Nucleic Acid Structure - Chapter 1 PDF

Chapter Topics I DNA as Genetic Material II The Composition and Structure of DNA and RNA III Nucleosides and Nucleotides Chapter1: Nucleic Acid Structure -Dr. KamelAdwan IV DNA double helix V Different DNA Forms...

Chapter Topics I DNA as Genetic Material II The Composition and Structure of DNA and RNA III Nucleosides and Nucleotides Chapter1: Nucleic Acid Structure -Dr. KamelAdwan IV DNA double helix V Different DNA Forms 1 I. DNA as Genetic Material 1. Griffith s Transformation Experiment In 1928, Frederick Griffith, wasworking with Streptococcus pneumoniae (also calledpneumococcus), a bacterium that causes pneumonia. Griffith used two strains of the bacterium:the S strain, which produces smooth, shiny colonies andis virulent (highly infectious); and the Rstrain, which produces rough colonies and is nonvirulent(harmless) (Figure 1.1). Figure 1.1The bacterium Streptococcus pneumoniae. The virulence of the S strain is dueto the presence of a capsule surrounding each cell. The capsule is also the reason for thesmooth, shiny appearance of S colonies. Chapter1: Nucleic Acid Structure -Dr. KamelAdwan Griffith injected mice with different strains of thebacterium and observed their effects on the mice(Figure 1.2). When mice were injected with R bacteria, themice lived. When mice were injected with living Sbacteria, the mice died. However, if the bacteriawere killed by heat before injection, the mice lived. In his key experiment, Griffith injected mice with amixture of living R bacteria and heat-killed S bacteria.The mice died, and living S bacteria were present in the blood. 2  Griffith concluded that someR bacteria hadsomehow been transformed into smooth, virulent S bacteria by uptake the Geneticmaterial that code for the capsule from the dead S bacteria. Griffith calledthis phenomenon the transforming principle. Figure 1.2 Griffith s transformation experiment. 2.Hershey and Chase s Bacteriophage Experiment In 1952, Hershey and Chase did experiments to determine which part of T2 Chapter1: Nucleic Acid Structure -Dr. KamelAdwan bacteriophage protein or DNA enters the bacterial cell. Bacteriophages (also called phages) are viruses that attack bacteria(bacteria eater). T2 reproduces by invading an Escherichia coli (E. coli) cell and using the bacterium s molecular machinery to make more viruses (Figure 1.3). To trace the two components of the virus, Hershey and Chase labeled each with a specific radioactive tracer:35S - labeled proteins and 32P - labeled DNA. 3  Figure 1.3 Diagram of bacteriophage T2 Hershey and Chase allowed bacteriophage containing either 32P or 35S to attach to bacteria. Then Hershey and Chase separated the bacteria from the rest of the material. They found that most of the 35S (and thus the protein) had separated from 32 the bacteria, and that most of the P (and thus the DNA) had stayed with the bacteria. These results suggested that the DNA was transferred to the bacteria, whereas the protein remained outside, and thus that it was DNA responsible for the function and reproduction of phage T2 (Figure 1.4). Chapter1: Nucleic Acid Structure -Dr. KamelAdwan Figure 1.4 The Hershey and Chase experiment. 4 II. The Composition and Structure of DNA and RNA DNA and RNA are linear polymers made of subunits known as nucleotides,and the polymersare known as "polynucleotide" (Figure 1.5). Figure 1.5Structure of a polynucleotide Each nucleotide has three components: a phosphate group, a five-carbon sugar, and a nitrogen- containing base (Figure1.6). Chapter1: Nucleic Acid Structure -Dr. KamelAdwan DNA and RNA Each Have Four Bases Figure 1.6A typical nucleotide. There are two classes of nitrogenous bases: 1. Adenine (A) and guanine (G) are purines, bicyclic structures (two fused rings) 2. Cytosine (C), thymine (T) and uracil (U) are monocyclicpyrimidines. In RNA, the thymine base is replaced by uracil. The chemical structures of the bases are shown in Figure 1.7. 5  Figure 1.7The Bases of the Nucleic Acids Structures of deoxyribose and ribose In DNA, the sugar is always deoxyribose; whereas, in RNA, it is ribose. Both sugars are pentoses, or five-carbon sugars. Deoxyribose has one less oxygen than ribose (Figure1.8). Figure 1.8Structures of deoxyribose and ribose Chapter1: Nucleic Acid Structure -Dr. KamelAdwan III. Nucleosides and Nucleotides The combination of a sugar and a base is called a nucleoside. Additionof a phosphate group (PO4-2) to a nucleoside yields a nucleotide (Figure 1.9a). Thus a nucleotide is a nucleoside plus a phosphate. Examples of a DNA nucleotide (a deoxyribonucleotide) and an RNA nucleotide (a ribonucleotide) are shown in Figure 1.9a. A complete list of the names of the bases, nucleosides, and nucleotides is in Table 1.1. 6  Inthe polynucleotide chain, adjacent nucleotides are joined by a phosphodiester linkage, which consists of a phosphate group that links the sugars of two nucleotides in 5' 3' 5' 3' orientation(Figure 1.9b). Chapter1: Nucleic Acid Structure -Dr. KamelAdwan Figure 1.9(a) Basic structures of DNA and RNA nucleosides and nucleotides. (b) A segment of a polynucleotide chain, in this case a single strand of DNA. 7 Table 1.1 Names of the base, nucleoside, and nucleotide components found in DNA and RNA Base Nucleoside Nucleotides Adenine (A) Deoxyadenosine dAMP dADP dATP Guanine (G) Deoxyguanosine dGMP dGDP dGTP DNA Cytosine (C) Deoxycytidine dCMP dCDP dCTP Thymine (T) Deoxythymidine dTMP dTDP dTTP Adenine (A) Adenosine AMP ADP ATP Guanine (G) Guanosine GMP GDP GTP RNA Cytosine (C) Cytidine CMP CDP CTP Uracil (U) Uridine UMP UDP UTP IV. DNA double helix Watson and Crick s double helix model of DNA based on the X-ray crystallography data has the following main features: 1. The DNA molecule consists of two polynucleotide chains wound around each other in a right-handed in a clockwise (right-handed) fashion. 2. The two chains are antiparallel; that is, the two strands are oriented in opposite directions. This means that the 5'-end of one strand is opposite the 3'-end of the other strand (Fig. 1.10) Chapter1: Nucleic Acid Structure -Dr. KamelAdwan 3. The sugar phosphate backbones are on the outsides of the double helix, with the bases oriented toward the central axis (see Figure 1.10). 4. The bases in each of the two polynucleotide chains are bonded together by hydrogen bonds, which are relatively weak chemical bonds. The specific pairings observed are A bonded with T by two hydrogen bonds; and G bonded with C by three hydrogen bonds (Figure 1.10). 8  The two chains are complementary to each other, so if one chain has the sequence 5'-TATTCCGA-3', then the opposite, antiparallel chain must bear the sequence 3'-ATAAGGCT-5'. 5. Acomplete (360°) turn of the helix takes 3.4 nm;therefore, there are 10 base pairs (bp) per turn. Theexternal diameter of the helix is 2 nm. 6. Between the backbone strands run the major and minor grooves. Chapter1: Nucleic Acid Structure -Dr. KamelAdwan Figure 1.10Molecular structure of DNA. V.Different DNA Forms DNA can exist in several different forms most notably, the A-, B-, and Z- DNA forms (Figure 1.11). 9 1. A-DNA Right-handed, short and broad;with about eleven base pairs per turn (23 Å).It is seen only in conditions of high salt concentrations. 2. B-DNA Right-handed, longer, thinner, with about ten base pairs per turn (34 Å) B-DNA forms under conditions of high humidity and its structure that most closely corresponds to that of DNA in the cell.It is the structure of DNA that Watson and Crick described 3. Z-DNA Left-handed, longest, thinnest, with about twelve base pairs per turn (46 Å). It is called the Z form, because its bases seem to zigzag. It is seen in DNA molecule with alternating G-C sequences 5-Methylcytosine in Z-DNA is related to gene regulation in eukaryotes. Chapter1: Nucleic Acid Structure -Dr. KamelAdwan Figure 1.11Different forms of DNA. 10 This document was created with Win2PDF available at http://www.daneprairie.com. The unregistered version of Win2PDF is for evaluation or non-commercial use only.