Compare the Phosphates Sugars and Bases of DNA and RNA

DNA and RNA are nucleic acids, which are basically made up of a nitrogenous base containing pentose sugars linked via phosphate groups. The building blocks of nucleic acids are called nucleotides. Nucleic acids serve as the cell’s genetic material by storing information, which is required for the development, functioning, and reproduction of organisms. Most organisms use DNA as their genetic material, while few of them like retroviruses use RNA as their genetic material. DNA is stable when compared to RNA due to the differences in phosphate sugars and bases shared by each of them.  One, two or three phosphate groups can be attached to the pentose sugar, producing mono-, di- and triphosphates respectively. Pentose sugar used by DNA is deoxyribose and the pentose sugar used by RNA is ribose. Nitrogenous bases found in DNA are adenine, guanine, cytosine and thymine. In RNA, thymine is replaced by uracil.

This article looks at,

1. What are Phosphates
2. What are Sugars
3. What are Bases
4. Comparison of Phosphates Sugars and Bases of DNA and RNA
      – Similarities
      -Differences

What are Phosphates

DNA and RNA are made up of repeating units of nucleotides; deoxyribonucleotides and ribonucleotides, respectively. Nucleotide is made up of a pentose sugar, which is attached to a nitrogenous base and one, two or three phosphate groups. Both DNA and RNA nucleotides can attach to one, two or three phosphate groups on their 5′ carbon of the pentose sugar. Phosphate-bound nucleosides are called mono-, di- and triphosphates, respectively. The phosphorylation reactions are catalyzed by a class of enzymes called ATP:D-ribose 5-phosphotransferase. Deoxyribonucleosides are phosphorylated by the enzyme called deoxyribokinase and RNA nucleosides are phosphorylated by the enzyme called ribokinase. The formation of phosphodiester bonds during the production of sugar-phosphate backbone is energized by cutting the high energy phosphate bonds in the nucleotide triphospahates. The formation of each nucleotide, nucleoside monophosphate, nucleoisde diphosphate and nucleoside triphosphate is shown in figure 1.

Figure 1: Three nucleotide types

What are Sugars

Both DNA and RNA contain pentose sugars. Deoxyribonucleotides contain deoxyribose and ribonucleotides contain ribose as their pentose sugars. Ribose is a pentose monosaccharide, containing a five-membered ring in its structure. It contains an aldehyde functional group in its open chain form. Hence, ribose is called aldopentose. Ribose contains two enantiomers: D-ribose and L-ribose. The naturally occurring conformation is D-ribose, where L-ribose is not found in nature. D-ribose is an epimer of D-arabinose, which differ by the stereochemistry at the 2′.carbon. This 2’ hydroxyl group is important in RNA splicing.

The pentose sugar found in DNA is deoxyribose. Deoxyribose is a modified form of the sugar, ribose. It is formed from ribose 5-phosphate by the action of the enzyme, ribonucleotide reductase. An oxygen atom is lost while forming deoxyribose from the second carbon atom of the ribose ring. Hence, deoxyribose is more precisely called 2-deoxyriose. The 2-deoxyribose contains two enantiomers: D-2-deoxyribose and L-2-deoxyribose. Only D-2-deoxyribose is involved in the formation of DNA backbone. Due to the absence of 2’ hydroxyl group in deoxyriboses, DNA is capable of folding into its double-helix structure, increasing the mechanical flexibility of the molecule. DNA can be tightly coiled in order to pack into a small nucleus as well. The difference between ribose and deoxyribose is with the 2’ hydroxyl group present in ribose. Deoxyribose, when compared to ribose is shown in figure 2.

Figure 2: Deoxyribose

What are Bases

Both DNA and RNA are attached to a nitrogenous base on 1’ carbon of the pentose sugar, replacing the hydroxyl group of deoxyribose. Five types of nitrogenous bases are found in both DNA and RNA. They are adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U).  Adenine and guanine are purines, which are found in two ring structured pyrimidine ring fused with an imidazole ring. Cytosine, thymine, and uracil are pyrimidines, which contain a single six-membered pyrimidine ring structure. DNA contains adenine, guanine, cytosine and thymine in its nucleotides. RNA contains uracil, instead of thymine. Adenine forms two hydrogen bonds with thymine and guanine forms three hydrogen bonds with cytosine. The complementary base pairing in DNA is called Watson-Crick DNA base pairing model. It brings two complementary DNA strands together, forming hydrogen bonds. Hence, the final structure of DNA is double-stranded and antiparallel. In RNA, uracil forms two hydrogen bonds with adenine, replacing thymine. The complementary base pairing of RNA within the same molecule form double-stranded RNA structures called hairpin loops. The double-stranded DNA is shown in figure 3.

Figure 3: DNA

The difference between thymine and uracil is in the methyl group present in the 5’ carbon atom of thymine. Uracil is capable of base pairing with other bases as well in addition adenine and the deamination of cytosine can produce uracil. Therefore, RNA is less stable when compared to DNA due to the presence of uracil instead of thymine. Uracil and thymine are shown in figure 4.

Figure 4: Uracil and thymine

Comparison of the Phosphates Sugars and Bases of DNA and RNA

Similarities Between Phosphates Sugars and Bases of DNA and RNA

Phosphates

• Both DNA and RNA contain one, two or three phosphate groups, attached to the 5′ carbon of the pentose sugar.

Pentose sugar

• Both DNA and RNA contain a pentose monosaccharide in their nucleotides, which is attached to a nitrogenous base and one, two or three phosphate groups.

Nitrogenous bases

• Both DNA and RNA share three types of nitrogenous bases: adenine, guanine, and cytosine.

Differences Between Phosphates Sugars and Bases of DNA and RNA

Pentose Sugar

DNA: The pentose sugar found in DNA is deoxyribose.

RNA: The pentose sugar found in RNA is ribose.

Conformation of the Sugar

DNA: D-2-deoxyribose is found in the sugar-phosphate backbone of DNA.

RNA: D-ribose is found in the sugar-phosphate backbone of RNA.

Significance of the Pentose Sugar in DNA/RNA

DNA: The 2-deoxyribose allows the formation of DNA double-helix.

RNA: Ribose does not allow the formation of an RNA double-helix due to the presence of 2’ hydroxyl group.

Thymine/Uracil

DNA: Thymine is found in DNA.

RNA: Uracil is found in RNA.

Significance of Thymine/Uracil

DNA: DNA is more stable than RNA due to the presence of thymine.

RNA: RNA is less stable due to the presence of uracil instead of thymine.

Phosphorylation

DNA: Deoxyribonucleosides are phosphorylated by deoxyribokinases.

RNA: Ribonucleosides are phosphorylated by ribokinases.

Phosphorylation Produces

DNA: Phosphorylation of deoxyribonucleosides produces deoxyribonucleotides.

RNA: Phosphorylation of ribonucleosides produces ribonucleotides.

Conclusion

Both DNA and RNA consist of a pentose sugar, which is attached to a nitrogenous base on the 1’ carbon and one or more phosphate groups to the 5’ carbon. The sugar-phosphate backbone of both nucleic acids types is formed by the polymerization of nucleotides via phosphate groups. The pentose sugar found in the sugar-phosphate backbone of DNA is D-2-deoxyribose. D-ribose is found in RNA. The nitrogenous bases found in DNA are adenine, guanine, cytosine and thymine. In RNA, uracil is found, replacing the thymine. One, two or three phosphate groups are found attached to the pentose sugar. When one phosphate group is attached to the nucleoside, it is called nucleotide monophosphate. When two phosphate groups are attached to the nucleoside, it is called nucleotide diphosphate. When three phosphate groups are attached to the nucleoside, it is called nucleotide triphosphate.

Reference:
1.”Class Notes.” The Basics: DNA, RNA, Protein. N.p., n.d. Web. 28 Apr. 2017.
2.”Structure of Nucleic Acids.” SparkNotes. SparkNotes, n.d. Web. 28 Apr. 2017.
3.”Why thymine instead of uracil?” Earthling Nature. N.p., 17 June 2016. Web. 28 Apr. 2017.

Image Courtesy:
1.”Nucleotides 1″ By Boris (PNG), SVG by Sjef – en:Image:Nucleotides.png (Public Domain) via Commons Wikimedia
2.”DeoxyriboseLabeled” By Adenosine (English Wikipedia User) – English Wikipedia (CC BY-SA 3.0) via Commons Wikimedia
3. “DNA Nucleotides” By OpenStax College – Anatomy & Physiology, Connexions Web site.  Jun 19, 2013 (CC BY 3.0) via Commons Wikimedia
4. “Pyrimidines2” By Mtov – Own work (Public Domain) via Commons Wikimedia