5.2.1.2. Secondary structure of DNA

Secondary structure of DNA

The secondary structure of DNA is the arrangement in space of two nucleotide chains or strands in a double helix, with the nitrogenous bases facing each other and linked by hydrogen bonds. This structure was deduced from the following experimental data:

It was observed that the density and viscosity of the DNA in aqueous dispersion were higher than expected due to its chemical composition and molecular weight, so it was assumed that there must be hydrogen bonds between the groups -NH ₂, -CO-, and = NH.

Chargaff found that all DNAs had the same number of adenine (A) and thymine (T) molecules, and as many cytosine (C) as guanine (G).

n° adenine molecules / n° thymine molecules = 1
n° cytosine molecules / n° guanine molecules = 1

From this it was deduced that hydrogen bonds were formed between A and T and between C and G.

With X-rays it was discovered that DNA has a structure of 20 Å (0.2 nm) in diameter , in which certain units were repeated every 3.4 Å (0.34 nm), and that there was another greater repetition every 34 Å (3.4 nm).

1 nm (nanometer) = 10 Å (angstrom) = 1 × 10^-9 meters = 1 × 10^-6 millimeters

With all these data, J. Watson and F. Crick devised, in 1953, the model of the double helix of DNA, which says that DNA is made up of two antiparallel chains of polynucleotides, with the 5 '→3' bonds oriented in different sense, complementary and wound one on top of the other in a double helix or plectonemic form (for the two chains to separate, they must be unwound).

The fact that they are complementary chains implies that if there is adenine in a chain, in its complement, there will be the nitrogenous base thymine. And if there is guanine in one, cytosine in the other.

As in proteins, in the secondary structure of DNA, the hydrophobic groups -CH ₃ and -CH= of the nitrogenous bases are oriented towards the interior of the molecule, establishing hydrophobic interactions between lipophilic groups, which collaborate with hydrogen bonds in give stability to the macromolecule. The pentoses and the phosphate groups are on the outside.

Estructura secundaria del ADN

By Deneapol [Public domain], via Wikimedia Commons

Complementarity between the bases

The two antiparallel chains that make up the DNA double helix are held together by hydrogen bonds between the complementary nitrogenous bases.

Adenine will always appear united with thymine, and cytosine with guanine, by means of hydrogen bonds between their polar groups. Thus, between adenine and thymine, two hydrogen bonds are established , and between guanine and cytosine, three.

A=T y G≡C

Between A and T, two hydrogen bonds are established.

La unión entre bases nitrogenadas timina y adenina se prodecue mediante dos puentes de hidrógeno

By Yikrazuul (Own work) [Public domain], via Wikimedia Commons

Between C and G, three hydrogen bonds are established.

La unión entre las bases nitrogenadas guanina y citosina se produce mediante tres puentes de hidrógeno

By Yikrazuul (Own work) [Public domain], via Wikimedia Commons

They can never join two bases that are not complementary, since the structure and size of the puric and pyrimidine bases prevents the creation of hydrogen bonds.

In summary, the bonds that contribute to the formation of the double helix are:

Link phosphodiester, at the junction of two nucleotides.
Link N-glycosidic, at the junction of the deoxyribose and a nitrogenous base.
Link hydrogen bridge at the junction of nucleobases (A=T and G≡C).

Alternative structures to the double helix (form B)

Although the double helix described by Watson and Crick, the so-called B-shape, has been considered the only possible spatial conformation, other possible shapes are currently known.

Form B is the one adopted by DNA in solution and in which it interacts with nuclear proteins.

Video: The structure of DNA: Watson and Crick.

DNA form A

Form A of DNA is a right-handed double helix, like form B, but the base pairs do not form a plane perpendicular to the axis, but are inclined 20º with respect to the axis of the helix. It is wider and shorter than form B.

Form A has only been observed in the laboratory, formed from Form B when the relative humidity drops to 75%.

By Thorwald at en.wikipedia (Transferred from en.wikipedia) [Public domain], from Wikimedia Commons

Z form of DNA

The Z form of DNA is longer and narrower than the B form. It is left-handed, it rotates counterclockwise. Its shape is due to the presence of numerous alternating guanine and cytosine nucleotides (GCGCGCGC).

Other secondary structures

In addition to the B, A, and Z forms of DNA, there are a few other types:

In prokaryotes, as in mitochondria and chloroplasts, DNA is circular double-stranded.
In some viruses, the DNA chains are single, not double, and can be circular or linear.

Fundamental ideas about the secondary structure of DNA

Secondary structure of DNA

It is the arrangement in space of two nucleotide chains or strands in a double helix, with the nitrogenous bases facing each other and joined by hydrogen bonds.
Diameter: 20 Å = 0.2 nm
Nucleotides are linked by phosphodiester bonds between the phosphate group at the 5' carbon of one nucleotide and the hydroxyl group at the 3' carbon of the next.
Nitrogenous bases are joined by hydrogen bonds (bridges), two bonds between A and T, and three bonds between G and C.

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Skip navigation Biology 2nd Baccalaureate Biology 2nd Bac. 1. Bioelements and biomolecules. Water and mineral salts 1.1. Chemical bonds in biology 1.1.1. Intramolecular bonds 1.1.1.1. Covalent bond 1.1.1.2. Ionic bond 1.1.2. Intermolecular bonds 1.1.2.1. Van der Waals forces 1.1.2.2. Hydrogen bonds 1.2. The chemical basis of life: inorganic and organic components 1.2.1. Primary bioelements 1.2.2. Secondary bioelements 1.2.3. Trace elements 1.3. The immediate principles or biomolecules 1.3.1. Water 1.3.1.1. Chemical structure of water 1.3.1.2. Properties and functions of water 1.3.2. Mineral salts 1.3.2.1. Functions of salts in solution 1.3.2.2. Colloidal solutions and dispersions 1.3.2.3. Properties of colloidal dispersions 1.3.2.4. Diffusion, osmosis and dialysis 1.3.2.4.1. Diffusion 1.3.2.4.2. Osmosis 1.3.2.4.3. Dialysis 1.4. Bibliography 2. Glucides 2.1. Glucid concept 2.2. Classification of carbohydrates 2.3. Monosaccharides 2.3.1. Trioses 2.3.1.1. Spatial isomerism or stereoisomerism 2.3.2. Tetroses 2.3.3. Pentoses 2.3.3.1. Monosaccharide cyclization 2.3.4. Hexoses 2.4. The N-glucosidic and O-glucosidic bonds 2.4.1. Substances derived from monosaccharides 2.5. Disaccharides 2.6. Polysaccharides 2.6.1. Homopolysaccharides 2.6.1.1. Reserve homopolysaccharides 2.6.1.2. Structural homopolysaccharides 2.6.2. Heteropolysaccharides 2.6.3. Heterosides 2.7. General functions of glucides 2.8. Bibliography 3. Lipids 3.1. Lipid concept 3.2. Classification of lipids 3.2.1. Fatty acids 3.2.1.1. Saturated and unsaturated fatty acids 3.2.1.2. Chemical properties of fatty acids 3.2.1.3. Physical properties of fatty acids 3.2.1.4. Fatty Acid Functions 3.2.2. Saponifiable lipids or with fatty acids 3.2.2.1. Simple lipids 3.2.2.1.1. Acylglycerides 3.2.2.1.2. Cerides 3.2.2.2. Complex lipids 3.2.2.2.1. Phospholipids 3.2.2.2.2. Glycolipids 3.2.3. Unsaponifiable lipids or without fatty acids 3.3. Lipid functions 3.4. Bibliography 4. Proteins 4.1. Introduction to proteins 4.2. Amino acids 4.2.1. Classification of amino acids 4.2.2. Properties of amino acids 4.3. The peptide bond 4.4. Protein 4.4.1. Protein structure 4.4.1.1. Primary structure of proteins 4.4.1.2. Secondary structure of proteins 4.4.1.3. Tertiary structure of proteins 4.4.1.4. Quaternary structure of proteins 4.4.2. Protein properties 4.4.3. Classification of proteins 4.4.3.1. Holoproteins 4.4.3.2. Heteroproteins 4.4.4. Protein functions 4.5. Enzymes 4.5.1. Structure of enzymes 4.5.2. The active center of enzymes 4.5.3. General Mechanism of Enzyme Catalysis 4.5.4. Regulation of enzyme activity 4.5.5. Allosteric enzymes 4.5.6. Nomenclature and classification of enzymes 4.6. The vitamins 4.6.1. Fat-soluble vitamins 4.6.2. Water soluble vitamins 4.7. Bibliography 5. Nucleotides and nucleic acids 5.1. The chemical composition of nucleic acids 5.1.1. Components of nucleic acids 5.1.2. Concept, types and functions of nucleic acids 5.1.3. Nucleosides 5.1.4. Nucleotides 5.1.4.1. Nucleotide functions 5.1.5. Nucleic acids 5.2. Deoxyribonucleic acid (DNA) 5.2.1. DNA structure 5.2.1.1. Primary structure of DNA 5.2.1.2. Secondary structure of DNA 5.2.1.3. Tertiary structure of DNA 5.2.1.3.1. Tertiary structure of DNA in prokaryotes 5.2.1.3.2. Tertiary structure of DNA in eukaryotes 5.2.1.4. Quaternary structure of DNA 5.2.2. DNA types 5.2.3. Genetic material: chromatin and chromosomes 5.2.3.1. Karyotype and karyogram 5.3. Ribonucleic acid (RNA) 5.3.1. RNA types 5.3.1.1. Transfer RNA 5.3.1.2. Messenger RNA 5.3.1.3. Ribosomal RNA 5.3.1.4. Nucleolar RNA 5.3.1.5. Small nuclear RNA 5.3.2. Functions of ribonucleic acids 5.4. Bibliography 6. Cell morphology 6.1. Cell concept 6.1.1. Cell history 6.1.2. Cell theory 6.2. Levels of cellular organization 6.2.1. General characteristics of cells 6.2.2. Prokaryotic cells 6.2.2.1. Prokaryotic cell morphology 6.2.2.2. Structure of prokaryotes 6.2.2.2.1. Bacterial capsule 6.2.2.2.2. Bacterial wall 6.2.2.2.3. Plasma membrane 6.2.2.2.4. Cytoplasm-Ribosomes-Inclusions 6.2.2.2.5. Bacterial DNA 6.2.2.2.6. Bacterial appendages 6.2.2.3. Bacteria Physiology 6.2.3. Eukaryotic cells 6.2.3.1. Animal and plant cell 6.2.3.1.1. Animal eukaryotic cell 6.2.3.1.2. Plant eukaryotic cell 6.2.3.2. Cell Evolution: Endosymbiont Theory 6.3. Size, shape and quantity 6.4. The plasma membrane 6.4.1. Chemical composition of the membrane 6.4.2. The structure of the membrane. The fluid mosaic model 6.4.3. Functions of the plasma membrane 6.4.4. Transport across the membrane 6.4.4.1. Small molecule transport 6.4.4.2. Macromolecule transport 6.4.5. Plasma membrane differentiations 6.5. The cell wall of plant cells 6.5.1. Chemical composition of the cell wall 6.5.2. Cell wall structure 6.5.3. Cell wall differentiations 6.5.4. Cell wall functions 6.6. Extracellular matrix or glucocalyx 6.7. Cytosol or hyaloplasm 6.8. The cytoskeleton 6.8.1. Microfilaments or actin filaments 6.8.2. Intermediate filaments 6.8.3. Microtubules 6.9. Cell membrane and organelle systems 6.9.1. Membrane systems 6.9.1.1. The endoplasmic reticulum 6.9.1.2. Golgi apparatus 6.9.2. Cell organelles 6.9.2.1. Lysosomes 6.9.2.2. Peroxisomes 6.9.2.3. Vacuoles 6.9.2.4. Mitochondria 6.9.2.4.1. Functions of the mitochondria 6.9.2.5. Plastids 6.9.2.5.1. Chloroplasts 6.9.2.6. Ribosomes 6.9.2.7. Centrosome 6.9.2.8. Cilia and flagella 6.10. Cell motility 6.11. The cell nucleus 6.11.1. Characteristics of the cell nucleus 6.11.2. The interphase nucleus 6.11.3. The mitotic nucleus or nucleus in division 6.12. Bibliography 7. Metabolism 7.1. Metabolism 7.1.1. Energetic Aspects of Cellular Chemical Reactions 7.2. Catabolism 7.2.1. Catabolism and obtaining energy 7.2.2. Carbohydrate catabolism 7.2.2.1. Glycolysis 7.2.2.2. Cellular respiration 7.2.2.2.1. Oxidative decarboxylation 7.2.2.2.2. Krebs cycle 7.2.2.2.3. Electron transport chain 7.2.2.2.4. Energy balance of cellular respiration 7.2.2.3. Fermentations 7.2.2.3.1. Alcoholic or ethyl fermentation 7.2.2.3.2. Lactic fermentation 7.2.2.3.3. Other types of fermentations 7.3. Anabolism 7.3.1. Autotrophic anabolism 7.3.2. Photosynthesis 7.3.2.1. Photochemical or light phase 7.3.2.1.1. Photosystems 7.3.2.1.2. Photophosphorylation 7.3.2.1.2.1. Non cyclic photophosphorylation 7.3.2.1.2.2. Cyclic photophosphorylation 7.3.2.2. Biosynthetic or dark phase 7.3.2.3. Factors influencing photosynthesis 7.3.2.4. Products of photosynthesis 7.3.3. Chemosynthesis 7.4. Bibliography 8. Cell reproduction 8.1. The cell cycle 8.1.1. Interphase 8.1.2. Cellular division 8.2. Cellular division 8.2.1. Mitosis 8.2.1.1. Prophase 8.2.1.2. Metaphase 8.2.1.3. Anaphase 8.2.1.4. Telophase 8.2.1.5. Cytokinesis 8.2.1.6. More on mitosis 8.2.2. Meiosis 8.2.2.1. Meiosis I 8.2.2.2. Meiosis II 8.2.3. Meiosis and sexual reproduction 8.2.4. Meiosis and life cycle 8.2.5. Biological importance of meiosis 8.3. Differences and similarities between mitosis and meiosis 8.4. Bibliography 9. Classical genetics 9.1. Genetics basics 9.2. Mendelian genetics 9.2.1. The method 9.2.2. Mendel's Laws 9.2.2.1. Mendel's first law or principle of uniformity in the first generation 9.2.2.2. Mendel's second law or principle of segregation 9.2.2.2.1. Backcross and test crossover 9.2.2.3. Mendel's third law or principle of independent combination 9.3. Gene interaction 9.3.1. Gene interaction between allelic genes 9.3.2. Gene interaction between non-allelic genes that influence for the same trait 9.4. Chromosomal theory of heredity 9.5. Ligation and recombination 9.6. Complex mendelism 9.6.1. Multiple allelism 9.6.1.1. Lethal genes 9.6.2. Pleiotropy 9.6.3. Expressiveness and genetic penetrance 9.7. Sex-linked inheritance 9.7.1. Y-linked inheritance 9.7.2. X-linked inheritance 9.8. Heredity influenced by sex 9.9. Bibliography 10. Molecular genetics 10.1. DNA as hereditary material 10.2. DNA replication 10.2.1. The need for DNA replication 10.2.2. First hypotheses about DNA duplication 10.2.3. Meselson and Stahl experiment 10.2.4. The sense of growth of the new strands 10.2.5. Mechanism of DNA replication 10.2.5.1. Replication in prokaryotes 10.2.5.2. Replication in eukaryotes 10.2.6. Error correction 10.2.7. Enzymes involved in replication 10.3. Gene concept 10.4. "One gene-one enzyme" theory 10.5. Transcription 10.5.1. Mechanism of transcription 10.5.1.1. Transcription in prokaryotes 10.5.1.2. Eukaryotic transcription 10.6. Translation or protein biosynthesis 10.6.1. The genetic code 10.6.2. Mechanism of translation of RNA to proteins 10.6.2.1. Translation in eukaryotes 10.7. Regulation of gene expression 10.8. Bibliography 11. Genetics and evolution 11.1. Mutations 11.2. Types of mutations 11.2.1. Gene or point mutation 11.2.2. Chromosomal or structural mutation 11.2.3. Mutation at the genomic level 11.3. Causes of mutations 11.4. Evolutionary implications of mutations 11.5. Metabolic implications of mutations 11.6. Bibliography 12. Microbiology and biotechnology 12.1. Microbiology 12.2. Viruses 12.2.1. Viral morphology 12.2.2. Viral physiology 12.2.2.1. Lytic cycle 12.2.2.2. Lysogenic cycle 12.2.2.3. Cycles of viruses of special interest 12.2.2.3.1. Flu virus life cycle 12.2.2.3.2. Life cycle of the AIDS virus 12.3. Other acellular forms 12.3.1. Viroids 12.3.2. Prions 12.4. Biotechnology 12.5. Bibliography 13. Immunology 13.1. Infection concept 13.2. Defense mechanisms against infections 13.2.1. Nonspecific mechanisms 13.2.1.1. Primary barriers: external defenses 13.2.1.2. Secondary barriers: internal defenses 13.2.2. Specific mechanisms 13.3. Immunity and immune system 13.3.1. Components of the immune system 13.3.2. Concept and nature of antigens 13.4. The immune response 13.4.1. Humoral immune response: the antibodies 13.4.1.1. Antibody-producing cells: B lymphocytes 13.4.1.2. Antibodies 13.4.1.2.1. Types of antibodies 13.4.1.2.2. Antigen-antibody reaction 13.4.1.3. Immune memory: primary and secondary responses 13.4.2. Cellular immune response: T lymphocytes 13.5. Types of immunity 13.5.1. Natural immunity 13.5.2. Artificial immunity 13.6. Immune system disorders 13.6.1. Autoimmunity 13.6.2. Hypersensitivity 13.6.3. Immunodeficiency 13.6.4. Transplants and the phenomenon of rejections 13.7. Bibliography « Previous \| Next » 5.2.1.2. Secondary structure of DNA Secondary structure of DNA The secondary structure of DNA is the arrangement in space of two nucleotide chains or strands in a double helix, with the nitrogenous bases facing each other and linked by hydrogen bonds. This structure was deduced from the following experimental data: It was observed that the density and viscosity of the DNA in aqueous dispersion were higher than expected due to its chemical composition and molecular weight, so it was assumed that there must be hydrogen bonds between the groups -NH ₂, -CO-, and = NH. Chargaff found that all DNAs had the same number of adenine (A) and thymine (T) molecules, and as many cytosine (C) as guanine (G). n° adenine molecules / n° thymine molecules = 1 n° cytosine molecules / n° guanine molecules = 1 From this it was deduced that hydrogen bonds were formed between A and T and between C and G. With X-rays it was discovered that DNA has a structure of 20 Å (0.2 nm) in diameter , in which certain units were repeated every 3.4 Å (0.34 nm), and that there was another greater repetition every 34 Å (3.4 nm). 1 nm (nanometer) = 10 Å (angstrom) = 1 × 10^-9 meters = 1 × 10^-6 millimeters With all these data, J. Watson and F. Crick devised, in 1953, the model of the double helix of DNA, which says that DNA is made up of two antiparallel chains of polynucleotides, with the 5 '→3' bonds oriented in different sense, complementary and wound one on top of the other in a double helix or plectonemic form (for the two chains to separate, they must be unwound). The fact that they are complementary chains implies that if there is adenine in a chain, in its complement, there will be the nitrogenous base thymine. And if there is guanine in one, cytosine in the other. As in proteins, in the secondary structure of DNA, the hydrophobic groups -CH ₃ and -CH= of the nitrogenous bases are oriented towards the interior of the molecule, establishing hydrophobic interactions between lipophilic groups, which collaborate with hydrogen bonds in give stability to the macromolecule. The pentoses and the phosphate groups are on the outside. By Deneapol [Public domain], via Wikimedia Commons Complementarity between the bases The two antiparallel chains that make up the DNA double helix are held together by hydrogen bonds between the complementary nitrogenous bases. Adenine will always appear united with thymine, and cytosine with guanine, by means of hydrogen bonds between their polar groups. Thus, between adenine and thymine, two hydrogen bonds are established , and between guanine and cytosine, three. A=T y G≡C Between A and T, two hydrogen bonds are established. By Yikrazuul (Own work) [Public domain], via Wikimedia Commons Between C and G, three hydrogen bonds are established. By Yikrazuul (Own work) [Public domain], via Wikimedia Commons They can never join two bases that are not complementary, since the structure and size of the puric and pyrimidine bases prevents the creation of hydrogen bonds. In summary, the bonds that contribute to the formation of the double helix are: *Link phosphodiester,* at the junction of two nucleotides. *Link N-glycosidic,* at the junction of the deoxyribose and a nitrogenous base. Link hydrogen bridge at the junction of nucleobases (A=T and G≡C). Alternative structures to the double helix (form B) Although the double helix described by Watson and Crick, the so-called *B-shape, has been considered the only possible spatial conformation, other possible shapes are currently known. Form B is the one adopted by DNA in solution and in which it interacts with nuclear proteins. Video: The structure of DNA: Watson and Crick. DNA form A Form A of DNA is a right-handed double helix, like form B, but the base pairs do not form a plane perpendicular to the axis, but are inclined 20º with respect to the axis of the helix. It is wider and shorter than form B. Form A has only been observed in the laboratory, formed from Form B when the relative humidity drops to 75%. By Thorwald at en.wikipedia (Transferred from en.wikipedia) [Public domain], from Wikimedia Commons* Z form of DNA The Z form of DNA is longer and narrower than the B form. It is left-handed, it rotates counterclockwise. Its shape is due to the presence of numerous alternating guanine and cytosine nucleotides (GCGCGCGC). Other secondary structures In addition to the B, A, and Z forms of DNA, there are a few other types: In prokaryotes, as in mitochondria and chloroplasts, DNA is circular double-stranded. In some viruses, the DNA chains are single, not double, and can be circular or linear. Fundamental ideas about the secondary structure of DNA Secondary structure of DNA It is the arrangement in space of two nucleotide chains or strands in a double helix, with the nitrogenous bases facing each other and joined by hydrogen bonds. Diameter: 20 Å = 0.2 nm Nucleotides are linked by phosphodiester bonds between the phosphate group at the 5' carbon of one nucleotide and the hydroxyl group at the 3' carbon of the next. Nitrogenous bases are joined by hydrogen bonds (bridges), two bonds between A and T, and three bonds between G and C. Licensed under the Creative Commons Attribution Share Alike License 4.0 « Previous \| Next » These pages are semi-automatically translated from the web Biology 2nd Baccalaureate. Biología de 2º de Bachillerato (biologia-geologia.com). You can make any suggestion, question, comment, ..., in our forum 2º Bachillerato Biología - Foro de biologia-geologia.com
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