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Genetic information is encoded in deoxyribonucleic acid (DNA) molecules. Therefore, DNA is an essential component of living organisms. Genes are segments of DNA that carry genetic information (1).
What Is The Monomer Of The Dna Molecule
Some DNA sequences do not encode genes and have a structural role (eg, in chromosome structure) or are involved in regulating the use of genetic information. For example, repressor sites are DNA sequences that allow repressors to bind, turning off gene expression.
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DNA consists of two long polymers that run in opposite directions and form the regular geometry of a double helix. Monomers of DNA are called nucleosomes. A nucleus has three components: a base, a sugar (deoxyribose), and a phosphate residue. These four bases are adenine (A), cytosine (C), guanine (G), and thymine (T). Sugar and phosphate form the backbone on either side of the double helix. These bases interact through hydrogen bonds.
It is the sequence of these four bases that encodes the genetic information. The interaction of two bases in opposite directions through hydrogen bonds is called base pairing. As shown in Figure 3, adenine pairs with thymine, and guanine forms a base pair with cytosine. These are the most common base pair patterns, but other patterns are possible.
Figure 3 Chemical structure of DNA Two polymers with a phosphate-deoxyribose backbone and four bases: A, C, G, T linked by two (A-T) or three (G-C) hydrogen bonds. Both lines run in opposite directions (image from Wikipedia).
Most of the DNA in cells is in the so-called B-DNA structure. However, it can also accommodate other 3D structures (Figure 4). Z-DNA, found in DNA that binds to certain proteins, is an even rarer structure. In Z-DNA, the bases are chemically modified so that the strands move in the opposite direction to a B-stranded form. Z-DNA formation is an important mechanism for regulating chromatin structure.
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Continue to the last page of this online course to find out what you’ll learn next and let us know what you think about the course. Home » Student Resources » Online Chemistry Courses » CH450 and CH451: Biochemistry – Defining Life at the Molecular Level » Chapter 4: DNA, RNA, and the Human Genome.
Chapter 4: DNA, RNA, and the Human Genome 4.1 The Structure of DNA and RNA 4.2 Chromosomes and Packaging 4.3 The Sequence of the Human Genome 4.4 References
Along with proteins, lipids, and complex carbohydrates (polysaccharides), nucleic acids are one of the four macromolecules essential to all life forms. Nucleic acid consists of two large macromolecules, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), which contain the genetic instructions for the growth, function, development, and reproduction of all known organisms and viruses. A DNA macromolecule (Figure 4.1) consists of two polyvalent chains wrapped around each other to form a double helix. RNA macromolecules usually exist as polycyclic chains and are much smaller than their counterpart DNA molecules.
Figure 4.1: Structure of the DNA double helix. Atoms in the structure are color-coded by element, and the bottom right shows the detailed structure of the two base pairs.
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The basic structure of a nucleic acid monomer is the nucleobase, which consists of a sugar residue + a nitrogenous base attached to the sugar residue at the 1′ position (Figure 4.2). The sugar used for RNA monomers is ribose, but DNA monomers use oxoxide, which has lost the hydroxyl functional group at the 2′ position of the ribose. For DNA molecules, the standard nitrogenous structure includes four nitrogenous bases. These include the purines: adenine (A) and guanine (G), and the amino acids: cytosine (C) and thiamine (T). RNA uses the same nitrogenous bases as DNA, except for thymine. Thymine replaces urayl (U) in the RNA structure.
When one or more phosphate groups are attached to a nucleobase at the 5′ position of the sugar residue, it is called a nucleobase. Nucleosides come in three flavors depending on how many phosphates are present: one phosphate group forms an atomic monophosphate, two phosphates form an atomic diphosphate, and three phosphates form an atomic triphosphate (Figure 4.2).
Figure 4.2 The monomeric structure of nucleic acids. The site where the nitrogenous base attaches to the sugar residue (glycosidic linkage) is shown in red.
Duplexes formed during DNA synthesis have several important physical properties (Figure 4.3). DNA is assembled so that nucleophilic monophosphates are incorporated into the growing DNA chain. Unlike the protein α-helix, where the R groups of the amino acids are located outside the helix, in the DNA double helix, the nitrogenous bases are inside and facing each other. The backbone of DNA is made up of repeating sugar phosphate residues. If a pyramid on one strand is always paired with a purine on the other side, it fits the double helix model. According to Chargaff’s rule, these two groups combine A with T and G with C. Two H bonds are formed between A and T, and three are formed between G and C. This third H bond in the G:C base pair is between the extracellular amino group of G and the C2 keto group of C.
Lesson Video: Nucleic Acids
Additionally, the orientation of the sugar molecules within the fiber determines the orientation of the fiber. The phosphate group that forms part of the basic monomer is always attached to the 5′ position of the oxy-oxy sugar residue. The free end that can accept the new nucleoside is the 3′ hydroxyl position of the deoxyribose sugar. Thus, DNA is directional and is always synthesized in the 5′ to 3′ direction. Interestingly, the two sides of the DNA double helix lie in opposite directions or tails.
Figure 4.3 Structure of DNA: The lower diagram shows the arrangement of nucleobase monophosphates within the structure of a nucleic acid. At the top right, the four nucleobases form two base pairs: thymine and adenine (bonded by double hydrogen bonds) and guanine and cytosine (bonded by triple hydrogen bonds). Mononuclear monomers are linked by sugar and phosphate molecules to form the two “backbones” (double helices) of nucleic acid shown on the left.
The nucleophile required as a monomer for the synthesis of DNA and RNA is the highly energetic nuclear triphosphate. During the addition of nucleobases to the polymer structure, two phosphate groups (Pi-Pi, called pyrophosphate) from each triphosphate are separated from the incoming nucleobase and further hydrolyzed during the reaction, forming the nucleic acid monophosphate incorporated into the growing RNA or DNA chayurein4 (DNA4). Addition of triphosphate to the incoming nucleoli is accomplished by attack of the 3′-OH of the growing DNA polymerase. Thus, DNA synthesis is directional and occurs only at the 3′ end of the molecule.
Further hydrolysis of pyrophosphate (Pi-Pi) releases large amounts of energy, ensuring a negative ΔG for the overall reaction. Hydrolysis of Pi-Pi -> 2Pi ΔG = -7 kcal/mol is important in providing an overall negative ΔG (-6.5 kcal/mol) for the DNA synthesis reaction. Hydrolysis of the pyrophosphate also ensures that the reverse reaction, pyrophosphorylation, of newly synthesized nucleotides in the growing DNA chain does not occur.
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This reaction is mediated by a family of enzymes in DNA called DNA polymerases. Similarly, RNA polymerase is required for RNA synthesis. A more detailed description of the mechanism of the polymerase reaction is included in Chapters X and Y, DNA Replication and Repair, and DNA Replication.
Figure 4.4 Nucleic acid conjugation: During nucleic acid conjugation, the 3′ OH of the growing strand attacks the subsequent NTP-conjugated (blue) α-phosphate, forming a phosphoester linkage and release of pyrophosphate (PPi). DNA polymerase further mediates the hydrolysis of the pyrophosphate to prevent the reverse reaction from occurring and releases enough energy to drive the reaction. This diagram shows the structure of DNA.
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It has been established that the structure of DNA is a double helix.
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