Deoxyribonucleic acids

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This diagram shows the chemical structure of deoxyribonucleic acid, with colored labels identifying the four nucleobases, the phosphate, and deoxyribose components. Credit: Madeleine Price Ball, Madprime.

Deoxyribonucleic acid (DNA) is a polymer composed of nucleic acids linked together by a sugar-phosphate backbone.

The nucleic acids are inorganic acids with phosphoric acid as the only acid.

Attached to each sugar is a nucleobase.

Polyphosphoric acids[edit]

Def. "[a] colourless liquid, H3PO4"[1] is called phosphoric acid, orthophosphoric acid, or monophosphoric acid.

"[A]n orthophosphoric acid molecule can dissociate up to three times, giving up an H+ each time, which typically combines with a water molecule, H2O, as shown in these [chemical] reactions:"[2]

H3PO4(s)   + H2O(l) ↔ H3O+(aq) + H2PO4(aq)       Ka1= 7.25×10−3
H2PO4(aq)+ H2O(l) ↔ H3O+(aq) + HPO42−(aq)       Ka2= 6.31×10−8
HPO42−(aq)+ H2O(l) ↔ H3O+(aq) +  PO43−(aq)        Ka3= 4.80×10−13

"The anion after the first dissociation, H2PO4, is the dihydrogen phosphate anion. The anion after the second dissociation, HPO42−, is the hydrogen phosphate anion. The anion after the third dissociation, PO43−, is the phosphate or orthophosphate anion. For each of the dissociation reactions shown above, there is a separate acid dissociation constant, called Ka1, Ka2, and Ka3 given at 25 °C. Associated with these three dissociation constants are corresponding pKa1=2.12, pKa2=7.21, and pKa3=12.67 values at 25 °C. Even though all three hydrogen (H) atoms are equivalent on an orthophosphoric acid molecule, the successive Ka values differ since it is energetically less favorable to lose another H+ if one (or more) has already been lost and the molecule/ion is more negatively charged."[2]

"For a given total acid concentration [A] = [H3PO4] + [H2PO4] + [HPO42−] + [PO43−] ([A] is the total number of moles of pure H3PO4 which have been used to prepare 1 liter of solution), the composition of an aqueous solution of phosphoric acid can be calculated using the equilibrium equations associated with the three reactions described above together with the [H+][OH] = 10−14 relation and the electrical neutrality equation. Possible concentrations of polyphosphoric molecules and ions is neglected. The system may be reduced to a fifth degree equation for [H+] which can be solved numerically, yielding:"[2]

[A] (mol/L) pH [H3PO4]/[A] (%) [H2PO4]/[A] (%) [HPO42−]/[A] (%) [PO43−]/[A] (%)
1 1.08 91.7 8.29 6.20×10−6 1.60×10−17
10−1 1.62 76.1 23.9 6.20×10−5 5.55×10−16
10−2 2.25 43.1 56.9 6.20×10−4 2.33×10−14
10−3 3.05 10.6 89.3 6.20×10−3 1.48×10−12
10−4 4.01 1.30 98.6 6.19×10−2 1.34×10−10
10−5 5.00 0.133 99.3 0.612 1.30×10−8
10−6 5.97 1.34×10−2 94.5 5.50 1.11×10−6
10−7 6.74 1.80×10−3 74.5 25.5 3.02×10−5
10−10 7.00 8.24×10−4 61.7 38.3 8.18×10−5

"For large acid concentrations, the solution is mainly composed of H3PO4. For [A] = 10−2, the pH is close to pKa1, giving an equimolar mixture of H3PO4 and H2PO4. For [A] below 10−3, the solution is mainly composed of H2PO4 with [HPO42−] becoming non negligible for very dilute solutions. [PO43−] is always negligible. Note that the above analysis does not take into account ion activity coefficients; as such, the pH and molarity of a real phosphoric acid solution may deviate substantially from the above values."[2]

Def. typically two to twenty, or three to seven, linked monophosphoric acids, or orthophosphoric acids, is called an oligophosphoric acid.

Def. "any of a class of inorganic polymers containing linked phosphate groups"[3], or more than five linked phosphoric acids, is called a polyphosphate, or polyphosphoric acid.

Nitrogenous bases[edit]

Nitrogenous bases, found in cell nuclei, are nucleobases.

"In normal spiral DNA the bases form pairs between the two strands: [Adenine] A with [Thymine] T and [Cytosine] C with [Guanine] G. Purines pair with pyrimidines mainly for dimensional reasons - only this combination fits the constant width geometry of the DNA spiral."[4]

Nitrogenous bases include purines: adenine, guanine, hypoxanthine, isoguanine, xanthine, and 7-methylguanine; and pyrimidines: cytosine, thymine, and isocytosine.

Sugars[edit]

This diagram shows the pentoses ribose and deoxyribose in the α-D-ribofuranose form. Credit: Boumphreyfr.

Def. "[a] derivative of the pentose sugar ribose in which the 2' hydroxyl (-OH) is reduced to a hydrogen (H)"[5] is called deoxyribose.

In the diagram of DNA at the page top, the pentose sugar deoxyribose is in a cyclic, furanose (5-membered ring) form. D-deoxyribose or L-deoxyribose is not demonstrated, but is determined by the hydroxyls being primarily below (D) or above (L) the plane of the ring. In Earth-based DNA, deoxyribose is in the dextro (D) configuration.

Deoxyribose may also occur in a pyranose (six-membered ring) form.

There are other pentose sugars including aldopentoses: apiose, arabinose, xylose, and lyxose, and ketopentoses: ribulose and xylulose. These may have a deoxy-form: deoxyapiose, deoxyarabinose, deoxyxylose, deoxylyxose, deoxyribulose, and deoxyxylulose. They may occur as a levo or dextro sugar and as a furanose or pyranose.

To occur in an Earth-like DNA, each of these six deoxypentoses and perhaps other sugars need to be dextro furanoses. Each is a DNA, for example, deoxyapionucleic acid.

Sugar phosphates[edit]

This is a structural drawing of glucose-6-phosphate. Credit: Yikrazuul.
The diagram shows the chemical structure of phytate. Credit: Shaddack.

Any of the various sugars can have one or more phosphates attached as in glucose-6-phosphate diagrammed on the right.

Nucleosides[edit]

Def. "an organic molecule in which a nitrogenous heterocyclic base (or nucleobase), which can be either a double-ringed purine or a single-ringed pyrimidine, is covalently attached to a five-carbon pentose sugar (deoxyribose in DNA or ribose in RNA)"[6] is called a nucleoside.

Nucleotides[edit]

"All five nucleotides (including the RNA base "uracil") are synthesized through complex metabolic pathways involving several multi-subunit enzymes. The pathways differ for both purines and pyrimidines (uracil falling in the pyrimidine category since it is thymine's counterpart.)"[7]

Nucleic acids[edit]

Main source: Nucleic acids
These images show natural and artificial nucleic acid polymers. Credit: Irina Anosova, Ewa A. Kowal, Matthew R. Dunn, John C. Chaput, Wade D. Van Horn1, and Martin Egli.

"Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms."[8]

Def. any "acidic, chainlike biological macromolecule consisting of multiply repeat units of phosphoric acid, sugar and purine and pyrimidine bases"[9] occurring in cell nuclei is called a nucleic acid.

Def. a nucleic acid "in which the sugar component is threose"[10] is called threose nucleic acid, or threonucleic acid (TNA).

Additional DNAs may be

  1. deoxyapionucleic acid,
  2. deoxyarabinonucleic acid,
  3. deoxyxylonucleic acid (dXyNA),
  4. deoxylyxonucleic acid,
  5. deoxyribulonucleic acid, and
  6. deoxyxylulonucleic acid.

Synthesis of deoxyapionucleic acid has been accomplished.[11]

Deoxyxylonucleic acid and xylose nucleic acid have been produced.[12]

"[X]ylonucleic acid (XyloNA) [contains] a potentially prebiotic xylose sugar (a 3′-epimer of ribose) in its backbone."[12]

A "number of sugar-modified nucleic acid variants has been revealed as new genetic polymers, (2) some of them are endowed with catalytic activity (for e.g. FANA and HNA) (3). The structure of these artificial nucleic acids, however, mimics natural nucleic acid helicity (4)."[12]

"Although helices display a distinct pitch and curvature, they feature ca. 11–12 base pairs per turn, and χ/δ covariance plots indicate that the backbones of XNA:RNA or XNA:DNA heteroduplexes adopt an architecture that is either closely related to the A-form, as in the case of [1,5-anhydrohexitol nucleic acid (HNA)] HNA:RNA (96), [locked nucleic acid (LNA)] LNA:RNA (83), [cyclohexene nucleic acid (CeNA)] CeNA:RNA (85) and PNA:RNA (59), or between the A- and B-forms, as seen in the structures of DNA:RNA (97), [arabinonucleic acid (ANA)] ANA:RNA (79), [2′-deoxy-2′-fluoro-arabinonucleic acid (FANA)]FANA:RNA (79) and [peptide nucleic acid (PNA)] PNA:DNA (98)."[8]

Additional XNAs include bridged nucleic acid (BNA) glycol nucleic acid (GNA), FANA and peptide nucleic acid (PNA).

On the right is a diagram displaying various artificial and natural nucleic acid polymers.

"Representative structures illustrate the structural diversity and plasticity of natural and artificial nucleic acid (XNA) backbones. Structures are shown in alphabetic order. (A) Natural genetic polymers: B-form DNA (black), DNA:RNA hybrid and A-form RNA (gray). (B) Representative structures of XNA heteroduplexes with RNA or DNA. The RNA strand is shown in gray, the DNA strand in black and the orientation of the XNA strand is indicated. (C) XNA homoduplexes. Homo-XNA duplexes adopt a variety of structures. (D) Representative XNA-only heteroduplexes. FAF:FAF stands for FANA(F)-ANA(A)-FANA(F) XNA:XNA heteroduplex. Alt and chim indicate the alternated or chimeric order of FANA-segments in the duplex sequences respectively. The depicted duplexes have the following PDB ID codes in the Protein Data Bank (http://www.rcsb.org): B-DNA (3BSE); DNA:RNA (1EFS); A-RNA (3ND4); ANA(purple):RNA (2KP3); CeNA(blue):RNA (3KNC); FANA(violet):RNA (2KP4); HNA(yellow):RNA (2BJ6); LNA(cyan):RNA (1H0Q); PNA(orange):DNA (1PDT); PNA(orange):RNA (176D); CeNA:CeNA (blue, 2H0N); hDNA:hDNA (sky blue, 2H9S); FRNA:FRNA (magenta, 3P4A); GNA:GNA (red, 2XC6); HNA:HNA (yellow, 481D); LNA:LNA (cyan, 2×2Q); PNA:PNA (orange, 2K4G), TNA:TNA (green, coordinates not deposited in the PDB [...]); dXyNA:dXyNA (brown, coordinates not deposited in the PDB [...]); XyNA:XyNA (light green, 2N4J); FAF:FAF (FANA in violet, ANA in purple, 2LSC), FRNA:FANA (alt) (FRNA in magenta, FANA in violet, 2M8A); FRNA:FANA (chim) (FRNA in magenta, FANA in violet, 2M84)."[8]

Mitochondrial DNA[edit]

Mitochondrial DNAs are the small circular chromosome found inside mitochondria. Credit: National Human Genome Research Institute.
Human mitochondrial DNA has 37 genes on their respective H- and L-strands. Credit: Emmanuel Douzery.

Mitochondrial DNA (mtDNA or mDNA)[13] consists of one or more strands making up the small circular chromosomes inside mitochondria. Mitochondria are passed only from mother to offspring.

The 16,569 base pairs of human mitochondrial DNA encode for 37 genes.[14]

The guanine-rich strand is the heavy strand (or H-strand) which encodes 28 genes and the cytosine-rich strand is the light strand (or L-strand) which encodes the other 9 genes.[14]

The H (heavy, outer circle) and L (light, inner circle) strands are given with their corresponding genes.

There are 22 transfer RNA (TRN) genes for the following amino acids: F, V, L1 (codon UUA/G), I, Q, M, W, A, N, C, Y, S1 (UCN), D, K, G, R, H, S2 (AGC/U), L2 (CUN), E, T and P (white boxes).

There are 2 ribosomal RNA (RRN) genes: S (small subunit, or 12S) and L (large subunit, or 16S) (blue boxes).

There are 13 protein-coding genes: 7 for NADH dehydrogenase subunits (ND, yellow boxes), 3 for cytochrome c oxidase subunits (COX, orange boxes), 2 for ATPase subunits (ATP, red boxes), and one for cytochrome b (CYTB, coral box).

Two gene overlaps are indicated (ATP8-ATP6, and ND4L-ND4, black boxes).

The control region (CR) is the longest non-coding sequence (grey box). Its three hyper-variable regions are indicated (HV, green boxes).

Noncoding DNA[edit]

"Non-coding DNA sequences do not code for amino acids. Most non-coding DNA lies between genes [intergenic] on the chromosome [...]. Other non-coding DNA, called introns, is found within genes. [...] Non-coding DNA [...] represents 98 percent of our genome sequence and it does all sorts of things, like regulate those genes to figure out where they should turn on, where they should turn off, how much we should turn on certain genes, how are we going to pack up the DNA into chromosomes, and so forth."[15][16]

Over 80% of human DNA "serves some purpose, biochemically speaking".[17]

Non-coding repetitive sequences[edit]

Over 50% of human DNA consists of non-coding repetitive sequences.[18]

Non-coding RNA sequences[edit]

"[S]ome DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression.[19]"[20]

Pseudogenes[edit]

Main sources: Genes/Pseudogenes and Pseudogenes

"An abundant form of noncoding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation.[21] 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.[22]"[20]

Genes[edit]

Main source: Genes

Def. "[a] unit of heredity; a segment of DNA or RNA that is transmitted from one generation to the next, and that carries genetic information such as the sequence of amino acids for a protein"[23] is called a gene.

"The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. 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."[20]

"[O]nly about 1.5% of the human genome consists of protein-coding exons".[20]

Telomeres[edit]

"Some noncoding DNA sequences [such as telomeres and centromeres] play structural roles in chromosomes."[20]

"[T]elomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.[24]"[20]

"Telomeres and centromeres typically contain few genes, but are important for the function and stability of chromosomes.[25][26]"[20]

Centromeres[edit]

Centromeres are chromosomal loci that ensure delivery of a copy of a chromosome to each daughter upon cell division. On the Spindle Apparatus, chromosome movement is run and maintained by the centromere during meiosis and mitosis.[27]

Introns[edit]

"An intron is any nucleotide sequence within a gene that is removed by RNA splicing while the final mature RNA product of a gene is being generated.[28][29] The term intron refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts."[30][31]

There are "several families of internal nucleic acid sequences that are not present in the final gene product, including inteins, untranslated sequences ([Untranslated region] UTR), and nucleotides removed by RNA editing, in addition to introns."[31]

"[I]ntrons are extremely common within the nuclear genome of higher vertebrates (e.g. humans and mice), where protein-coding genes almost always contain multiple introns"[31].

"[S]ome introns themselves encode specific proteins or can be further processed after splicing to generate noncoding RNA molecules.[32] Alternative splicing is widely used to generate multiple proteins from a single gene. Furthermore, some introns represent mobile genetic elements and may be regarded as examples of selfish DNA.[33]"[31]

"[T]he human genome contains an average of 8.4 introns/gene (139,418 in the genome)"[31].

"Some introns are known to enhance the expression of the gene that they are contained in by a process known as intron-mediated enhancement (IME)."[31]

Human DNA[edit]

Main source: Human DNA
This diagram of the structure of DNA shows the four bases; adenine, cytosine, guanine and thymine, and the location of the major and minor groove. Credit: Zephyris.

"[H]uman DNA has millions of on-off switches and complex networks that control the genes' activities. ... [A]t least 80% of the human genome is active, which opposed the previously held idea that most of the DNA are useless."[34]

"DNA contains genes, which hold the instructions for [life. But, these] take up only about 2 percent of the genome ... The human genome is made up of about 3 billion “letters” along strands that make up the familiar double helix structure of DNA. Particular sequences of these letters form genes, which tell cells how to make proteins. People have about 20,000 genes, but the vast majority of DNA lies outside of genes. ... [A]t least three-quarters of the genome is involved in making RNA [...] it appears to help regulate gene activity."[35]

Hypotheses[edit]

Main source: Hypotheses
  1. As both ribose and deoxyribose nucleic acids exist, each pentose or hexose sugar should be usable to make a nucleic acid.

See also[edit]

References[edit]

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External links[edit]

{{Chemistry resources}}{{Gene project}}{{Phosphate biochemistry}}

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