Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information Genetics (from Ancient Greek grc-Latn genetikos, “genitive” and that from grc-Latn genesis, “origin” a discipline of Biology, is Developmental Biology is the official journal of the Society for Developmental Biology. Life is a state that distinguishes Organisms from non-living objects such as non-life and dead organisms being manifested by growth through Metabolism A virus (from the Latin virus meaning Toxin or Poison) is a sub-microscopic infectious agent that is unable The main role of DNA molecules is the long-term storage of information. In Chemistry, a molecule is defined as a sufficiently stable electrically neutral group of at least two Atoms in a definite arrangement held together by Information as a concept has a diversity of meanings from everyday usage to technical settings DNA is often compared to a set of blueprints or a recipe, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. A blueprint is a type of paper-based reproduction usually of a Technical drawing, documenting an Architecture or an Engineering design The cell is the structural and functional unit of all known living Organisms It is the smallest unit of an organism that is classified as living and is often called Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. History See also History of genetics The existence of genes was first suggested by Gregor Mendel (1822-1884 who in the 1860s studied inheritance
Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds. A polymer is a large Molecule ( Macromolecule) composed of repeating Structural units typically connected by Covalent Chemical bonds Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group Esters are a class of Chemical compounds and Functional groups Esters consist of an inorganic or organic Acid in which at least Attached to each sugar is one of four types of molecules called bases. Structure The "skeleton" of adenine It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription. Transcription is the synthesis of RNA under the direction of DNA
Within cells, DNA is organized into structures called chromosomes. A chromosome is an organized structure of DNA and Protein that is found in cells. These chromosomes are duplicated before cells divide, in a process called DNA replication. Cell division is a process by which a cell, called the parent cell divides into two or more cells called daughter cells. DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules Eukaryotic organisms (animals, plants, and fungi) store their DNA inside the cell nucleus, while in prokaryotes (bacteria and archae) it is found in the cell's cytoplasm. Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex Plants are living Organisms belonging to the kingdom Plantae. A fungus (ˈfʌŋgəs is a eukaryotic Organism that is a member of the kingdom Fungi (ˈfʌndʒaɪ In Cell biology, the nucleus (pl nuclei; from Latin la ''nucleus'' or la ''nuculeus'' "little nut" or kernel is a membrane-enclosed The prokaryotes (proʊˈkærioʊts singular prokaryote /proʊˈkæriət/ are a group of Organisms that lack a Cell nucleus (= karyon or any other The Bacteria ( singular: bacterium) are a large group of unicellular Microorganisms Typically a few Micrometres in length bacteria have The cytoplasm is the contents of a cell that is enclosed within the Plasma membrane. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. Chromatin is the complex basis of DNA and protein that makes up Chromosomes It is found inside the nuclei of eukaryotic cells, and within the In Biology, histones are the chief Protein components of Chromatin. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
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Physical and chemical properties
DNA is a long polymer made from repeating units called nucleotides. A polymer is a large Molecule ( Macromolecule) composed of repeating Structural units typically connected by Covalent Chemical bonds Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group [1][2] The DNA chain is 22 to 26 Ångströms wide (2. An ångström or angstrom (symbol Å) (ˈɔːŋstrəm Swedish: ˈɔ̀ŋstrœm is an internationally recognized non- SI unit of length equal 2 to 2. 6 nanometres), and one nucleotide unit is 3. A nanometre ( American spelling: nanometer, symbol nm) ( Greek: νάνος nanos dwarf; μετρώ metrό count) is a 3 Å (0. 33 nm) long. [3] Although each individual repeating unit is very small, DNA polymers can be enormous molecules containing millions of nucleotides. For instance, the largest human chromosome, chromosome number 1, is approximately 220 million base pairs long. In Molecular biology, two Nucleotides on opposite complementary DNA or RNA strands that are connected via Hydrogen bonds are called [4]
In living organisms, DNA does not usually exist as a single molecule, but instead as a tightly-associated pair of molecules. [5][6] These two long strands entwine like vines, in the shape of a double helix. A helix (pl helixes or helices) from the Greek word έλιξ, is a special kind of Space curve, i The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix. In general, a base linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. See also Adenosine triphosphate (ATP Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group If multiple nucleotides are linked together, as in DNA, this polymer is called a polynucleotide. A polynucleotide molecule is an organic Polymer molecule composed of Nucleotide Monomers covalently bonded in a chain [7]
The backbone of the DNA strand is made from alternating phosphate and sugar residues. A phosphate, an Inorganic chemical, is a salt of Phosphoric acid. Carbohydrates (from ' Hydrates of Carbon ' or saccharides ( Greek σάκχαρον meaning " Sugar " are the most [8] The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. A pentose is a Monosaccharide with five Carbon Atoms They either have an Aldehyde Functional group in position 1 ( aldopentoses Carbon (kɑɹbən is a Chemical element with the symbol C and its Atomic number is 6 The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. A phosphodiester bond is a group of strong covalent bonds between the phosphorus atom in a Phosphate group and two other Molecules over two History See also Atomic theory, Atomism The concept that matter is composed of discrete units and cannot be divided into arbitrarily tiny These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand. This arrangement of DNA strands is called antiparallel. The asymmetric ends of DNA strands are referred to as the 5′ (five prime) and 3′ (three prime) ends, with the 5' end being that with a terminal phosphate group and the 3' end that with a terminal hydroxyl group. Directionality, in Molecular biology, refers to the end-to-end chemical orientation of a single strand of Nucleic acid. Directionality, in Molecular biology, refers to the end-to-end chemical orientation of a single strand of Nucleic acid. One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar ribose in RNA. Ribose (ɹˈaɪbəʊs ɹˈaɪbəɹʊs primarily seen as D-ribose, is an Aldopentose — a Monosaccharide containing five Carbon [6]
The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands. A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). Adenine is a Purine with a variety of roles in Biochemistry including Cellular respiration, in the form of both the energy-rich Adenosine Cytosine is one of the five main bases found in DNA and RNA. It is a Pyrimidine derivative with a Heterocyclic Aromatic ring Guanine is one of the five main Nucleobases found in the Nucleic acids DNA and RNA, the others being Adenine, Cytosine, Thymine is one of the four bases in the Nucleic acid of DNA that make up the letters ATGC These four bases are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.
These bases are classified into two types; adenine and guanine are fused five- and six-membered heterocyclic compounds called purines, while cytosine and thymine are six-membered rings called pyrimidines. Purine ( 1) is a heterocyclic Aromatic Organic compound, consisting of a Pyrimidine ring fused to an Imidazole ring Pyrimidine is a Heterocyclic Aromatic Organic compound similar to Benzene and Pyridine, containing two Nitrogen Atoms [6] A fifth pyrimidine base, called uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. Uracil is a common and naturally occurring Pyrimidine derivative In Chemistry, a methyl group is a Hydrophobic Alkyl Functional group named after Methane (4 Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine.
Major and minor grooves
The double helix is a right-handed spiral. As the DNA strands wind around each other, they leave gaps between each set of phosphate backbones, revealing the sides of the bases inside (see animation). There are two of these grooves twisting around the surface of the double helix: one groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide. [10] The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove. In the field of Molecular biology, a transcription factor (sometimes called a sequence-specific DNA binding factor is a Protein that binds to specific sequences [11]
Base pairing
- Further information: Base pair
Each type of base on one strand forms a bond with just one type of base on the other strand. In Molecular biology, two Nucleotides on opposite complementary DNA or RNA strands that are connected via Hydrogen bonds are called This is called complementary base pairing. In Molecular biology, two Nucleotides on opposite complementary DNA or RNA strands that are connected via Hydrogen bonds are called Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G. A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen This arrangement of two nucleotides binding together across the double helix is called a base pair. The double helix is also stabilized by the hydrophobic effect and pi stacking, which are not influenced by the sequence of the DNA. The hydrophobic effect is the property that non-polar molecules tend to form intermolecular aggregates in an aqueous medium and analogous intramolecular interactions Stacking in Supramolecular chemistry refers to a stacked arrangement of Aromatic Molecules which interact through aromatic interactions [12] As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature. Temperature is a physical property of a system that underlies the common notions of hot and cold something that is hotter generally has the greater temperature [13] As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms. [1]
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The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). The GC base pair is therefore stronger than the AT base pair. As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands. [14] In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart. The Pribnow box (also known as the Pribnow-Schaller box) is the sequence TATAAT of six Nucleotides ( Thymine - Adenine - Thymine In Biology, a promoter is a region of DNA that facilitates the transcription of a particular Gene. [15] In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). DNA denaturation, also called DNA melting, is the process by which double-stranded Deoxyribonucleic acid unwinds and separates into single-stranded strands through When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules have no single common shape, but some conformations are more stable than others. [16]
Sense and antisense
- Further information: Sense (molecular biology)
A DNA sequence is called "sense" if its sequence is the same as that of a messenger RNA copy that is translated into protein. Sense, when applied in a Molecular biology context is a general concept used to compare the polarity of Nucleic acid molecules such as DNA or RNA Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product [17] The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA (i. e. both strands contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the functions of these RNAs are not entirely clear. [18] One proposal is that antisense RNAs are involved in regulating gene expression through RNA-RNA base pairing. Gene expression is the process by which inheritable information from a Gene, such as the DNA sequence, is made into a functional Gene product, such [19]
A few DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, blur the distinction between sense and antisense strands by having overlapping genes. A plasmid is an extra-chromosomal DNA molecule separate from the chromosomal DNA which is capable of replicating independently of the chromosomal DNA A virus (from the Latin virus meaning Toxin or Poison) is a sub-microscopic infectious agent that is unable [20] In these cases, some DNA sequences do double duty, encoding one protein when read along one strand, and a second protein when read in the opposite direction along the other strand. In bacteria, this overlap may be involved in the regulation of gene transcription,[21] while in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome. The Bacteria ( singular: bacterium) are a large group of unicellular Microorganisms Typically a few Micrometres in length bacteria have [22]
Supercoiling
- Further information: DNA supercoil
DNA can be twisted like a rope in a process called DNA supercoiling. In a "relaxed" double-helical segment of DNA, the two strands twist around the helical axis once every 10 In a "relaxed" double-helical segment of DNA, the two strands twist around the helical axis once every 10 With DNA in its "relaxed" state, a strand usually circles the axis of the double helix once every 10. 4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound. [23] If the DNA is twisted in the direction of the helix, this is positive supercoiling, and the bases are held more tightly together. If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily. In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins Topoisomerases (type I, type II) are Isomerase Enzymes that act on the topology of DNA. [24] These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication. Transcription is the synthesis of RNA under the direction of DNA DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules [25]
Alternative double-helical structures
- Further information: Mechanical properties of DNA
DNA exists in many possible conformations. The mechanical properties of DNA, which are directly related to its structure are a significant problem for cells. In Chemistry, conformational isomerism is a form of Stereoisomerism in which Molecules with the same Structural formula (same connectivity [8] However, only A-DNA, B-DNA, and Z-DNA have been observed in organisms. A-DNA is one of the many possible double helical structures of DNA. Z-DNA is one of the many possible double helical structures of DNA. Which conformation DNA adopts depends on the sequence of the DNA, the amount and direction of supercoiling, chemical modifications of the bases and also solution conditions, such as the concentration of metal ions and polyamines. The M acro E xpansion T emplate A ttribute L anguage complements TAL, providing macros which allow the reuse of code across An ion is an Atom or Molecule which has lost or gained one or more Valence electrons giving it a positive or negative electrical charge The polyamines are organic compounds having two or more primary Amino groups - such as Putrescine, Cadaverine, Spermidine, and Spermine [26] Of these three conformations, the "B" form described above is most common under the conditions found in cells. [27] The two alternative double-helical forms of DNA differ in their geometry and dimensions.
The A form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes. [28][29] Segments of DNA where the bases have been chemically-modified by methylation may undergo a larger change in conformation and adopt the Z form. Methylation is a term used in the chemical sciences to denote the attachment or substitution of a methyl group on various substrates. Z-DNA is one of the many possible double helical structures of DNA. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form. [30] These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription. [31]
Quadruplex structures
- Further information: G-quadruplex
At the ends of the linear chromosomes are specialized regions of DNA called telomeres. Nucleic acid sequences which are rich in Guanine are capable of forming four-stranded structures called G-quadruplexes (Also known as G-tetrads or G4-DNA A telomere is a region of repetitive DNA at the end of Chromosomes which protects the end of the chromosome from destruction The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes. Telomerase is an Enzyme that adds specific DNA sequence repeats ("TTAGGG" in all vertebrates to the 3' ("three prime" end of DNA strands in the [33] These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected. DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its Genome. [34] In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence. [35]
These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure. Nucleic acid sequences which are rich in Guanine are capable of forming four-stranded structures called G-quadruplexes (Also known as G-tetrads or G4-DNA [36] These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit. Chelation is the binding or complexation of a bi- or multidentate Ligand. [37] Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.
In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins. [38] At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop. A triple-stranded DNA is a structure of DNA in which three oligonucleotides wind around each other and form a triple helix In Molecular biology, a displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch [36]
Chemical modifications
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| cytosine | 5-methylcytosine | thymine |
Base modifications
- Further information: DNA methylation
The expression of genes is influenced by the chromatin structure of a chromosome and regions of that have low or no gene expression usually contain high levels of methylation of cytosine bases. DNA methylation is a type of chemical modification of DNA that can be inherited and subsequently removed without changing the original DNA sequence Chromatin is the complex basis of DNA and protein that makes up Chromosomes It is found inside the nuclei of eukaryotic cells, and within the Methylation is a term used in the chemical sciences to denote the attachment or substitution of a methyl group on various substrates. Cytosine is one of the five main bases found in DNA and RNA. It is a Pyrimidine derivative with a Heterocyclic Aromatic ring For example, cytosine methylation, producing 5-methylcytosine, is important for X-chromosome inactivation. 5-Methylcytosine is a methylated form of Cytosine in which a Methyl group is attached to carbon 5 altering its structure without altering its base-pairing X-inactivation (also called lyonization) is a process by which one of the two copies of the X chromosome present in Female Mammals is inactivated [39] The average level of methylation varies between organisms, with Caenorhabditis elegans lacking cytosine methylation, while vertebrates show higher levels, with up to 1% of their DNA containing 5-methylcytosine. Caenorhabditis elegans (ˌsiːnoʊræbˈdaɪtɪs ˈɛlɪgænz is a free-living Nematode (roundworm about 1 mm in length which Vertebrates are members of the Subphylum Vertebrata, Chordates with backbones or spinal columns The grouping sometimes includes [40] Despite the biological role of 5-methylcytosine it can deaminate to leave a thymine base, methylated cytosines are therefore particularly prone to mutations. Deamination is the removal of an Amine group from a Molecule. In biology mutations are changes to the Nucleotide sequence of the Genetic material of an organism [41] Other base modifications include adenine methylation in bacteria and the glycosylation of uracil to produce the "J-base" in kinetoplastids. Glycosylation is the enzymatic process that links Saccharides to produce glycans, either free or attached to Proteins and Lipids This enzymatic The kinetoplastids are a group of Flagellate Protozoa, including a number of Parasites responsible for serious diseases in humans and other animals as well [42][43]
DNA damage
- Further information: Mutation
DNA can be damaged by many different sorts of mutagens, which are agents that change the DNA sequence. In biology mutations are changes to the Nucleotide sequence of the Genetic material of an organism Benzopyrene, C20H12 is a five-ring Polycyclic aromatic hydrocarbon that is Mutagenic and highly Carcinogenic It is a crystalline Tobacco Smoking is the inhalation of smoke from burned dried or cured leaves of the Tobacco plant most often in the form of a Cigarette. In Biology, a mutagen ( Latin, literally origin of change) is a physical or chemical agent that changes the genetic information (usually DNA) These agents include oxidizing agents, alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and X-rays. An oxidizing agent or oxidising agent (also called an oxidant, oxidizer or oxidiser) can be defined as either a Chemical compound Alkylation is the transfer of an Alkyl group from one Molecule to another Electromagnetic radiation takes the form of self-propagating Waves in a Vacuum or in Matter. Ultraviolet ( UV) light is Electromagnetic radiation with a Wavelength shorter than that of Visible light, but longer than X-rays X-radiation (composed of X-rays) is a form of Electromagnetic radiation. The type of DNA damage produced depends on the type of mutagen. For example, UV light mostly damages DNA by producing thymine dimers, which are cross-links between adjacent pyrimidine bases in a DNA strand. A thymine dimer is the covalent bonding of two adjacent Thymine residues within a DNA molecule often catalyzed by ultraviolet radiation or chemical mutagenic agents [45] On the other hand, oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage, including base modifications, particularly of guanosine, as well as double-strand breaks. In Chemistry, radicals (often referred to as free radicals) are atoms molecules or ions with Unpaired electrons on an otherwise Open shell Hydrogen peroxide (H2O2 is a very pale blue liquid which appears colorless in a dilute solution slightly more Viscous than water [46] It has been estimated that in each human cell, about 500 bases suffer oxidative damage per day. [47][48] Of these oxidative lesions, the most dangerous are double-strand breaks, as these are difficult to repair and can produce point mutations, insertions and deletions from the DNA sequence, as well as chromosomal translocations. A point mutation, or single base substitution, is a type of Mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic Genetic Insertion is the addition of one or more Nucleotide Base pairs into a genetic sequence In Genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) is a Mutation (a genetic aberration In Genetics, a chromosome translocation is a Chromosome abnormality caused by rearrangement of parts between nonhomologous Chromosomes. [49]
Many mutagens intercalate into the space between two adjacent base pairs. In Chemistry, intercalation is the reversible inclusion of a Molecule (or group between two other molecules (or groups Intercalators are mostly aromatic and planar molecules, and include ethidium, daunomycin, doxorubicin and thalidomide. Ethidium bromide (sometimes abbreviated as "EtBr", the abbreviation also confusingly used for Bromoethane) is an intercalating agent Daunorubicin or daunomycin (daunomycin cerubidine is Chemotherapy of the Anthracycline family that is given as a treatment for some types of Cancer Doxorubicin ( INN,; trade name Adriamycin; also known as hydroxydaunorubicin) is a drug used in cancer Chemotherapy. Thalidomide is a Sedative - Hypnotic, and Multiple myeloma Medication. In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix. These structural changes inhibit both transcription and DNA replication, causing toxicity and mutations. As a result, DNA intercalators are often carcinogens, with benzopyrene diol epoxide, acridines, aflatoxin and ethidium bromide being well-known examples. The term carcinogen refers to any substance Radionuclide or radiation that is an agent directly involved in the promotion of Cancer or in the fatation of its propagation Benzopyrene, C20H12 is a five-ring Polycyclic aromatic hydrocarbon that is Mutagenic and highly Carcinogenic It is a crystalline Acridine, C13H9N is an Organic compound and a nitrogen heterocycle. Aflatoxins are naturally occurring Mycotoxins that are produced by many species of Aspergillus, a Fungus, most notably Aspergillus Ethidium bromide (sometimes abbreviated as "EtBr", the abbreviation also confusingly used for Bromoethane) is an intercalating agent [50][51][52] Nevertheless, due to their properties of inhibiting DNA transcription and replication, they are also used in chemotherapy to inhibit rapidly-growing cancer cells. Chemotherapy, in its most general sense refers to treatment of disease by chemicals that kill cells specifically those of micro-organisms or Cancer. Cancer (medical term Malignant Neoplasm) is a class of Diseases in which a group of cells display uncontrolled [53]
Overview of biological functions
DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. A chromosome is an organized structure of DNA and Protein that is found in cells. The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes. In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby The human genome is the Genome of Homo sapiens, which is stored on 23 chromosome pairs [54] The information carried by DNA is held in the sequence of pieces of DNA called genes. A DNA sequence or genetic sequence is a succession of letters representing the Primary structure of a real or hypothetical DNA Molecule History See also History of genetics The existence of genes was first suggested by Gregor Mendel (1822-1884 who in the 1860s studied inheritance Transmission of genetic information in genes is achieved via complementary base pairing. Genetic transmission is the transfer of genetic information from genes to another generation or from one location in a cell to another For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation which depends on the same interaction between RNA nucleotides. Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) Alternatively, a cell may simply copy its genetic information in a process called DNA replication. The details of these functions are covered in other articles; here we focus on the interactions between DNA and other molecules that mediate the function of the genome.
Genes and genomes
- Further information: Cell nucleus, Chromatin, Chromosome, Gene, Noncoding DNA
Genomic DNA is located in the cell nucleus of eukaryotes, as well as small amounts in mitochondria and chloroplasts. In Cell biology, the nucleus (pl nuclei; from Latin la ''nucleus'' or la ''nuculeus'' "little nut" or kernel is a membrane-enclosed Chromatin is the complex basis of DNA and protein that makes up Chromosomes It is found inside the nuclei of eukaryotic cells, and within the A chromosome is an organized structure of DNA and Protein that is found in cells. History See also History of genetics The existence of genes was first suggested by Gregor Mendel (1822-1884 who in the 1860s studied inheritance In Genetics, non-coding DNA describes DNA which does not contain instructions for making Proteins (or other cell products such as Noncoding In Cell biology, the nucleus (pl nuclei; from Latin la ''nucleus'' or la ''nuculeus'' "little nut" or kernel is a membrane-enclosed In Cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed Organelle found in most eukaryotic cells. Chloroplasts are Organelles found in Plant cells and eukaryotic Algae that conduct Photosynthesis. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid. In Prokaryotes, the nucleoid (meaning nucleus-like) is an irregularly-shaped region within the cell of Prokaryotes where the Genetic material [55] The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. The genotype is the genetic constitution of a cell an organism or an individual (i A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain an open reading frame that can be transcribed, as well as regulatory sequences such as promoters and enhancers, which control the transcription of the open reading frame. An open reading frame ( ORF) is a portion of an organism's Genome which contains a sequence of bases that could potentially encode a Protein A regulatory sequence (also called a regulatory region or a regulatory area) is a segment of DNA where regulatory proteins such as Transcription In Biology, a promoter is a region of DNA that facilitates the transcription of a particular Gene. In Genetics, an enhancer is a short region of DNA that can be bound with Proteins (namely the Trans-acting factors much like a set of Transcription
In many species, only a small fraction of the total sequence of the genome encodes protein. In Biology, a species is one of the basic units of Biological classification and a Taxonomic rank. In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby For example, only about 1. 5% of the human genome consists of protein-coding exons, with over 50% of human DNA consisting of non-coding repetitive sequences. An exon is a Nucleic acid sequence that is represented in the mature form of an RNA molecule after a portions of a precursor RNA Introns have been In the study of DNA sequences one can distinguish two main types of repeated sequence: Tandem repeats Satellite DNA, [56] The reasons for the presence of so much non-coding DNA in eukaryotic genomes and the extraordinary differences in genome size, or C-value, among species represent a long-standing puzzle known as the "C-value enigma. In Genetics, non-coding DNA describes DNA which does not contain instructions for making Proteins (or other cell products such as Noncoding Genome size refers to the total amount of DNA contained within one copy of a Genome. The term C-value refers to the amount of DNA contained within a Haploid nucleus (e The C-value enigma or C-value paradox is a term used to describe the complex puzzle surrounding the extensive variation in nuclear Genome size among Eukaryotic "[57] However, DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression. A non-coding RNA ( ncRNA) is any RNA molecule that is not translated into a Protein. [58]
Some non-coding DNA sequences play structural roles in chromosomes. Telomeres and centromeres typically contain few genes, but are important for the function and stability of chromosomes. A telomere is a region of repetitive DNA at the end of Chromosomes which protects the end of the chromosome from destruction A centromere is a region of DNA typically found near the middle of a Chromosome where two Sister chromatids come in contact [34][60] An abundant form of non-coding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation. Pseudogenes are defunct relatives of known Genes that have lost their Protein -coding ability or are otherwise no longer expressed [61] These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the creation of new genes through the process of gene duplication and divergence. FOSSIL is a standard protocol for allowing serial communication for Telecommunications programs under the DOS Operating system. Gene duplication (or chromosomal duplication) is any duplication of a region of DNA that contains a Gene; it may occur as an error in Homologous Divergent evolution is the accumulation of differences between groups which can lead to the formation of new species usually a result of different groups of the same species adapting to different [62]
Transcription and translation
- Further information: Genetic code, Transcription (genetics), Protein biosynthesis
A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins Transcription is the synthesis of RNA under the direction of DNA Protein biosynthesis (synthesis is the process in which cells build Proteins The term is sometimes used to refer only to protein translation but more A phenotype is any observable characteristic of an Organism, such as its morphology, Development, biochemical or physiological properties Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides (e. g. ACT, CAG, TTT).
In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. RNA polymerase ( RNAP or RNApol) is an Enzyme that produces RNA. This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids. Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at Since there are 4 bases in 3-letter combinations, there are 64 possible codons (43 combinations). These encode the twenty standard amino acids, giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA and TAG codons.
Replication
- Further information: DNA replication
Cell division is essential for an organism to grow, but when a cell divides it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules Cell division is a process by which a cell, called the parent cell divides into two or more cells called daughter cells. The double-stranded structure of DNA provides a simple mechanism for DNA replication. DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins A DNA Polymerase is an Enzyme that assists in DNA replication. This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to copy the antiparallel strands of the double helix. [63] In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.
Interactions with proteins
All the functions of DNA depend on interactions with proteins. These protein interactions can be non-specific, or the protein can bind specifically to a single DNA sequence. Enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.
DNA-binding proteins
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Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called chromatin. Chromatin is the complex basis of DNA and protein that makes up Chromosomes It is found inside the nuclei of eukaryotic cells, and within the In eukaryotes this structure involves DNA binding to a complex of small basic proteins called histones, while in prokaryotes multiple types of proteins are involved. In Biology, histones are the chief Protein components of Chromatin. [64][65] The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. Nucleosomes form the fundamental repeating units of eukaryotic Chromatin, which is used to pack the large eukaryotic genomes into the nucleus while still ensuring These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence. An ionic bond (or electrovalent bond) is a type of Chemical bond that can often form between Metal and Non-metal Ions (or [66] Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation. Methylation is a term used in the chemical sciences to denote the attachment or substitution of a methyl group on various substrates. Phosphorylation is the addition of a Phosphate (PO4 group to a Protein molecule or a small molecule Acetylation (or in IUPAC nomenclature ethanoylation) describes a reaction that introduces an Acetyl Functional group into an Organic compound [67] These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription. In the field of Molecular biology, a transcription factor (sometimes called a sequence-specific DNA binding factor is a Protein that binds to specific sequences [68] Other non-specific DNA-binding proteins found in chromatin include the high-mobility group proteins, which bind preferentially to bent or distorted DNA. [69] These proteins are important in bending arrays of nucleosomes and arranging them into more complex chromatin structures. [70]
A distinct group of DNA-binding proteins are the single-stranded-DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-characterised member of this family and is essential for most processes where the double helix is separated, including DNA replication, recombination and DNA repair. [71] These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem-loops or being degraded by nucleases. Stem-loop intramolecular Base pairing is a pattern that can occur in single-stranded DNA or more commonly in RNA. A nuclease is an Enzyme capable of cleaving the Phosphodiester bonds between the nucleotide subunits of Nucleic acids Older papers may use terms such as
In contrast, other proteins have evolved to specifically bind particular DNA sequences. In Proteins the helix-turn-helix ( HTH) is a major Structural motif capable of binding DNA. The most intensively studied of these are the various classes of transcription factors, which are proteins that regulate transcription. In the field of Molecular biology, a transcription factor (sometimes called a sequence-specific DNA binding factor is a Protein that binds to specific sequences Each one of these proteins bind to one particular set of DNA sequences and thereby activates or inhibits the transcription of genes with these sequences close to their promoters. The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription. [73] Alternatively, transcription factors can bind enzymes that modify the histones at the promoter; this will change the accessibility of the DNA template to the polymerase. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins [74]
As these DNA targets can occur throughout an organism's genome, changes in the activity of one type of transcription factor can affect thousands of genes. [75] Consequently, these proteins are often the targets of the signal transduction processes that mediate responses to environmental changes or cellular differentiation and development. In Biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. Most of these base-interactions are made in the major groove, where the bases are most accessible. [76]
DNA-modifying enzymes
Nucleases and ligases
Nucleases are enzymes that cut DNA strands by catalyzing the hydrolysis of the phosphodiester bonds. A restriction enzyme (or restriction Endonuclease) is an Enzyme that cuts double-stranded DNA at specific recognition Nucleotide Eco RV (pronounced "eco R five" is a type II restriction Endonuclease isolated from certain strains of Escherichia coli. A nuclease is an Enzyme capable of cleaving the Phosphodiester bonds between the nucleotide subunits of Nucleic acids Older papers may use terms such as Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins Hydrolysis is a Chemical reaction during which one or more water molecules are split into hydrogen and hydroxide ions which may go on to participate in further reactions A phosphodiester bond is a group of strong covalent bonds between the phosphorus atom in a Phosphate group and two other Molecules over two Nucleases that hydrolyse nucleotides from the ends of DNA strands are called exonucleases, while endonucleases cut within strands. Exonucleases are enzymes (found as individual enzymes or as parts of larger enzyme complexes that cleave Nucleotides one at a time from an end of a polynucleotide chain Endonucleases are Enzymes that cleave the Phosphodiester bond within a Polynucleotide chain in contrast to Exonucleases which cleave Phosphodiester The most frequently-used nucleases in molecular biology are the restriction endonucleases, which cut DNA at specific sequences. Molecular biology is the study of Biology at a molecular level A restriction enzyme (or restriction Endonuclease) is an Enzyme that cuts double-stranded DNA at specific recognition Nucleotide For instance, the EcoRV enzyme shown to the left recognizes the 6-base sequence 5′-GAT|ATC-3′ and makes a cut at the vertical line. In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system. The Bacteria ( singular: bacterium) are a large group of unicellular Microorganisms Typically a few Micrometres in length bacteria have This article is about a biological infectious particle for other uses see Phage (disambiguation. The restriction modification system ( RM system) is used by Bacteria, and perhaps other prokaryotic organisms to protect themselves from foreign DNA [78] In technology, these sequence-specific nucleases are used in molecular cloning and DNA fingerprinting. Molecular cloning refers to the procedure of isolating a defined DNA sequence and obtaining multiple copies of it In vivo.
Enzymes called DNA ligases can rejoin cut or broken DNA strands. In Molecular biology, DNA ligase is a special type of Ligase ( that can link together two DNA strands that have single-strand breaks (a break in both complementary [79] Ligases are particularly important in lagging strand DNA replication, as they join together the short segments of DNA produced at the replication fork into a complete copy of the DNA template. The replication fork is a structure that forms during DNA replication. The replication fork is a structure that forms during DNA replication. They are also used in DNA repair and genetic recombination. DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its Genome. Genetic recombination is the process by which a strand of genetic material (usually DNA; but can also be RNA) is broken and then joined to a different DNA molecule [79]
Topoisomerases and helicases
Topoisomerases are enzymes with both nuclease and ligase activity. Topoisomerases (type I, type II) are Isomerase Enzymes that act on the topology of DNA. These proteins change the amount of supercoiling in DNA. In a "relaxed" double-helical segment of DNA, the two strands twist around the helical axis once every 10 Some of these enzyme work by cutting the DNA helix and allowing one section to rotate, thereby reducing its level of supercoiling; the enzyme then seals the DNA break. [24] Other types of these enzymes are capable of cutting one DNA helix and then passing a second strand of DNA through this break, before rejoining the helix. [80] Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription. [25]
Helicases are proteins that are a type of molecular motor. Helicases are a class of Enzymes vital to all living Organisms They are motor proteins that move directionally along a Nucleic acid phosphodiester backbone Molecular motors are biological Molecular machines that are the essential agents of movement in living organisms They use the chemical energy in nucleoside triphosphates, predominantly ATP, to break hydrogen bonds between bases and unwind the DNA double helix into single strands. Nucleoside triphosphate (NTP is a Nucleoside with three Phosphates Natural nucleoside triphosphates include Adenosine triphosphate (ATP Guanosine Adenosine-5'-triphosphate ( ATP) is a multifunctional Nucleotide that is most important as a " molecular currency" of intracellular Energy [81] These enzymes are essential for most processes where enzymes need to access the DNA bases.
Polymerases
Polymerases are enzymes that synthesize polynucleotide chains from nucleoside triphosphates. A polymerase (EC 2776/7/19/48/49 is an Enzyme whose central function is associated with Polymers of Nucleic acids such as RNA and DNA Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins Nucleoside triphosphate (NTP is a Nucleoside with three Phosphates Natural nucleoside triphosphates include Adenosine triphosphate (ATP Guanosine The sequence of their products are copies of existing polynucleotide chains - which are called templates. These enzymes function by adding nucleotides onto the 3′ hydroxyl group of the previous nucleotide in a DNA strand. Hydroxyl in Chemistry stands for a molecule consisting of an Oxygen atom and a Hydrogen atom connected by a Covalent bond. Consequently, all polymerases work in a 5′ to 3′ direction. [82] In the active site of these enzymes, the incoming nucleoside triphosphate base-pairs to the template: this allows polymerases to accurately synthesize the complementary strand of their template. The active site of an Enzyme contains the catalytic and Binding sites. Polymerases are classified according to the type of template that they use.
In DNA replication, a DNA-dependent DNA polymerase makes a DNA copy of a DNA sequence. A DNA Polymerase is an Enzyme that assists in DNA replication. Accuracy is vital in this process, so many of these polymerases have a proofreading activity. Proofreading traditionally means reading a proof copy of a text in order to detect and correct any errors Here, the polymerase recognizes the occasional mistakes in the synthesis reaction by the lack of base pairing between the mismatched nucleotides. If a mismatch is detected, a 3′ to 5′ exonuclease activity is activated and the incorrect base removed. Exonucleases are enzymes (found as individual enzymes or as parts of larger enzyme complexes that cleave Nucleotides one at a time from an end of a polynucleotide chain [83] In most organisms DNA polymerases function in a large complex called the replisome that contains multiple accessory subunits, such as the DNA clamp or helicases. The replication of the DNA of Escherichia coli proceeds via the replisome, a multiprotein workhorse that in other organisms may vary in complexity A DNA clamp, also known as a sliding clamp, is a Protein fold that serves as a Processivity -promoting factor in DNA replication. Helicases are a class of Enzymes vital to all living Organisms They are motor proteins that move directionally along a Nucleic acid phosphodiester backbone [84]
RNA-dependent DNA polymerases are a specialized class of polymerases that copy the sequence of an RNA strand into DNA. They include reverse transcriptase, which is a viral enzyme involved in the infection of cells by retroviruses, and telomerase, which is required for the replication of telomeres. In Biochemistry, a reverse transcriptase, also known as RNA-dependent DNA polymerase, is a DNA polymerase Enzyme that transcribes A virus (from the Latin virus meaning Toxin or Poison) is a sub-microscopic infectious agent that is unable A retrovirus is any Virus belonging to the viral family Retroviridae. Telomerase is an Enzyme that adds specific DNA sequence repeats ("TTAGGG" in all vertebrates to the 3' ("three prime" end of DNA strands in the [85][33] Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure. [34]
Transcription is carried out by a DNA-dependent RNA polymerase that copies the sequence of a DNA strand into RNA. RNA polymerase ( RNAP or RNApol) is an Enzyme that produces RNA. To begin transcribing a gene, the RNA polymerase binds to a sequence of DNA called a promoter and separates the DNA strands. It then copies the gene sequence into a messenger RNA transcript until it reaches a region of DNA called the terminator, where it halts and detaches from the DNA. Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product In genetics a terminator, or transcription terminator is a section of genetic sequence that marks the end of Gene or Operon on genomic DNA As with human DNA-dependent DNA polymerases, RNA polymerase II, the enzyme that transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits. [86]
Genetic recombination
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- Further information: Genetic recombination
A DNA helix usually does not interact with other segments of DNA, and in human cells the different chromosomes even occupy separate areas in the nucleus called "chromosome territories". [88] This physical separation of different chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is during chromosomal crossover when they recombine. Genetic recombination is the process by which a strand of genetic material (usually DNA; but can also be RNA) is broken and then joined to a different DNA molecule Chromosomal crossover is when two DNA helices break, swap a section and then rejoin.
Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of natural selection and can be important in the rapid evolution of new proteins. Natural selection is the process by which favorable Heritable traits become more common in successive Generations of a Population of [89] Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks. [90]
The most common form of chromosomal crossover is homologous recombination, where the two chromosomes involved share very similar sequences. Homologous recombination is a type of Genetic recombination, a process of physical rearrangement occurring between two strands of DNA. Non-homologous recombination can be damaging to cells, as it can produce chromosomal translocations and genetic abnormalities. In Genetics, a chromosome translocation is a Chromosome abnormality caused by rearrangement of parts between nonhomologous Chromosomes. The recombination reaction is catalyzed by enzymes known as recombinases, such as RAD51. RAD51 is a human Gene. The Protein encoded by this gene is a member of the RAD51 protein family which assist in repair of DNA double strand breaks. [91] The first step in recombination is a double-stranded break either caused by an endonuclease or damage to the DNA. Endonucleases are Enzymes that cleave the Phosphodiester bond within a Polynucleotide chain in contrast to Exonucleases which cleave Phosphodiester [92] A series of steps catalyzed in part by the recombinase then leads to joining of the two helices by at least one Holliday junction, in which a segment of a single strand in each helix is annealed to the complementary strand in the other helix. A Holliday junction is a mobile junction between four strands of DNA. The Holliday junction is a tetrahedral junction structure that can be moved along the pair of chromosomes, swapping one strand for another. The recombination reaction is then halted by cleavage of the junction and re-ligation of the released DNA. [93]
Evolution of DNA metabolism
- Further information: RNA world hypothesis
DNA contains the genetic information that allows all modern living things to function, grow and reproduce. The RNA world hypothesis proposes that a world filled with life based on Ribonucleic acid (RNA predated current life based on Deoxyribonucleic acid (DNA However, it is unclear how long in the 4-billion-year history of life DNA has performed this function, as it has been proposed that the earliest forms of life may have used RNA as their genetic material. This timeline of the evolution of life outlines the major events in the development [82][94] RNA may have acted as the central part of early cell metabolism as it can both transmit genetic information and carry out catalysis as part of ribozymes. Catalysis is the process in which the rate of a Chemical reaction is increased by means of a Chemical substance known as a catalyst A ribozyme (from ribo nucleic acid en' zyme', also called RNA Enzyme or catalytic RNA is an RNA Molecule that catalyzes [95] This ancient RNA world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based on four nucleotide bases. The RNA world hypothesis proposes that a world filled with life based on Ribonucleic acid (RNA predated current life based on Deoxyribonucleic acid (DNA eVolution is the third Album by eLDee, it was due to be released in 2008 This would occur since the number of unique bases in such an organism is a trade-off between a small number of bases increasing replication accuracy and a large number of bases increasing the catalytic efficiency of ribozymes. [96]
Unfortunately, there is no direct evidence of ancient genetic systems, as recovery of DNA from most fossils is impossible. This is because DNA will survive in the environment for less than one million years and slowly degrades into short fragments in solution. [97] Claims for older DNA have been made, most notably a report of the isolation of a viable bacterium from a salt crystal 250-million years old,[98] but these claims are controversial. [99][100]
Uses in technology
Genetic engineering
- Further information: Molecular biology and genetic engineering
Modern biology and biochemistry make intensive use of recombinant DNA technology. Molecular biology is the study of Biology at a molecular level Genetic engineering, Recombinant DNA technology, genetic modification/manipulation (GM and gene splicing are terms that apply to the direct Foundations of modern biology There are five unifying principles Biochemistry is the study of the chemical processes in living Organisms It deals with the Structure and function of cellular components such as Recombinant DNA is a man-made DNA sequence that has been assembled from other DNA sequences. Recombinant DNA is a form of synthetic DNA that is engineered through the combination or insertion of one or more DNA strands thereby combining DNA sequences They can be transformed into organisms in the form of plasmids or in the appropriate format, by using a viral vector. In Molecular biology, transformation is the genetic alteration of a cell resulting from the uptake genomic incorporation and expression of foreign A plasmid is an extra-chromosomal DNA molecule separate from the chromosomal DNA which is capable of replicating independently of the chromosomal DNA Viral vectors are a tool commonly used by molecular Biologists to deliver Genetic material into cells This process can be performed inside a living organism [101] The genetically modified organisms produced can be used to produce products such as recombinant proteins, used in medical research,[102] or be grown in agriculture. Genetic engineering, Recombinant DNA technology, genetic modification/manipulation (GM and gene splicing are terms that apply to the direct Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl Agriculture refers to the production of goods through the growing of plants and fungi and the raising of domesticated Animals The study of agriculture [103][104]
Forensics
- Further information: Genetic fingerprinting
Forensic scientists can use DNA in blood, semen, skin, saliva or hair at a crime scene to identify a perpetrator. Blood is a specialized Bodily fluid that delivers necessary substances to the body's cells such as nutrients and oxygen—and transports Waste products Physiological aspects Internal and external fertilization Depending on the Species, spermatozoa can fertilize The skin is the outer covering of living tissue of an animal (or plant For the band see Saliva (band; for the village in Azerbaijan see Səliva. Hair is a keratinised protein filament that grows through the epidermis from follicles deep within the Dermis. This process is called genetic fingerprinting, or more accurately, DNA profiling. In DNA profiling, the lengths of variable sections of repetitive DNA, such as short tandem repeats and minisatellites, are compared between people. A short tandem repeat (STR in DNA is a class of polymorphisms that occurs when a pattern of two or more Nucleotides are repeated and the repeated sequences This article is about the DNA sequence See also Miniaturized satellite for the size class of orbiting spacecraft A minisatellite is a section This method is usually an extremely reliable technique for identifying a criminal. [105] However, identification can be complicated if the scene is contaminated with DNA from several people. [106] DNA profiling was developed in 1984 by British geneticist Sir Alec Jeffreys,[107] and first used in forensic science to convict Colin Pitchfork in the 1988 Enderby murders case. Sir Alec John Jeffreys, FRS (born 9 January 1950 at Oxford in Oxfordshire) is a British Geneticist, who developed techniques Colin Pitchfork (born 1961 Bristol, England) was the first criminal convicted for murder based on DNA fingerprinting evidence and the first to be [108] People convicted of certain types of crimes may be required to provide a sample of DNA for a database. This has helped investigators solve old cases where only a DNA sample was obtained from the scene. DNA profiling can also be used to identify victims of mass casualty incidents. [109]
Bioinformatics
- Further information: Bioinformatics
Bioinformatics involves the manipulation, searching, and data mining of DNA sequence data. Bioinformatics is the application of information technology to the field of molecular biology Bioinformatics is the application of information technology to the field of molecular biology Data mining is the process of Sorting through large amounts of data and picking out relevant information The development of techniques to store and search DNA sequences have led to widely-applied advances in computer science, especially string searching algorithms, machine learning and database theory. Computer science (or computing science) is the study and the Science of the theoretical foundations of Information and Computation and their String searching algorithms, sometimes called string matching algorithms, are an important class of String algorithms that try to find a place where one or several Machine learning is a subfield of Artificial intelligence that is concerned with the design and development of Algorithms and techniques that allow computers to "learn" Database theory encapsulates a broad range of topics related to the study and research of the theoretical realm of Databases and Database management systems Theoretical [110] String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, were developed to search for specific sequences of nucleotides. [111] In other applications such as text editors, even simple algorithms for this problem usually suffice, but DNA sequences cause these algorithms to exhibit near-worst-case behaviour due to their small number of distinct characters. A text editor is a type of program used for editing plain Text files Text editors are often provided with Operating systems or software development The related problem of sequence alignment aims to identify homologous sequences and locate the specific mutations that make them distinct. In Bioinformatics, a sequence alignment is a way of arranging the Primary sequences of DNA, RNA, or Protein to identify regions of In Evolutionary biology, homology has come to mean any similarity between characters that is due to their shared ancestry. In biology mutations are changes to the Nucleotide sequence of the Genetic material of an organism These techniques, especially multiple sequence alignment, are used in studying phylogenetic relationships and protein function. A multiple sequence alignment (MSA is a Sequence alignment of three or more Biological sequences generally Protein, DNA, or RNA [112] Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are difficult to use without annotations, which label the locations of genes and regulatory elements on each chromosome. The Human Genome Project (HGP was an international Scientific research project with a primary goal to determine the sequence of chemical base pairs which make up DNA Regions of DNA sequence that have the characteristic patterns associated with protein- or RNA-coding genes can be identified by gene finding algorithms, which allow researchers to predict the presence of particular gene products in an organism even before they have been isolated experimentally. Gene finding typically refers to the area of Computational biology that is concerned with algorithmically identifying stretches of sequence usually genomic DNA A gene product is the biochemical material either RNA or Protein, resulting from expression of a Gene. [113]
DNA nanotechnology
![The DNA structure at left (schematic shown) will self-assemble into the structure visualized by atomic force microscopy at right. DNA nanotechnology is the field which seeks to design nanoscale structures using the molecular recognition properties of DNA molecules. Image from Strong, 2004. [1]](http://upload.wikimedia.org/wikipedia/commons/thumb/5/55/DNA_nanostructures.png/400px-DNA_nanostructures.png)
- Further information: DNA nanotechnology
DNA nanotechnology uses the unique molecular recognition properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties. DNA nanotechnology is a subfield of Nanotechnology which seeks to use the unique Molecular recognition properties of DNA and other Nucleic acids The term molecular recognition refers to the specific interaction between two or more Molecules through Noncovalent bonding such as including hydrogen bonding DNA is thus used as a structural material rather than as a carrier of biological information. This has led to the creation of two-dimensional periodic lattices (both tile-based as well as using the "DNA origami" method) as well as three-dimensional structures in the shapes of polyhedra. Nanoscale folding of DNA, also known as DNA origami, is a process which allows researchers to create arbitrary two-dimensional shapes at the Nanoscale using DNA What is a polyhedron? We can at least say that a polyhedron is built up from different kinds of element or entity each associated with a different number of dimensions Nanomechanical devices and algorithmic self-assembly have also been demonstrated, and these DNA structures have been used to template the arrangement of other molecules such as gold nanoparticles and streptavidin proteins. A DNA machine is a Molecular machine constructed from DNA. Research into DNA machines was pioneered in the late 1980s by Nadrian Seeman and co-workers DNA computing is a form of Computing which uses DNA, Biochemistry and Molecular biology, instead of the traditional silicon-based Computer Colloidal gold, also known as "nanogold" is a suspension (or Colloid) of sub- Micrometre -sized particles of Gold in a fluid — usually Streptavidin is a 53000 dalton tetrameric Protein purified from the Bacterium Streptomyces avidinii.
History and anthropology
- Further information: Phylogenetics and Genetic genealogy
Because DNA collects mutations over time, which are then inherited, it contains historical information and by comparing DNA sequences, geneticists can infer the evolutionary history of organisms, their phylogeny. Genetic genealogy is the application of Genetics to traditional genealogy. [114] This field of phylogenetics is a powerful tool in evolutionary biology. Evolutionary biology is a sub-field of Biology concerned with the origin of Species from a Common descent, and Descent of species If DNA sequences within a species are compared, population geneticists can learn the history of particular populations. Population genetics is the study of the Allele frequency distribution and change under the influence of the four evolutionary forces Natural selection, Genetic This can be used in studies ranging from ecological genetics to anthropology; for example, DNA evidence is being used to try to identify the Ten Lost Tribes of Israel. Ecological genetics is the study of Genetics in the context of the interactions among organisms and between the organisms and their environment Anthropology (/ˌænθɹəˈpɒlədʒi/ from Greek grc ἄνθρωπος anthrōpos, "human" -λογία -logia) is the study of The phrase Ten Lost Tribes of Israel refers to the ancient Tribes of Israel that disappeared from the Biblical account after the Kingdom of Israel was destroyed [115][116]
DNA has also been used to look at modern family relationships, such as establishing family relationships between the descendants of Sally Hemings and Thomas Jefferson. Sally Hemings ( Shadwell, Albemarle County Virginia, circa 1773 &ndash Charlottesville Virginia, 1835 was an American slave owned by Thomas Jefferson (April 13 1743 – July 4 1826 was the third President of the United States (1801–1809 the principal author of the Declaration of Independence This usage is closely related to the use of DNA in criminal investigations detailed above. Indeed, some criminal investigations have been solved when DNA from crime scenes has matched relatives of the guilty individual. [117]
History of DNA research
- Further information: History of molecular biology
DNA was first isolated by the Swiss physician Friedrich Miescher who, in 1869, discovered a microscopic substance in the pus of discarded surgical bandages. Rosalind Elsie Franklin ( 25 July, 1920 Notting Hill, London – 16 April, 1958 Chelsea London) was an Francis Harry Compton Crick OM FRS (8 June 1916 – 28 July 2004 Ph The history of molecular biology begins in the 1930s with the convergence of various previously distinct biological disciplines Biochemistry, Genetics, Microbiology Switzerland (English pronunciation; Schweiz Swiss German: Schwyz or Schwiiz Suisse Svizzera Svizra officially the Swiss Confederation Johannes Friedrich Miescher ( 13 August 1844, Basel - 26 August 1895, Davos) was a Swiss Biologist Pus is a whitish-yellow yellow or yellow-brown substance produced during Inflammatory responses of the body that can be found in regions of Pyogenic bacterial As it resided in the nuclei of cells, he called it "nuclein". [118] In 1919 this discovery was followed by Phoebus Levene's identification of the base, sugar and phosphate nucleotide unit. Phoebus Aaron Theodore Levene MD ( 25 February, 1869 &mdash 6 September, 1940) was a Russian-American Biochemist who studied the [119] Levene suggested that DNA consisted of a string of nucleotide units linked together through the phosphate groups. However, Levene thought the chain was short and the bases repeated in a fixed order. In 1937 William Astbury produced the first X-ray diffraction patterns that showed that DNA had a regular structure. William Thomas Astbury FRS (Bill Astbury 25 February, 1898 &mdash 4 June, 1961) was an English Physicist and X-ray scattering techniques are a family of non-destructive analytical techniques which reveal information about the crystallographic structure chemical composition [120]
In 1928, Frederick Griffith discovered that traits of the "smooth" form of the Pneumococcus could be transferred to the "rough" form of the same bacteria by mixing killed "smooth" bacteria with the live "rough" form. Frederick Griffith (1879 - 1941 was a British medical officer and geneticist. A trait is a distinct phenotypic character of an organism that may be inherited environmentally determined or somewhere in between [121] This system provided the first clear suggestion that DNA carried genetic information, when Oswald Avery, along with coworkers Colin MacLeod and Maclyn McCarty, identified DNA as the transforming principle in 1943. Oswald Theodore Avery ( October 21, 1877 &ndash 2 February, 1955) was a Canadian -born American Physician and Colin Munro MacLeod ( January 28, 1909 &mdash February 11, 1972) was a Canadian-American geneticist Maclyn McCarty ( South Bend Indiana, June 9 1911 &ndash January 2 2005) was an American Geneticist. Griffith's experiment, conducted in 1928 by Frederick Griffith, was one of the first experiments suggesting that bacteria are capable of transferring genetic information [122] DNA's role in heredity was confirmed in 1952, when Alfred Hershey and Martha Chase in the Hershey-Chase experiment showed that DNA is the genetic material of the T2 phage. Alfred Day Hershey ( December 4, 1908 &ndash May 22 1997) was an American Nobel Prize -winning Bacteriologist and Martha Cowles Chase (1927 &ndash August 8, 2003) also known as Martha C The Hershey-Chase experiments were a series of Experiments conducted in 1952 by Alfred Hershey and Martha Chase, confirming that DNA Genetic material is used to store the genetic information of an organic life form Enterobacteria phage T2 is a virulent bacteriophage of the T4-like viruses genus in the family Myoviridae. [123]
In 1953, based on X-ray diffraction images[124] taken by Rosalind Franklin and the information that the bases were paired, James D. Watson and Francis Crick suggested[124] what is now accepted as the first accurate model of DNA structure in the journal Nature. Photo 51 is the nickname given to an X-ray diffraction image of DNA taken by Rosalind Franklin in 1952 that was critical evidence in identifying Rosalind Elsie Franklin ( 25 July, 1920 Notting Hill, London – 16 April, 1958 Chelsea London) was an Francis Harry Compton Crick OM FRS (8 June 1916 – 28 July 2004 Ph The Molecular structure of Nucleic Acids A Structure for Deoxyribose Nucleic Acid was an article published by James D Nature is a prominent Scientific journal, first published on 4 November 1869 [5] Experimental evidence for Watson and Crick's model were published in a series of five articles in the same issue of Nature. [125] Of these, Franklin and Raymond Gosling's paper was the first publication of X-ray diffraction data that supported the Watson and Crick model,[126][127] this issue also contained an article on DNA structure by Maurice Wilkins and his colleagues. Rosalind Elsie Franklin ( 25 July, 1920 Notting Hill, London – 16 April, 1958 Chelsea London) was an Raymond Gosling (born 1926 is a distinguished scientist who worked with both Maurice Wilkins and Rosalind Franklin at King's College London in deducing Maurice Hugh Frederick Wilkins CBE FRS ( 15 December 1916 – 5 October 2004) was a New Zealand -born British [128] In 1962, after Franklin's death, Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine. The Nobel Prize (Nobelpriset (Nobelprisen is a Swedish prize established in the 1895 will of Swedish chemist Alfred Nobel; it was first awarded in Peace, Literature The Nobel Prize in Physiology or Medicine (Nobelpriset i fysiologi eller medicin is awarded once a year by the Swedish Karolinska Institute. [129] However, debate continues on who should receive credit for the discovery. [130]
In an influential presentation in 1957, Crick laid out the "Central Dogma" of molecular biology, which foretold the relationship between DNA, RNA, and proteins, and articulated the "adaptor hypothesis". The central dogma of molecular biology was first enunciated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970 [131] Final confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 through the Meselson-Stahl experiment. The Meselson-Stahl experiment was an experiment by Matthew Meselson and Franklin Stahl which demonstrated that DNA replication was semiconservative [132] Further work by Crick and coworkers showed that the genetic code was based on non-overlapping triplets of bases, called codons, allowing Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg to decipher the genetic code. Har Gobind Khorana, or Hargobind Khorana (born January 9, 1922) is an Indian-American molecular biologist Robert William Holley ( January 28, 1922 &ndash February 11, 1993) was an American Biochemist, he was awarded the Nobel Prize Marshall Warren Nirenberg (born April 10, 1927) is a US Biochemist and geneticist. [133] These findings represent the birth of molecular biology. Molecular biology is the study of Biology at a molecular level
See also
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Further reading
- Clayton, Julie. (Ed. ). 50 Years of DNA, Palgrave MacMillan Press, 2003. ISBN 978-1-40-391479-8
- Judson, Horace Freeland. The Eighth Day of Creation: Makers of the Revolution in Biology, Cold Spring Harbor Laboratory Press, 1996. ISBN 978-0-87-969478-4
- Olby, Robert. Robert Cecil Olby (born in 1933 is a research professor in the Department of History and Philosophy of Science at the University of Pittsburgh. The Path to The Double Helix: Discovery of DNA, first published in October 1974 by MacMillan, with foreword by Francis Crick; ISBN 978-0-48-668117-7; the definitive DNA textbook, revised in 1994, with a 9 page postscript.
- Ridley, Matt. The Hon Matthew White Ridley (born February 7, 1958, in Northumberland) is an English science Francis Crick: Discoverer of the Genetic Code (Eminent Lives) HarperCollins Publishers; 192 pp, ISBN 978-0-06-082333-7 2006
- Rose, Steven. The Chemistry of Life, Penguin, ISBN 978-0-14-027273-4.
- Watson, James D. and Francis H. C. Crick. A structure for Deoxyribose Nucleic Acid (PDF). Nature 171, 737–738, 25 April 1953. Nature is a prominent Scientific journal, first published on 4 November 1869 Events 1607 - Eighty Years' War: The Dutch fleet destroys the anchored Spanish fleet at Gibraltar. Year 1953 ( MCMLIII) was a Common year starting on Thursday (link will display full calendar of the Gregorian calendar.
- Watson, James D. DNA: The Secret of Life ISBN 978-0-375-41546-3.
- Watson, James D. The Double Helix: A Personal Account of the Discovery of the Structure of DNA (Norton Critical Editions). The Double Helix A Personal Account of the Discovery of the Structure of DNA is an autobiographical account of the discovery of the Double helix structure of ISBN 978-0-393-95075-5
- Watson, James D. "Avoid boring people and other lessons from a life in science" (2007) New York: Random House. ISBN 978-0-375-41284-4
- Calladine, Chris R. ; Drew, Horace R. ; Luisi, Ben F. and Travers, Andrew A. Understanding DNA, Elsevier Academic Press, 2003. ISBN 978-0-12155089-9
External links
- The Secret Life of DNA - DNA Music compositions
- The Register of Francis Crick Personal Papers 1938 - 2007 at Mandeville Special Collections Library, Geisel Library, University of California, San Diego
- DNA Interactive This site from the Dolan DNA Learning Center included dozens of animations as well as interviews with James Watson and others (requires Adobe Flash)
- DNA from the Beginning Another DNA Learning Center site on DNA, genes, and heredity from Mendel to the human genome project. Adobe Flash (previously called Shockwave Flash and Macromedia Flash) is a set of Multimedia software created by Macromedia and currently
- Double Helix 1953–2003 National Centre for Biotechnology Education
- Double helix: 50 years of DNA, Nature
- Rosalind Franklin's contributions to the study of DNA
- U.S. National DNA Day — watch videos and participate in real-time chat with top scientists
- Genetic Education Modules for Teachers — DNA from the Beginning Study Guide
- Listen to Francis Crick and James Watson talking on the BBC in 1962, 1972, and 1974
- PDB Molecule of the Month pdb23_1
- DNA under electron microscope
- DNA at the Open Directory Project
- DNA coiling to form chromosomes
- DISPLAR: DNA binding site prediction on protein
- Dolan DNA Learning Center
- Olby, R. (2003) "Quiet debut for the double helix" Nature 421 (January 23): 402–405. Nature is a prominent Scientific journal, first published on 4 November 1869 The Protein Data Bank ( PDB) is a repository for 3-D structural data of Proteins and Nucleic acids These data typically obtained by X-ray crystallography The Open Directory Project ( ODP) also known as dmoz (from directory Robert Cecil Olby (born in 1933 is a research professor in the Department of History and Philosophy of Science at the University of Pittsburgh.
- Basic animated guide to DNA cloning
- DNA the Double Helix Game From the official Nobel Prize web site
- DNA Lab, demonstrates how to extract DNA from wheat using readily available equipment and supplies.
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