The Deoxyribose , Also known as 2-deoxy-D-ribose or 2-deoxy-D-erythro-pentosa is a 5-carbon monosaccharide (pentose) whose empirical formula is C 5 H 10 OR 4 . Its structure is presented in figure 1 (EMBL-EBI, 2016).
The molecule is a component of the DNA structure (deoxyribonucleic acid), where it alternates with phosphate groups to form the"backbone"of the DNA polymer and binds to nitrogenous bases
Figure 1: Structure of deoxyribose.
The presence of deoxyribose instead of ribose is a Difference between DNA and RNA (Ribonucleic acid). Deoxyribose was synthesized in 1935, but was not isolated from DNA until 1954 (Encyclopædia Britannica, 1998).
In deoxyribose all hydroxyl groups are on the same side in Fischer's projection (figure 2). D-2-deoxyribose is a precursor of nucleic acid DNA. 2-deoxyribose is an aldopentosa, ie a monosaccharide with five carbon atoms and having an aldehyde functional group.
It is noteworthy that for the case of these sugars, the carbons are denoted with an apostrophe to differentiate them from the carbons of the nitrogenous bases present in the DNA chain. Thus, the deoxyribose is said to lack an OH at the C2 'carbon.
Figure 2: Fisher's projection of deoxyribose.
Cyclic structure of deoxyribose
All carbohydrates are cyclized in aqueous medium since this gives stability. Depending on their carbon number, they may adopt a structure analogous to furan or pyran as shown in figure 3 (MURRAY, BENDER, & BOTHAM, 2013).
Figure 3: structure of pyran and furan and their analogues for the case of glucose.
Deoxyribose exists mainly as a mixture of three structures: the linear form H- (C = O) - (CH2) - (CHOH) 3-H and two ring forms, deoxyribofuranose (C3'-endo) with a ring of five Members and deoxyribopyranose ("C2'-endo"), with a six-membered ring. The latter shape is predominant as shown in Figure 4.
Figure 4: Cyclic isomers of deoxyribose in aqueous medium.
Differences between ribose and deoxyribose
As the name implies, deoxyribose is a deoxygenated sugar, meaning it is derived from ribose sugar by the loss of an oxygen atom.
It lacks the hydroxyl group (OH) at the C 2 'carbon as shown in Figure 5 (Carr, 2014). Deoxyribose sugar forms part of the DNA strand while ribose forms part of the RNA chain.
Figure 5: structures of deoxyribose vs ribose.
Since the sugars of pentosa, arabinose and ribose differ only by stereochemistry at C2 '(ribose is R and arabinose is L according to the Fisher convention), 2-deoxyribose and 2-deoxyarabinose are equivalent, although the latter Term is rarely used because ribose, not arabinose, is the precursor of deoxyribose.
Physical and chemical properties
Ribose is a white solid that forms a colorless liquid in aqueous solution (National Center for Biotechnology Information, 2017). It has a molecular weight of 134.13 g / mol, a melting point of 91 ° C and like all carbohydrates is very soluble in water (Royal Society of Chemistry, 2015).
Deoxyribose originates in the phosphate pentose pathway from 5-phosphate ribose by enzymes called ribonucleotide reductases. These enzymes catalyze the deoxygenation process (COMPOUND: C01801, S.F.).
Deoxyribose in DNA
As mentioned above, deoxyribose is a component of the DNA chain which gives it great biological importance. The DNA molecule (deoxyribonucleic acid), is the main repository of genetic information in life.
In standard nucleic acid nomenclature, a DNA nucleotide consists of a deoxyribose molecule with an organic base (usually adenine, thymine, guanine or cytosine) attached to the 1 'carbon.
The 5 'hydroxyl of each deoxyribose unit is replaced by a phosphate (which forms a nucleotide) which is attached to the 3' carbon of the deoxyribose in the preceding unit (Crick, 1953).
For the formation of the DNA strand first nucleoside formation is required. Nucleosides precede nucleotides. DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are formed by nucleotide chains.
A nucleoside is formed by a heterocyclic amine, called a nitrogenated and a sugar molecule that can be ribose or deoxyribose. When a phosphate group is connected to a nucleoside, the nucleoside is converted to a nucleotide.
The bases in DNA nucleoside precursors are adenine, guanine, cytosine and thymine. The latter substitutes uracil in the RNA chain. The deoxyribose sugar molecules bind to the bases in the precursors of nucleoside DNA.
DNA nucleosides are denoted adenosine, guanosine, thymidine and cytosine. Figure 6 illustrates the nucleoside structures of DNA.
Figure 6: Structure of nucleosides of DNA.
When a nucleoside acquires a phosphate group it becomes a nucleotide; One, two or three phosphate groups can bind to a nucleoside. Examples are adenine ribonucleoside monophosphate (AMP), adenine ribonucleoside diphosphate (ADP) and adenine ribonucleoside triphosphate (ATP).
Nucleotides (phosphate-linked nucleosides) are not only the basic components of RNA and DNA, they also serve as energy sources and transmitters of information in cells.
For example, ATP serves as an energy source in many biochemical interactions in the cell, GTP (guanosine triphosphate) provides energy for protein synthesis and cyclic AMP (cyclic adenosine monophosphate), a cyclic nucleotide, transduces signals in Hormonal responses and in the nervous system (Blue, SF).
Figure 7: Structure of a nucleotide.
For the case of DNA, the monophosphate nucleotides are linked through a fofodiester bond between the 5 'and 3' carbon of another nucleotide to form a strand of the strand as shown in Figure 8.
Figure 8: strand of the DNA strand conformed by nucleotides.
Subsequently, the strand formed by the nucleotides bound by the phosphodiester bond is attached to the complementary strand to form the DNA molecule as shown in Figure 9.
Figure 9: DNA strand.
Biological importance of deoxyribose
The configuration of the DNA strand is highly stable due in part to the stacks of the deoxyribose molecules.
The deoxyribose molecules interact by Van der Waals forces between them by means of permanent dipole interactions and dipoles induced by the oxygens of the hydroxyl (OH) groups conferring an additional stability to the DNA chain
The absence of the 2 'hydroxyl group in the deoxyribose is apparently responsible for the greater mechanical flexibility of the DNA compared to the RNA, which allows it to assume the double helix conformation, and also Eukaryotes ) Is tightly wound within the cell nucleus.
Double-stranded DNA molecules are also typically much longer than RNA molecules. The backbone of RNA and DNA are structurally similar, but the RNA is single-stranded and is made from ribose rather than deoxyribose.
Due to the lack of the hydroxyl group, DNA is more resistant to hydrolysis than RNA. The lack of the partially negative hydroxyl group also favors DNA over the RNA in stability.
There is always a negative charge associated with the phosphodiester bridges that bind two nucleotides that repel the hydroxyl group in the RNA, making it less stable than DNA (Structural Biochemistry / Nucleic Acid / Sugars / Deoxyribose Sugar, 2016).
Other biologically important derivatives of deoxyribose include mono-, di- and triphosphates, as well as 3'-5 'cyclic monophosphates. It should also be noted that the sense of the DNA strand is denoted as a function of the ribose carbons. This is particularly useful for understanding DNA replication.
As already noted, the DNA molecules are double stranded and the two strands are antiparallel, i.e. run in opposite directions. DNA replication in prokaryotes and eukaryotes occurs simultaneously in both chains.
However, there is no enzyme in any organism capable of polymerizing DNA in the 3 'to 5' direction, so that both newly replicated DNA strands can not grow in the same direction simultaneously.
However, the same enzyme reproduces both chains at the same time. The single enzyme replicates a strand ("conductive strand") in a continuous manner in the 5 'to 3' direction, with the same general direction of advancement.
It replicates the other strand ("delayed strand") discontinuously while polymerizing the nucleotides in short jets of 150-250 nucleotides, again in the 5 'to 3' direction, but at the same time faces towards the posterior end of the RNA Preceding Instead of the non-replicated portion.
Because the DNA strands are antiparallel, the enzyme DNA polymerase functions asymmetrically. In the main chain (forward), the DNA is continuously synthesized. In the delayed strand, the DNA is synthesized into short fragments (1-5 kilo bases), the so-called Okazaki fragments.
Several Okazaki fragments (up to 250) must be synthesized, in sequence, for each replication hairpin. To ensure this happens, the helicase acts on the delayed strand to unwind the dsDNA in a 5 'to 3' direction.
In the mammalian nuclear genome, most RNA primers are eventually removed as part of the replication process, whereas after replication of the mitochondrial genome the small part of RNA remains as an integral part of the closed circular DNA structure.
References
- Blue, M.-L. (S.F.). What is the Difference Between Nucleotide & Nucleoside? Retrieved from sciencing.com.
- Carr, S. M. (2014). Deoxyribose versus Ribose sugars . Recovered from mun.ca.
- COMPOUND: C01801 . (S.F.). Retrieved from genome.jp.
- Crick, J.D. (1953). A Structure for Deoxyribose Nucleic Acid. Nature . Retrieved from genius.com.
- EMBL-EBI. (2016, July 4). 2-deoxy-D-ribose . Retrieved from ebi.ac.uk.
- Encyclopædia Britannica. (1998, September 20). Deoxyribose . Retrieved from britannica.com.
- MURRAY, R.K., BENDER, D.A., & BOTHAM, K. M. (2013). Harper's Biochemistry 28th edition. Mcgraw-Hill.
- National Center for Biotechnology Information. . (2017, April 22). PubChem Compound Database; CID = 5460005 . Retrieved from pubchem.ncbi.nlm.nih.gov.
- Royal Society of Chemistry. (2015). 2-Deoxy-D-Ribose . Recovered from chemspider.com.
- Structural Biochemistry / Nucleic Acid / Sugars / Deoxyribose Sugar . (2016, September 21). Retrieved from wikibooks.org.