariant, and even in complex and highly differ-entiated organisms, all cells contain the same amount of this substance. By contrast, the quantity of RNA per cell varies substantially, depending on the rate of protein synthesis. The latter is influenced in its turn by exteRNAl conditions of growth such as the carbon source, temperature, and nutrient supplements. The synthesis of each specific enzyme or protein is determined by a special kind of RNA which contains the necessary information in the form of a chemical code akin to that of DNA. But in addition to carrying information about protein structure, RNA also plays a role in controlling the rate of synthesis of each protein. The mechanism by which protein synthesis is regulated depends in large measure on interactions bet-ween the cell and its surrounding medium. In this chapter we shall consider the feedback loop which permits the cell to initiate the synthesis of just the enzyme or enzymes it needs to cope with a particular change in the environment. We should emphasize at this point that the number of informational RNA molecules of a given type present in the cell at any one time is a material reflection of the operation of this mechanism. The result will be the rapid synthesis of one or more enzymes for which there is a 449 450 V. RNA Function need and the inhibition or decline in the synthesis of others not as essential for efficient growth.
eBook - PDF- Lizabeth A. Allison(Author)
- 2021(Publication Date)
- Wiley-Blackwell(Publisher)
48 Ch 3 The Versatility of RNA versatility of functional RNA molecules. RNA is involved in a wide range of cellular pro-cesses, including DNA replication, RNA processing, mRNA turnover, protein synthesis, and protein targeting. What makes RNA such a versatile molecule? The bottom line is that RNA has a much greater structural versatility compared with DNA. RNA chains fold into unique three-dimensional structures that act similarly to globular proteins. The folding patterns provide the basis for their chemical reactivity and specific interactions with other molecules, includ-ing proteins, nucleic acids, and small ligands. The known world of RNA is expanding at an astonishing pace, triggered by the discovery of a large and growing family of non-protein-coding RNAs. 3.2 RNA is involved in a wide range of cellular processes To depict a eukaryotic cell with all types of RNA actively carrying out their functions would be overwhelmingly cluttered. Instead, eight of the major types of RNA that play critical roles in mediating the flow of genetic information are shown in Figure 3.1: Ribosomal RNA (rRNA): an essential component of the ribosome , where protein synthesis takes place. Transcription DNA snRNA snoRNA 5S rRNA rRNA processing IncRNA piRNA mRNA splicing miRNA miRNA mRNA degradation or translation repression mRNA mRNA tRNA AAAA Translation Ribosome 5 uni2032 pre-mRNA pre-rRNA Transcriptional regulation Figure 3.1 Relationships among the eight major types of RNA during gene expression. Overview of the role of ribosomal RNA (rRNA), messenger RNA (mRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), microRNA (miRNA), PIWI-interacting RNA (piRNA), and long noncoding RNA (lncRNA) in transcriptional regulation, RNA processing, and protein synthesis. 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.
eBook - PDF- Belal E. Baaquie, Frederick H. Willeboordse(Authors)
- 2009(Publication Date)
- CRC Press(Publisher)
It turns out that this is achieved with the genetic code discussed in Section 18.10 in the context of information pro-cessing where groups of three successive nucleotides encode for a specific amino acid. Contrary to the case of proteins, DNA and RNA consist of very similar build-ing blocks, with almost identical monomers. Both DNA and RNA are built up of nucleotides containing the bases adenine (A), guanine (G) and cytosine (C), while DNA further uses thymine (T) and RNA uracil (U), the unmethylated form of thymine (a methyl group has the formula CH 3 and is named after methane that has the formula CH 4 , see also p. 305 for the structure of the amino bases). Thus both DNA and RNA use four distinct nucleotides. The sugar in the DNA nucleotides lacks an oxygen atom in the five-carbon sugar ribose — which the RNA nucleotides do have — and is, hence, called de-oxyribose. A special property essential for the process of information storage and processing is that these nucleotides can pair up in predetermined and generally fixed ways. The base adenine (A) can pair up with the base thymine (T) or uracil (U) while the base guanine (G) can pair up with cytosine (C). Since the pairs are formed between the bases of these nucleotides, such pairs are generally referred to as base pairs . See Figure 16.3. 16: RNA 343 The bonds between the base pairs are hydrogen bonds and as a consequence quite weak. That means that they can fairly easily be broken, if so required. Let us now have a bit closer look at how RNA assists in the process of obtaining a protein from a sequence of nucleotides in DNA. When a gene encoding a protein needs to be expressed, first the relevant sequence of nucleotides is copied onto a strand of so-called messenger RNA (mRNA) with the help of RNA polymerase such that the mRNA strand is exactly complementary to the DNA being copied.
- David Van Vranken, Gregory A. Weiss(Authors)
- 2018(Publication Date)
- Garland Science(Publisher)
LEARNING OBJECTIVES • Understand the chemical and structural differences between RNA and DNA. • Describe the features of a DNA gene sequence that determine when genes will be expressed and what part of the gene will be transcribed. • Draw a scheme showing the synthesis, processing, and translation of RNA in eukaryotic cells. • Explain how RNA interference can be used to control gene expression in cells. • Describe the features of an mRNA sequence that control ribosomal binding and what part of the mRNA will be translated. • Explain the role of tRNA and elongation factors in translation. • Describe the steps needed to produce a combinatorial library of proteins. ChAptER 4 131 RNA 4 P hoebus Aaron Theodore Levene (Figure 4.1) studied both RNA and DNA, and con- tributed key insights into the structures of both biopolymers. When Levene began his research at the Rockefeller Institute for Medical Research, precipitation techniques had been used to isolate two different types of nucleic acids—one from yeast and the other from calf thymus. In 1909, Levene showed that the carbohydrate in the nucleic acids isolated from yeast was the pentose sugar ribose, correctly identifying the mate- rial from yeast as RNA. Twenty years later, Levene also correctly identified the equiva- lent carbohydrate in material extracted from calf thymus as deoxyribose. Additionally, Levene deduced key structural elements of nucleic acids; for example, he coined the term “nucleoside” to describe a carbohydrate linked through a glycosidic bond to the base of a nucleic acid. With tour de force experimentation, he also discovered that the phosphodiesters link to the 3ʹ and 5ʹ carbons of the nucleic acid carbohydrate. Thus, Levene earned a spot in the pantheon of chemical biology through key insights into the chemical structures of RNA and DNA. When Francis Crick first proposed the central dogma in 1956, RNA was considered a minor league player charged merely with transducing information.
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