Biological Sciences
DNA Structure
The DNA structure refers to the double helix shape formed by two strands of nucleotides, which are composed of a sugar, a phosphate group, and a nitrogenous base. The nitrogenous bases adenine, thymine, cytosine, and guanine form complementary base pairs, with adenine pairing with thymine and cytosine pairing with guanine. This structure allows DNA to store and transmit genetic information.
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11 Key excerpts on "DNA Structure"
eBook - PDFDNA Replication
Current Advances
- Herve Seligmann(Author)
- 2011(Publication Date)
- IntechOpen(Publisher)
There are hairpins from single-strands, structures with overhangs, etc., and a plethora of forms seen in complexes with proteins. We will discuss some of these in greater detail in Section 4 along with their relevant cellular functions, focusing on replication and the associated processes. First, we must delve into the detailed vocabulary used to describe DNA Structure and provide a common language for the remainder of the chapter. 3. A vocabulary lesson for DNA Structure As with any description of a biopolymer, we will start the discussion of DNA Structure at the simplest unit (the nucleotide building block), then develop the concepts of structure with increasing size and complexity. In order to reach this stage of complexity, we must first define terms that will be used in discussing DNA Structure at all levels. 3.1 General principles Almost every student today knows that DNA is composed of four basic building blocks, each defined by the unique chemical structure of the aromatic base, and each base attached to a phosphodeoxyribose backbone. The four common deoxyribonucleotides are categorized as the purine (deoxyadenosine, dA, and deoxyguanosine, dG) or pyrimidine (deoxythymidine, dT, and deoxycytosine, dC) nucleotides. The atoms of sugars are distinguished from those of the bases by a “prime” added to the atom name, so that the sugar carbons are C1’, C2’, C3’, C4’, C5’ (Fig. 2), starting with the carbon at the glycosidic bond that attaches the base to the sugar, and so forth around the ring. The deoxynucleotides of DNA lack a O2’ oxygen, which distinguishes them from ribonucleotides (RNA). For simplicity, we will simply assume the deoxyform and drop the “deoxy” and “d” prefixes from this point on (Hendrickson et al. , 1988). 3.2 What defines a stable DNA Structure? DNA in its functional form is not the isolated nucleotides, but a polymer built from the mononucleotides (G, C, A, T).
eBook - PDF- Lizabeth A. Allison(Author)
- 2021(Publication Date)
- Wiley-Blackwell(Publisher)
19 C H A P T E R T W O Fundamental Molecular Biology, Third Edition. Edited by Lizabeth A. Allison. © 2021 John Wiley & Sons Inc. Published 2021 by John Wiley & Sons Inc. Companion Website: www.wiley.com/go/allison/FMB3 2.1 Introduction The DNA double helix is an icon for modern biology, a form represented from art galleries to corporate logos. In chemical terms, DNA is a polymer of build-ing blocks called nucleotides. Each nucleotide consists of a sugar, a phosphate, and a base – adenine (A), thymine (T), cytosine (C), or guanine (G). How the sugar, phosphate, and base are arranged in a nucleotide and how nucleotides are joined together was known by 1953. What Watson and Crick addressed was the way in which the two strands are arranged in space as a double helix. While the structure of DNA is aesthetically pleasing, it is relatively meaningless without an understanding of how it relates to function. Recall that Watson and Crick’s proposed structure for DNA didn’t create wide excitement until its role in protein synthesis was understood (see Chapter 1). On the flip side, function cannot truly be understood without knowledge of structure. One goal of this chapter is to describe the structure of DNA, while keeping its function within living cells in mind. The Structure of DNA The metaphors for DNA keep multiplying. It is a string of code, a spiral staircase, and, now, something very like origami. Source: From Pennisi, E. (2015). Science , 347(6217), 10. © 2015 AAAS. O U T L I N E ▶ 2.1 Introduction ▶ 2.2 Primary structure: the components of nucleic acids ▶ 2.3 Secondary structure of DNA ▶ 2.4 Unusual DNA secondary structures ▶ 2.5 Tertiary structure of DNA The double helix in art. (Julie Newdoll/www.brushwithscience.com, “Dawn of the Double Helix,” oil and mixed media on canvas, © 2003.)
eBook - PDF- Donald Voet, Judith G. Voet, Charlotte W. Pratt(Authors)
- 2018(Publication Date)
- Wiley(Publisher)
In this chapter, we briefly examine the structures of nucleotides and the nucleic acids DNA and RNA. We also consider how the chemistry of these molecules allows them to carry biological information in the form of a sequence of nucleo- tides. This information is expressed by the transcription of a segment of DNA to yield RNA, which is then translated to form protein. Because a cell’s structure and function ultimately depend on its genetic makeup, we discuss how genomic sequences provide information about evolution, metabolism, and disease. Finally, 1 Nucleotides 2 Introduction to Nucleic Acid Structure A Nucleic Acids Are Polymers of Nucleotides B DNA Forms a Double Helix C RNA Is a Single-Stranded Nucleic Acid 3 Overview of Nucleic Acid Function A DNA Carries Genetic Information B Genes Direct Protein Synthesis 4 Nucleic Acid Sequencing A Restriction Endonucleases Cleave DNA at Specific Sequences B Electrophoresis Separates Nucleic Acids According to Size C Traditional DNA Sequencing Uses the Chain- Terminator Method D Next-Generation Sequencing Technologies Are Massively Parallel E Entire Genomes Have Been Sequenced F Evolution Results from Sequence Mutations 5 Manipulating DNA A Cloned DNA Is an Amplified Copy B DNA Libraries Are Collections of Cloned DNA C DNA Is Amplified by the Polymerase Chain Reaction D Recombinant DNA Technology Has Numerous Practical Applications C H A P T E R T H R E E Overview of DNA Structure, Function, and Engineering Families of genes shared by five different species of grains are depicted by overlapping shapes. By identifying the genes in samples of DNA, researchers can focus on the genetic features that have a common purpose or provide some unique function to an organism. Jizeng Jia et al., Nature, 496, 91–95 (04 April 2013), doi:10.10138/nature/2028 1,031 1,441 2,980 8,443 1,635 278 Brachypodium 26,552 22,405 Rice 39,049 25,489 Sorghum 34,496 26,722 Barley fl-cDNA 23,585 17,345 Ae.
eBook - PDF- Donald Voet, Charlotte W. Pratt, Judith G. Voet(Authors)
- 2014(Publication Date)
- Wiley(Publisher)
Because a cell’s structure and function ultimately depend on its genetic makeup, we discuss how genomic sequences provide information about evo- lution, metabolism, and disease. Finally, we consider some of the techniques used in manipulating DNA in the laboratory. In later chapters, we will exam- ine in greater detail the participation of nucleotides and nucleic acids in meta- bolic processes. Chapter 24 includes additional information about nucleic acid structures, DNA’s interactions with proteins, and DNA packaging in cells, as a prelude to several chapters discussing the roles of nucleic acids in the stor- age and expression of genetic information. 1 Nucleotides K E Y C O N C E P T S • The nitrogenous bases of nucleotides include two types of purines and three types of pyrimidines. • A nucleotide consists of a nitrogenous base, a ribose or deoxyribose sugar, and one or more phosphate groups. • DNA contains adenine, guanine, cytosine, and thymine deoxyribonucleotides, whereas RNA contains adenine, guanine, cytosine, and uracil ribonucleotides. Nucleotides are ubiquitous molecules with considerable structural diversity. There are eight common varieties of nucleotides, each composed of a nitrogenous base linked to a sugar to which at least one phosphate group is also attached. The bases of nucleotides are planar, aromatic, heterocyclic molecules that are struc- tural derivatives of either purine or pyrimidine (although they are not syn- thesized in vivo from either of these organic compounds). The most common purines are adenine (A) and guanine (G), and the major pyrimidines are cytosine (C), uracil (U), and thymine (T). The purines form bonds to a five-carbon sugar (a pentose) via their N9 atoms, whereas pyrimidines do so through their N1 atoms (Table 3-1). In ribonucleotides, the pentose is ribose, while in deoxyribonucleotides (or just deoxynucleotides), the sugar is 2-deoxyribose (i.e., the carbon at position 2¿ lacks a hydroxyl group).
eBook - PDF- Julianne Zedalis, John Eggebrecht(Authors)
- 2018(Publication Date)
- Openstax(Publisher)
Only 32 P entered the bacterial cells, indicating that DNA is the genetic material. Around this same time, Austrian biochemist Erwin Chargaff examined the content of DNA in different species and found that the amounts of adenine, thymine, guanine, and cytosine were not found in equal quantities, and that it varied from species to species, but not between individuals of the same species. He found that the amount of adenine equals the amount of thymine, and the amount of cytosine equals the amount of guanine, or A = T and G = C. This is also known as Chargaff’s rules. This finding proved immensely useful when Watson and Crick were getting ready to propose their DNA double helix model. 14.2 | DNA Structure and Sequencing In this section, you will explore the following questions: • What is the molecular structure of DNA? • What is the Sanger method of DNA sequencing? What is an application of DNA sequencing? • What are the similarities and differences between eukaryotic and prokaryotic DNA? Connection for AP ® Courses The currently accepted model of the structure of DNA was proposed in 1953 by Watson and Crick, who made their model after seeing a photograph of DNA that Franklin had taken using X-ray crystallography. The photo showed the molecule’s double-helix shape and dimensions. The two strands that make up the double helix are complementary and anti-parallel in nature. That is, one strand runs in the 5' to 3' direction, whereas the complementary strand runs in the 3' to 5' direction. (The significance of directionality will be important when we explore how DNA copies itself.) DNA is a polymer of nucleotides that consists of deoxyribose sugar, a phosphate group, and one of four nitrogenous bases—A, T, C, and G—with a purine always pairing with a pyrimidine (as Chargaff found). The genetic “language” of DNA is found in sequences of the nucleotides. During cell division each daughter cell receives a copy of DNA in a process called replication.
eBook - PDF- R.S. Verma(Author)
- 1998(Publication Date)
- Elsevier Science(Publisher)
105 B. DNA Unwinding Elements ...................................... 107 C. Parallel-Stranded DNA ......................................... 108 D. Four-Stranded DNA ........................................... 109 E. Higher Order Pu.Py Structures ................................... 113 INTRODUCTION TO THE STRUCTURE, PROPERTIES, AND REACTIONS OF DNA A. Introduction DNA occupies a critical role in the cell, inasmuch as it is the source of all intrin- sic genetic information. Chemically, DNA is a very stable molecule, a character- istic important for a macromolecule that may have to persist in an intact form for a long period of time before its information is accessed by the cell. Although DNA plays a critical role as an informational storage molecule, it is by no means as unexciting as a computer tape or disk drive. Rather, DNA can adopt a myriad of alternative conformations, including cruciforms, intramolecular triplexes, left handed Z-DNA, and quadruplex DNA, to name a few. Local variations in the shape of the canonical B-form DNA helix are most certainly important in DNA- protein interactions that modulate and control gene expression. Moreover, the ability of DNA to adopt many alternative helical structures, the ability to bend and twist, and the ability to modulate the potential energy of the molecule through variations in DNA supercoiling provide enormous potential for the involvement of DNA: Structure and Function 3 the DNA itself in its own expression and replication. This chapter will focus on alternative structures of DNA and their potential involvement in biology. For more detail on some subjects, see books by S inden 1 and Soyfer and Potaman. 2 B. The Structure of Nucleic Acids 3. Bases Two different heterocyclic aromatic bases with purine heterocycles, adenine and guanine, exist in DNA (Figure 1). Adenine has an amino group (-NH 2) at the C6 position, whereas guanine has an amino group at the C2 position and a carbonyl group at the C6 position.
eBook - PDF- D. Peter Snustad, Michael J. Simmons(Authors)
- 2016(Publication Date)
- Wiley(Publisher)
Each nucleotide is composed of (1) a phosphate group, (2) a five-carbon sugar, or pentose, and (3) a cyclic nitrogen-containing compound called a base (◾ Figure 9.5). In DNA, the sugar is 2-deoxyribose (thus the name DNA is usually double-stranded, with adenine paired with thymine and guanine paired with cytosine. RNA is usually single-stranded and contains uracil in place of thymine. The Structures of DNA and RNA deoxyribonucleic acid); in RNA, the sugar is ribose (thus ribonucleic acid). Four different bases commonly are found in DNA: adenine (A), guanine (G), thymine (T), and cytosine (C). RNA also usually contains adenine, guanine, and cytosine but has a different base, uracil (U), in place of thymine. Adenine and guanine are double-ring bases called purines; cytosine, thymine, and uracil are single-ring bases called pyrimidines. Both DNA and RNA, therefore, contain four different subunits, or nucleotides: two purine nucleotides and two pyrimidine nucleotides (◾ Figure 9.6). In polynucleotides such as DNA and RNA, these subunits are joined together in long chains (◾ Figure 9.7). RNA usually exists as a single-stranded polymer that is composed of a long sequence of nucleotides. DNA has one additional—and very important—level of organization: it is usually a double-stranded molecule. DNA Structure: THE DOUBLE HELIX One of the most exciting breakthroughs in the history of biology occurred in 1953 when James Watson and Francis Crick (◾ Figure 9.8) deduced the correct structure of DNA. Their double-helix model of the DNA molecule immediately suggested an elegant mechanism for the transmission of genetic information (see A Milestone in Genetics: The Double Helix on the Student Companion site). Watson and Crick’s double-helix structure was based on two major kinds of evidence: 1.
eBook - PDFBiology
Concepts and Applications
- Cecie Starr, Christine Evers, Lisa Starr, , Cecie Starr, Christine Evers, Lisa Starr(Authors)
- 2017(Publication Date)
- Cengage Learning EMEA(Publisher)
A P P L I C AT I O N : S C I E N C E & S O C I E T Y Figure 8.15 James Symington and his dog Trakr assisting in the search for victims at Ground Zero, September 2001. A H E R O D O G ’ S G O L D E N C L O N E S 143 C H A P T E R 8 DNA Structure AND FUNCTION Copyright 2018 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. WCN 02-300 Section 8.1 It took many scientists and decades of research using cells and viruses called bacteriophage to determine that deoxyribonu- cleic acid (DNA), not protein, is the hereditary material of life. Section 8.2 Each DNA nucleotide has a five-carbon sugar, three phosphate groups, and one of four nitrogen-containing bases after which the nucleotide is named: adenine, thy- mine, guanine, or cytosine. A DNA molecule consists of two strands of these nucleotides coiled into a double helix. Hydrogen bonding between the internally positioned bases holds the strands together. The bases pair in a consistent way: adenine with thymine (A–T), and guanine with cytosine (G–C). The order of bases along a strand of DNA (the DNA sequence) varies among species and among individuals, and this variation is the basis of life’s diversity. Section 8.3 The DNA of eukaryotes is divided among a characteristic number of chro- mosomes that differ in length and shape. In eukaryotic chromosomes, the DNA wraps around histone proteins to form nucleosomes. When duplicated, a eukaryotic chromosome consists of two sister chromatids attached at a centromere. Diploid (2n) cells have two sets of chromosomes. Chromosome number is the total number of chromosomes in a cell of a given species. A human body cell has twenty-three pairs of chromosomes. Members of a pair of sex chromosomes differ among males and females. Members of a pair of autosomes are the same in males and females. Autosomes of a pair have the same length, shape, and centromere location. A karyotype reveals an individual’s complete set of chromosomes.
eBook - PDFKarp's Cell and Molecular Biology
Concepts and Experiments
- Gerald Karp, Janet Iwasa, Wallace Marshall(Authors)
- 2016(Publication Date)
- Wiley(Publisher)
Proteins that bind to DNA often contain domains that fit into these grooves. In many cases, a protein bound in a groove is able to read the sequence of nucleotides along the DNA without having to separate the strands. 11. The double helix makes one complete turn every 10 residues ( . ) 3 4 nm , or 150 turns per million daltons of molecular mass. 12. Because an A on one strand is always bonded to a T on the other strand, and a G is always bonded to a C, the nucleotide sequences of the two strands are always fixed relative to one another. Because of this relationship, the two chains of the dou- ble helix are said to be complementary to one another. For example, A is complementary to T, 5 3 -AGC- is complemen- tary to 3 5 -TCG- , and one entire chain is complementary to the other. As we shall see, complementarity is of overriding importance in nearly all the activities and mechanisms in which nucleic acids are involved. The Importance of the Watson‐Crick Proposal From the time biologists first considered DNA as the genetic mate- rial, it was expected to fulfill three primary functions (FIGURE 10.12): 1. Storage of genetic information . As genetic material, DNA must contain a stored record of instructions that determine all the inheritable characteristics that an organism exhibits. In molecular terms, DNA must contain the information needed to assemble all of the proteins that are synthesized by an organism (Figure 10.12 a) 2. Replication and inheritance. DNA must contain the informa- tion for synthesis of new DNA strands (replication). DNA repli- cation allows genetic instructions to be transmitted from one cell to its daughter cells and from one individual to its offspring (Figure 10.12 b) 3. Expression of the genetic message . DNA is more than a storage center; it is also a director of cellular activity. Consequently, the information encoded in DNA has to be expressed in some form that can take part in events that are taking place within the cell.
eBook - PDFHuman Heredity
Principles and Issues
- Michael Cummings(Author)
- 2015(Publication Date)
- Cengage Learning EMEA(Publisher)
■ Originally, proteins were regarded as the only molecular component of the cell with the complexity necessary to encode genetic information. This changed in 1944 when Avery and his colleagues demonstrated that DNA is the ge-netic material in bacteria. 8-3 The Chemistry of DNA ■ DNA and RNA are nucleic acids composed of subunits called nucleotides. Each nucleotide has three components: a base, a sugar, and a phosphate group. DNA contains four bases (adenine, guanine, cytosine, and thymine), and RNA contains four bases (adenine, guanine, cytosine, and ura-cil). The sugar in DNA is deoxyribose; RNA contains the sugar ribose. Nucleotides can be linked together to form Summary Pasieka/Science Source Copyright 2016 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it. Questions and Problems | 189 chains called polynucleotides. DNA contains two polynucle-otide chains; RNA contains one chain. 8-4 The Watson–Crick Model of DNA Structure ■ In 1953, Watson and Crick con-structed a model of DNA Structure that incorporated information from the chemical studies of Chargaff and the X-ray diffraction work of Wilkins and Franklin. Watson and Crick proposed that DNA is com-posed of two polynucleotide chains oriented in opposite directions and held together by hydrogen bonds be-tween complementary bases in the opposite strand. The two strands are wound around to form a right-handed helix. 8-5 RNA Is a Single-Stranded Nucleic Acid ■ RNA is another type of nucleic acid. It contains a different sugar than DNA and uses the base uracil in place of thy-mine.
eBook - PDF- Mary Ann Clark, Jung Choi, Matthew Douglas(Authors)
- 2018(Publication Date)
- Openstax(Publisher)
The two strands are anti-parallel in nature; that is, the 3' end of one strand faces the 5' end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside, like the rungs of a ladder. Each base pair is separated from the next base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, 10 base pairs are present per turn of the helix. The diameter of the DNA double-helix is 2 nm, and it is uniform throughout. Only the pairing between a purine and pyrimidine and the antiparallel orientation of the two DNA strands can explain the uniform diameter. The twisting of the two strands around each other results in the formation of uniformly spaced major and minor grooves (Figure 14.7). 384 Chapter 14 | DNA Structure and Function This OpenStax book is available for free at http://cnx.org/content/col24361/1.8 Figure 14.7 DNA has (a) a double helix structure and (b) phosphodiester bonds; the dotted lines between Thymine and Adenine and Guanine and Cytosine represent hydrogen bonds. The (c) major and minor grooves are binding sites for DNA binding proteins during processes such as transcription (the copying of RNA from DNA) and replication. DNA Sequencing Techniques Until the 1990s, the sequencing of DNA (reading the sequence of DNA) was a relatively expensive and long process. Using radiolabeled nucleotides also compounded the problem through safety concerns. With currently available technology and automated machines, the process is cheaper, safer, and can be completed in a matter of hours. Fred Sanger developed the sequencing method used for the human genome sequencing project, which is widely used today (Figure 14.8). Visit this site (http://openstaxcollege.org/l/DNA_sequencing) to watch a video explaining the DNA sequence-reading technique that resulted from Sanger’s work. The sequencing method is known as the dideoxy chain termination method.
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