DNA and RNA

9 Key excerpts on "DNA and RNA"

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  eBook - ePub

  Molecular Biology

  Structure and Dynamics of Genomes and Proteomes

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

    (Publisher)

  Nucleic Acids

  DOI: 10.1201/9781003132929-4

  Learning objectives

  Information storage and transmission involve two kinds of nucleic acids: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Nucleic acids are polymers built on a repetitive backbone of sugar moieties linked by phosphodiester bonds. In RNA the sugar is ribose; in DNA the sugar is 2′-deoxyribose. Attached to each sugar is a basic unit, either a purine or a pyrimidine. In DNA, the purines are adenine (A) and guanine (G), and the pyrimidines are cytosine (C) and thymine (T); in RNA uracil (U) substitutes for T. The sequence of bases along the polynucleotide chain provides the information for protein structure. Here, we present the Watson and Crick double-helical structure of the DNA, with base pairing of A with T and G with C in the complementary strands. This structure of DNA allows for copying and information transfer from one cell generation to the next.

  We also describe the possible structures of circular DNA molecules, introducing the concepts of supercoiling and linking number, Lk, the total number of times one strand crosses the other. We also introduce the classes of enzymes (topoisomerases) that can change the linking number of DNA molecules in the cell.

  RNA molecules are usually found in vivo as single-stranded molecules that have been copied (transcribed) from one strand of genomic DNA. RNAs are intermediaries in the transfer of genetic information from DNA to proteins. They can also perform many other functions, from regulation of transcription to the enzyme functions of ribozymes.

  4.1 Introduction

  Protein sequences are dictated by nucleic acids

  We have seen that proteins, in their enormous variety, can play a host of roles in the cell, both structural and functional. Each protein accomplishes this by having a unique amino acid sequence, which determines its secondary, tertiary, and quaternary structures. The information that dictates these sequences must somehow be stored in the cell, expressed in proteins, and transmitted through generations of cells and organisms. These vital functions are provided by biopolymers called nucleic acids, or polynucleotides, of which there are two kinds: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA

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  The Handy Biology Answer Book

  • Patricia Barnes-Svarney, Thomas E. Svarney(Authors)
  • 2014(Publication Date)
  • Visible Ink Press

    (Publisher)

  DNA, RNA, CHROMOSOMES, AND GENES

  HISTORY OF NUCLEIC ACIDS

  What are nucleic acids?

  DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids. They are molecules comprised of monomers (structural unit of a polymer) known as nucleotides. These molecules may be relatively small (as in the case of certain kinds of RNA) or quite large (a single DNA strand may have millions of monomer units). Individual nucleotides and their derivatives are important in living organisms. For example, ATP, the molecule that transfers energy in cells, is built from a nucleotide, as are a number of other molecules crucial to metabolism.

  Which came first—DNA or RNA?

  The first molecule had to be able to reproduce itself and carry out tasks similar to those done by proteins. However, proteins, even though bigger and more complicated than DNA, can’t make copies of themselves without the help of DNA and RNA. Therefore, RNA was the likely candidate as the first “information” molecule—mainly because scientists have found that RNA, unlike DNA, can replicate and then self-edit.

  What is the difference between DNA and RNA?

  DNA and RNA are both nucleic acids formed from a repetition of the simple building blocks called nucleotides. A nucleotide consists of a phosphate (PO4 ), sugar, and a nitrogen base, of which five types exist: adenine (A), thymine (T), guanine (G), cytosine (C), and uracil (U). In a DNA molecule, this basic unit is repeated in a double helix structure made from two chains of nucleotides linked between the bases; these links are either between A and T or between G and C. (The structure of the bases does not allow other kinds of links.)

  The structures of DNA (left) and RNA (right) are shown here. The arrangement of adenine, thymine, guanine, cytosine, and uracil nucleotydes are used to send instructions to cells to make proteins.

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  Biophysics for Beginners

  A Journey through the Cell Nucleus

  • Helmut Schiessel(Author)
  • 2013(Publication Date)
  • Jenny Stanford Publishing

    (Publisher)

  Whereas the one-dimensional DNAs are more like academic people living in a world of knowledge, the three-dimensional proteins belong to the working class—being out there in the real world doing real work. Proteins catalyze certain chemical reactions, others form the building blocks of a cellular network of stiff fibers, the cytoskeleton. To move our muscles there are motor proteins, and in plants proteins harvest the energy of the sun light. Also, the two copying machines, the DNA-and the RNA polymerase, are made from proteins. At first sight RNA seems to play only a minor role in this whole game, being merely the messenger between the DNA and the protein factories. But note that single-stranded RNAs occur in various roles: as mRNAs they carry information just like DNA, as tRNA they fold into unique 3-dimensional shapes just like proteins. The translation machine, the ribosome, is made from several proteins and from so-called ribosomal RNAs (rRNAs) that are also uniquely folded. This double role of RNAs suggests that in an early stage of evolution life consisted just of an RNA world with self-replicating RNA molecules. At a later stage it became advantageous to divide information storage and catalytic activities between specialists, the 8 Molecular Biology of the Cell DNAs and the proteins. That way the role of the universal RNA molecules was reduced mainly to act as the interface between the DNA and protein world—even though modern molecular biology now somewhat restores its reputation by discovering various RNAs that also play important roles in modern cells. In this book I shall focus mainly on biophysical problems that are related to the central dogma of molecular biology. The molecules we will deal with are DNA in Chapter 4, RNA and proteins in Chapter 6 and complexes made from DNA and proteins in Chapter 8. I discuss some key processes of the central dogma. Transcription will be described in detail in Section 8.2.

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  Chemistry for Today

  General, Organic, and Biochemistry

  • Spencer Seager, Michael Slabaugh, Maren Hansen, , Spencer Seager, Spencer Seager, Michael Slabaugh, Maren Hansen(Authors)
  • 2021(Publication Date)
  • Cengage Learning EMEA

    (Publisher)

  You learned in Section 21.3 that DNA is the storehouse of genetic information in the cell and that the stored information can be passed on to new cells as DNA undergoes replication. In this section, you will discover how the information stored in DNA is ex- pressed within the cell. This process of expression is so well established that it is called the central dogma of molecular biology. The accepted dogma, or principle, says that genetic information contained in DNA molecules is transferred to RNA molecules. The transferred informa- tion of RNA molecules is then expressed in the structure of synthesized proteins. In other words, the genetic information in DNA (genes) directs the synthesis of certain proteins. In fact, there is a specific DNA gene for every protein in the body. DNA does not direct the synthesis of carbohydrates, lipids, or the other nonprotein substances essential for life. However, these other materials are manufactured by the cell through reactions made possible by enzymes (proteins) produced under the direction of DNA. Thus, in this re- spect, the information stored in DNA really does determine every characteristic of the living organism. Two steps are involved in the flow of genetic information: transcription and transla- tion. In higher organisms (eukaryotes), the DNA containing the stored information is located in the nucleus of the cell, and protein synthesis occurs in the cytoplasm. Thus, the stored information must first be carried out of the nucleus. This is accomplished by transcription, or transferring the necessary information from a DNA molecule onto a molecule of messenger RNA. The appropriately named messenger RNA carries the in- formation (the message) from the nucleus to the site of protein synthesis in the cellular cytoplasm. In the second step, the mRNA serves as a template on which amino acids are assembled in the proper sequence necessary to produce the specified protein.

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  Biomedical Science

  • Ian Lyons(Author)
  • 2011(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  2 Molecular biology and genetics

  The human genome contains all the information necessary to generate all the components of the human body; it is found in almost every cell in the body. This information is encoded through the four different nucleotide types in deoxyribonucleic acid (DNA). DNA contains functional units known as genes, which encode protein or nucleic acid molecules with a specific function.

  The process by which a gene is converted into its product is well established, as are the mechanisms that regulate the expression of a gene. Changes to a gene, or deletions of parts of the genome, can result in disease, through changes to the proteins produced.

  DNA and genes

  The basic unit of genetic information is the gene. Genes are stretches of DNA that encode protein or RNA molecules with a specific function (or group of functions). The DNA in a cell (in almost every case) is the same as the DNA found in the zygote and possesses all the genetic information for creating a complete organism; the ability to reliably copy DNA to ensure accurate transmission of the genome is aided by the structure of DNA and its method of replication.

  Structure of nucleic acids

  DNA and RNA are made up of chains of nucleotides that are linked together to form a long continuous molecule. Each nucleotide base has common elements (Fig. 2.1 ):

  • A phosphate group
  • A deoxyribose (in DNA) or a ribose (in RNA) sugar
  • A base group made up of carbon–nitrogen rings; there are two types of bases used in nucleic acids:
    – purine bases (adenine and guanine) are made up of two carbon–nitrogen rings. The bases differ in the side chains attached to the rings
    – pyrimidine bases (cytosine and thymine) are made up of a single carbon–nitrogen ring; the different pyrimidine bases also have different side chains.

  The bases are the only part of the nucleotides that vary, and this variation stores information in the genetic code.

  The precursors for DNA synthesis are the deoxynucleotide triphosphates

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  Exploring Integrated Science

  • 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.

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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)

  8 The Ribosome and Protein Synthesis

  Paul HuterMichael Graf and Daniel N. Wilson

  University of Hamburg, Institute for Biochemistry and Molecular Biology,, 20146 Hamburg, Germany

  8.1 Central Dogma of Molecular Biology

  Conservation of the genome, its transfer, and faithful implementation of the information stored within are fundamentally important steps in every cell. About 50–60 years ago, the central dogma of molecular biology gained prominence for establishing the sequential occurrence of these vital events and their interconnectedness [1 , 2 ]. The classical view describes a consecutive order of events, in which deoxyribonucleic acid (DNA ) can either replicate itself to maintain the genomic integrity (replication) or transfer its information into ribonucleic acid (RNA ) molecules (transcription), which in turn serve as templates for the synthesis of proteins (translation). Together, replication, transcription, and translation form the three founding pillars of the dogma of molecular biology. This model is valid to this day; however, extensive studies over the past decades have broadened our understanding of the molecular mechanisms behind it. Both replication and transcription require the recruitment of macromolecular machines. While replication of the genome requires the action of DNA polymerases, transcription of information from DNA to RNA is mediated by RNA polymerases. RNA molecules are a heterogeneous population that fulfill various roles in a cell and can be divided into two major classes, namely, noncoding RNA (ncRNA ) and messenger RNA (mRNA ). Recent studies have shown that ncRNAs pursue different functions such as catalysis of chemical reactions (e.g. ribosomal RNA [rRNA ]), serving as adaptor molecules (e.g. transfer RNA [tRNA ]) or structural scaffolds (e.g. rRNA) and regulating gene expression (e.g. micro RNA [miRNA ]) [3 , 4 ]. On the other hand, mRNAs contain the information of genes, which can be decoded and translated into proteins. This process is called translation and is mediated by ribosomes. In contrast to the other two molecular machines, the ribosome consists predominantly of rRNA, and the structural and mechanistic themes of the core components are conserved among the three phylogenetic kingdoms of life. However, there are certain differences between, and as well as within, each kingdom concerning size, regulation, and composition, to name but a few [5 , 6 ]. Here we focus exclusively on the prokaryotic ribosomal machinery of Escherichia coli. Unless mentioned otherwise, all ribosomes within this chapter refer to the E. coli

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  Introduction to General, Organic, and Biochemistry

  • Frederick Bettelheim, William Brown, Mary Campbell, Shawn Farrell(Authors)
  • 2019(Publication Date)
  • Cengage Learning EMEA

    (Publisher)

  24.4 RNA Types We previously noted that there are several types of RNA with more being discovered every year. 1. Messenger RNA (mRNA) mRNA molecules are produced in the pro-cess called transcription , and they carry the genetic information from the DNA in the nucleus directly to the cytoplasm, where most of the protein is synthesized. Messenger RNA consists of a chain of nucleo-tides whose sequence is exactly complementary to that of one of the strands of the DNA. This type of RNA is not long-lived. It is synthesized as needed and then degraded, so its concentration at any given time is rather low. The size of mRNA varies widely, with the average unit containing perhaps 750 nucleotides. Figure 24.7 shows the basic flow of genetic information and the three types of RNA that form the basis of this process. 2. Transfer RNA (tRNA) Containing from 73 to 93 nucleotides per chain, tRNAs are relatively small molecules. There is at least one dif-ferent tRNA molecule for each of the 20 amino acids from which the body makes its proteins. The three-dimensional tRNA molecules are L-shaped, but they are conventionally represented as a cloverleaf in two Transfer RNA (tRNA) The RNA that transports amino acids to the site of protein synthesis in ribosomes match those of the suspect. This result is a negative identification and excluded the suspect from the case. When a positive identification occurs, the probability that a positive match is due to chance is 1 in 100 billion. Thus, while the identity is not absolutely proven, the law of averages says that there are not enough people on the planet for two of them to have the same DNA pattern. DNA fingerprints are now routinely accepted in court cases. Many convictions are based on such evidence, and, just as important, many jailed suspects have been re-leased when DNA fingerprinting proved them innocent. In one bizarre case, a convicted rapist demanded a DNA test.

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  Karp's Cell and Molecular Biology

  • Gerald Karp, Janet Iwasa, Wallace Marshall(Authors)
  • 2021(Publication Date)
  • Wiley

    (Publisher)

  The use of a messenger RNA also allows a cell to greatly amplify its synthetic output. One DNA molecule can serve as the tem- plate in the formation of many mRNA molecules, each of which can be used in the formation of a large number of polypeptide chains. The concept of a DNA-based gene encoding an RNA- based message that is then translated into a protein is known as the central dogma. Proteins are synthesized in the cytoplasm by a complex process called translation. Translation requires the participa- tion of dozens of different components, including ribosomes. Ribosomes are complex, cytoplasmic “machines” that can be programmed, like a computer, to translate the information encoded by any mRNA. Ribosomes contain both protein and RNA. The RNAs of a ribosome are called ribosomal RNAs (or rRNAs), and like mRNAs, each is transcribed from one of the DNA strands of a gene. Rather than functioning in an informa- tional capacity, rRNAs provide structural support to build the ribosome and help catalyze the chemical reaction in which amino acids are covalently linked to one another. Transfer RNAs (or tRNAs) constitute a third major class of RNA required during protein synthesis. Transfer RNAs are required to trans- late the information in the mRNA nucleotide code into the amino acid “alphabet” of a polypeptide. Both rRNAs and tRNAs owe their activity to their complex secondary and tertiary structures. Unlike DNA, which has a similar double-stranded, helical structure regardless of the source, many RNAs fold into a complex three-dimensional shape, which is markedly different from one type of RNA to another. Thus, like proteins, RNAs carry out a diverse array of functions because of their different shapes. As with proteins, the folding of RNA molecules follows certain rules. Whereas protein folding is driven by the withdrawal of hydrophobic res- idues into the interior, RNA folding is driven by the formation of regions having complementary base pairs (Figure 11.3).

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