Comparing RNA and DNA

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are both made from nucleic acid subunits and, although they have many similarities, they are different in four important areas. While DNA has thymine as one of its bases, RNA has uracil. While DNA is a triple helix, RNA is single-stranded. While DNA has deoxyribose as its sugar base, RNA has ribose as its sugar base. Finally, DNA is only found within the nucleus of prokaryotic cells while RNA is typically found in the cytoplasm of cells; RNA can be found in the nucleus of a cell, however, as messenger RNA (mRNA) during the transcription step of protein synthesis. Interestingly, eukaryotic cells have no nucleus and so DNA must be in the cytoplasm, and human red blood cells are anucleate and do not have DNA in them. We can look into more detail at each of these differences to discover the similarities between DNA and RNA.

Both DNA and RNA are composed of individual nucleic acids, which are in turn composed of three smaller constituents, the nitrogenous bases, the five-carbon sugar rings, and the phosphate groups. The phosphate groups in both DNA and RNA are the same, consisting of one phosphorous with three single bonds to three oxygens and with one double bond to a fourth bond. Each of the single-bonded oxygens has a negative charge on it while the double-bonded oxygen has no charge. In RNA, the carbon sugar ring is ribose. In DNA, the carbon sugar ring is the pentose deoxyribose, which is a four carbon ring that does not have the same hydroxyl on the second carbon as does RNA, and which has a methyl group off the fifth carbon. The nitrogenous bases consist of two subtypes, pyrimidines and purines. Pyrimidines are single-ring structures with six carbons and two nitrogens. In DNA, the pyrimidines found are cytosine (C) and thymine (T) while the purines found are guanine (G) and adenine (A). In RNA, the purines found are guanine (G) and adenine (A) are also found, and the pyrimidine cytosine (C) is present, but thymine (T) is replaced by uracil (U). Uracil (U) is similar to thymine except that the methyl group at the fifth carbon position of thymine has been deleted. In both DNA and RNA, nucleosides are formed when a nitrogenous base forms a glycosidic bond to the first carbon on the sugar ring, and then nucleotides are formed when the hydroxyl group of the fifth carbon of the sugar forms an ester bond with the phosphate group, creating 5’-monophosphate nucleotides. Finally, polymers of nucleotides are formed when the hydroxyl group on the third carbon of the first sugar combines with the phosphate group on the fifth carbon of the second sugar. These phosphodiester bonds create long chains of nucleotides in which one end has an unreacted 5’ phosphate terminal group and the opposite end has an unreacted 3’ hydroxyl group.

The structure of DNA has been highly studied and many theories have been offered over the years about its structure. In 1928, Phoebus Levene theorized that the nucleic acids were organized in a circular molecule which he referred to as a “tetranucleotide.” In 1951, Erwin Chargaff presented research from which he concluded that the ratio of purines to pyrimidines as always one-to-one, and more specifically, that adenine to thymine and cytosine to guanine were always one-to-one ratios. Today, this biochemical concept of complementarity is known as Chargaff’s Law. In 1953, Linus Pauling presented his theory that DNA was a triple helix, causing many modern biologists to smirk when they discuss the triple helix tertiary structure of proteins. After Rosalind Franklin’s x-ray diffractions of DNA were done, however, the thinking about DNA structure began to change. Although she was never acknowledged with a Nobel Prize, her research and photomicrographs played a great part in the early 1950’s discovery by Francis Crick and James Watson of the currently accepted double helix theory of DNA structure. According to Crick and Watson, DNA is arranged in such a way that there are two strands of DNA, with the nitrogenous bases on the inside like ladder rungs and with alternating sugar-phosphate sides to the ladder-like helix. Following Chargaff’s Law, there is complementary base pairing between the nitrogenous bases so that adenine and thymine are always connected by two hydrogen bonds and cytosine and guanine are always connected by three hydrogen bonds. In addition, while one strand of DNA runs in a 5’ to 3’ direction, the opposite strand will run in a 3’ to 5’ direction, so that the final helical structure will give a right-handed spiral. Instead of a rigid double helix structure, RNA exists as a more flexible single strand that can fold on itself to give complex shapes.

While DNA always exists as long chains of nucleic acids within the nucleus (with the above noted exception of eukaryotic cells), RNA exists in three different forms and may be in either the nucleus or in the cytoplasm of a cell. Messenger RNA, mRNA, is a smaller unit of RNA that transfers genetic information from the DNA to the ribosome, serving as a translator in the process of protein synthesis. Due to complementary base pairing and the existing nucleotides, a strand of DNA that reads AATTCCGGATCG would result in a strand of mRNA that reads UUAAGGCCUAGC. After going through an editing process that removes nonessential introns while retaining and splicing the essential exons, mRNA exits the nucleus and enters the cytoplasm to join with transfer RNA, tRNA, at the ribosome. The ribosome is the site of protein synthesis, and it is made of ribosomal RNA, rRNA, combined with proteins in one small and one large subunit that join to read a string of mRNA. During the transcription step of protein synthesis, tRNA’s are joined to mRNA’s at the ribosome. Transfer RNA’s, tRNA’s, interpret the genetic code on mRNA into amino acid sequences through complementary base pairing on the mRNA codon and the tRNA anticodon. The codon and anticodon are three unit areas that code for specific amino acids. Due to the complementary base pairing, an mRNA string that reads UUA-AGG-CCU-AGC would connect to first an AAU tRNA, then a UCC tRNA, then a GGA tRNA, and finally a UCG tRNA, and each tRNA will have its own unique amino acid attached to the acceptor region of its cloverleaf stem. It is important to note that while a ribosome may only work on one mRNA at a time, there may be multiple ribosomes working on a single mRNA simultaneously, forming a polysome. After being read, mRNA’s may be broken down into units or may be re-read repeatedly until the cell has enough of the protein for which the mRNA codes. After reading an mRNA, the ribosome and its rRNA will fall into the small and large subunits and will reconnect on a separate mRNA strand. After delivering an amino acid to the growing polypeptide on the ribosome, the tRNA will attach to a new free amino acid within the cytoplasm and then will attach to the same or a different mRNA, and repeat the cycle of protein synthesis.

DNA only Both DNA and RNA RNA only
Cytosine, Adenine, Guanine, and Thymine Nitrogenous bases that are pyrimidines or purines Cytosine, Adenine, Guanine, and Uracil
Deoxyribose Five carbon sugar rings Ribose
Phosphate groups
Nucleosides with glycosidic bonds
CMP, AMP, GMP, TMP 5’-monophosphate nucleotides CMP, AMP, GMP, UMP
Phosphodiester bonds between units
Double helix that is right-handed and runs antiparallel Single strand
Chargoff’s Law within DNA; DNA to mRNA Complementary base pairing DNA to mRNA; mRNA codon to tRNA anticodon
Found in nucleus only – not found in red blood cells (anucleate cells) Found in cytoplasm – except mRNA during transcription
Single type – DNA – carries genetic information Function in protein synthesis Three types – messenger RNA (mRNA); ribosomal RNA (rRNA); transfer RNA (tRNA) – with three distinct functions

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