2.7: Nucleic Acids

Biotech Focus

Figure \(\PageIndex{1}\): Mary Maynard Daly. (CCO)

Marie Maynard Daly's early research provided key insights into how DNA is structured and regulated within the cell nucleus. She particularly identified the four nucleic acid bases of DNA (adenine, guanine, thymine and cytosine) leading the way to understanding the structure of DNA. She continued to make significant contributions to science by identifying histones, the proteins around which DNA is wrapped within cells and by researching the relationship between cholesterol and heart disease among others.

If you would like to know more, read: Marie Maynard Daly: A National Historic Chemical Landmark

Introduction

Nucleic acids are the most important macromolecules for the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Learning Objectives

By the end of this section, you will be able to:

• Describe the structure of nucleic acids and define the two types of nucleic acids
• Explain the structure and role of DNA
• Explain the structure and roles of RNA

DNA and RNA are Nucleic Acids

DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multi-cellular mammals. In eukaryotes, the majority of DNA is found in the nucleus, with smaller amounts found in the organelles, such as the chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope but is found in a section of the cytoplasm called the nucleoid. More about the structure and function of DNA can be found in Chapter 3.1 DNA Structure.

The other type of nucleic acid, RNA, plays critical roles in the gene expression and its regulation. In eukaryotic cells, because the DNA molecules never leave the nucleus, an intermediary nucleic acid is needed to communicate with the rest of the cell. This intermediary is RNA. There are several kinds of RNA, with more being discovered. The most studied RNA types are mRNA, tRNA, and rRNA - all of which play key roles in protein synthesis. For more about the the types of RNA and their functions, go to Chapter 3.3 Transcription of RNA.

Nucleotides are the Building Blocks of DNA and RNA

DNA and RNA are polymers known as polynucleotides. The building blocks of DNA and RNA are monomers called nucleotides.

Each nucleotide is made up of three components (Figure \(\PageIndex{2}\)):

1. a nitrogenous base
2. a pentose (five-carbon) sugar
3. a phosphate group

To build a nucleotide, the pentose sugar is linked to a specific nitrogenous base at its first carbon and to one or more phosphate groups at its fifth carbon. The base and sugar linked together are called a nucleoside. Adding the phosphate group(s) creates a nucleotide.

Figure \(\PageIndex{2}\): Nucleotide structure. Left image: a nucleotide is made up a nitrogenous base (green box), a pentose sugar (blue box), and one or more phosphate groups (pink box). Carbon residues in the pentose are numbered clockwise from the oxygen as 1 "prime" (1′) through 5 "prime" (5′) . The base attaches to the 1′ carbon of the pentose sugar, and the phosphate is attached to the 5′ carbon. Two types of pentose sugars are found in nucleotides, deoxyribose (DNA) and ribose (RNA). Top right image: the nitrogenous bases are classified as either purines and pyrimidines. The purine bases, adenine and guanine and the pyrimidine base, cytosine, are found in DNA and RNA. The pyrimidine base thymine is found only in DNA while the pyrimidine, uracil, is only found in RNA. Bottom right image: deoxyribose is similar in structure to ribose, but it has an H instead of an OH at the 2′ position. (Nucleotide Structure by Patricia Zuk, CC BY 4.0; modified from Molecular structure of a nucleotide by Openstax, CC BY-NC 4.0)

The nitrogenous bases are organic molecules containing carbon and nitrogen. Because of the presence of an amino group with the potential of binding an extra hydrogen, the nitrogenous base is capable of decreasing the hydrogen ion concentration in its environment, thus acting as a base. The nitrogenous bases of nucleic acids are adenine (A), guanine (G) cytosine (C), thymine (T), and uracil. These nitrogenous bases are classified as either purines or pyrimidines. The primary structure of a purine (i.e. adenine and guanine) is two carbon-nitrogen rings, while the pyrimidine (cytosine, thymine, uracil) has a single carbon-nitrogen ring (Figure \(\PageIndex{2}\)). The nitrogenous base is specific to the nucleic acid. DNA contains A, T, G, and C, whereas RNA contains A, U, G, and C.

The pentose sugar in DNA is called deoxyribose, and in RNA, the sugar is ribose. The carbon atoms of the sugar are numbered clockwise from the oxygen within the ring. They are numbered from 1′ to 5′ (e.g. 1′ is read as “one prime”). The use of the term "prime" to number the carbons in the pentose sugar is meant to distinguish between these carbons and those found in the rings of the nitrogenous base. While the overall structure of deoxyribose and ribose are the same, there is an important difference - deoxyribose lacks an oxygen at the 2' carbon.

DNA and RNA nucleotides are named based on the nitrogenous base, the type of sugar and the number of phosphate groups. For example, adenosine triphosphate (ATP) is an RNA nucleotide with an adenine base and three phosphate groups attached to the ribose sugar. The DNA nucleotide counterpart would be deoxynucleotide triphosphate (dATP). If these nucleotides have only one phosphate group bound to the pentose sugar, they would be named adenosine monophosphate (AMP) and deoxynucleotide monophosphate (dAMP), respectively. Table \(\PageIndex{1}\) below summarizes the nomenclature for DNA and RNA nucleotides.

Table \(\PageIndex{1}\): Nucleotide Nomenclature

Nucleoside Name	Number of phosphates	Abbreviation	Name
adenosine/deoxyadenosine	1 2 3	AMP/dAMP ADP/dADP ATP/dATP	adenosine monophosphate/deoxyadenosine monophosphate adenosine diphosphate/deoxyadenosine diphosphate adenosine triphosphate/deoxyadenosine diphosphate
guanosine/deoxyguanosine	1 2 3	GMP/dGMP GDP/dGDP GTP/dGTP	guanosine monophosphate/deoxyguanosine monophosphate guanosine diphosphate/deoxyguanosine diphosphate guanosine triphosphate/deoxyguanosine triphosphate
cytidine/deoxycytidine	1 2 3	CMP/dCMP CDP/dCDP CTP/dCTP	cytidine monophosphate/deoxycytidine monophosphate cytidine diphosphate/deoxycytidine diphosphate cytidine triphosphate/deoxycytidine triphosphate
deoxythymidine (found in DNA only)	1 2 3	dTMP dTDP dTTP	deoxythymidine monophosphate deoxythymidine diphosphate deoxythymidine triphosphate
uridine (found in RNA only)	1 2 3	UMP UDP UTP	uridine monophosphate uridine diphosphate uridine triphosphate

Phosphodiester Bonds Join Nucleotides

Nucleotides join to one another through phosphodiester bonds (Figure \(\PageIndex{3}\)). In phosphodiester bond formation, the hydroxyl on the 3' carbon of one nucleotide forms a bond with the phosphate group closest to the pentose sugar in another nucleotide. When the diphosphate or triphosphate forms of the nucleotides are used in this reaction, water is not released and it is not considered a dehydration synthesis reaction. However, if a monophosphate nucleotide is used, water is removed through dehydration synthesis. When forming DNA and RNA, the phosphodiester bond forms in a specific direction. Specifically, the bond forms between the phosphate group(s) of an incoming nucleotide and the 3' hydroxyl of the existing polynucleotide chain. Because of this, one end of a nucleic acid has an exposed phosphate group and is named the "5' end" while the other end has a 3' hydroxyl and is called the "3' end". The phosphodiester bond is said to form "in the 5' to 3' direction".

Figure \(\PageIndex{3}\): The phosphodiester bond forms in a specific direction. Left image: the addition of the monophosphate form of the nucleotide (bottom) to a nucleotide chain (top) via a phosphodiester bond. Bond formation involves the removal of a water molecule (atoms shown in blue). Right image: the addition of the triphosphate form (bottom) to the nucleotide chain (top). The phosphodiester bond forms as a result of a "nucleophilic attack" by the 3' OH group (blue) on the first phosphate group of the incoming nucleotide. This attack removes the remaining two phosphate groups (green). The atoms involved in the phosphodiester bond are shown in red. The direction of phosphodiester bond formation from 5' to 3' is indicated with an arrow. (Phosphodiester bond by Patricia Zuk, CC BY 4.0)

DNA is Double-Helix Structure

DNA exists as a double-helix (Figure \(\PageIndex{4}\)), consisting of two long strands of DNA polynucleotides that twist like a "spiral staircase". In the DNA helix, the sugars and phosphates are found on the outside of the helix, not unlike the rails of the spiral staircase. The nitrogenous bases project to the interior of the helix, like the steps. The two polynucleotide strands of the helix run in opposite directions, or anti-parallel to one another, meaning that the 5′ end of one strand will be next to the 3′ end of the other strand. The bases from each nucleotide chain pair up with one another and are bound to each other by hydrogen bonds. This base pairing is restricted in the DNA helix and is known as complementary base pairing. In this pairing scheme, purines pair with pyrimidines. Specifically, adenine (A, the purine) pairs with thymine (T, the pyrimidine) through the formation of two hydrogen bonds and guanine (G, the purine) pairs with cytosine (C, the pyrimidine) through the formation of three hydrogen bonds. What results is a DNA helix in which the two DNA strands are complementary to each other. This complementary base pairing has implications for cellular processes like DNA replication. During DNA replication, each of the DNA strands are "copied" to produce two new DNA helices. However, the term copy is misleading, as a identical copy is not made rather a complementary copy is. For example, if the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG. For more information about DNA replication, read Chapter 3.2 Replication of DNA.

Figure \(\PageIndex{4}\): The DNA Helix. (A) Two phosphate-sugar backbones (curved blue lines) run on the outside of the DNA helix with the bases (adenine, thymine, guanine, cytosine) projecting to the inside. The two DNA strands run "anti-parallel" to one another. (B) Each base from one strand interacts with a "complementary" base from the opposing strand via hydrogen bonding (dotted black lines); adenine pairs with thymine and cytosine pairs with guanine. (DNA Helix by Jerome Walker and Denis Myts, Concepts of Biology; CC BY-SA 4.0)

Comparison between DNA and RNA

Like DNA, RNA is a polynucleotide chain made up of nucleotides joined by phosphodiester bonds that form in the 5' to 3' direction. However, RNA does differ from DNA in several aspects. Table \(\PageIndex{2}\) below outlines these differences.

Table \(\PageIndex{2}\): Differences between DNA and RNA

	DNA	RNA
Function	Stores and carries genetic information	Transfers genetic information; involved in protein synthesis
Types	One type	Several types
Location	Mostly in the nucleus; some in organelles	Nucleus and cytoplasm
Structure	Double-stranded; forms a helix	Usually single-stranded
Pentose Sugar	Deoxyribose (lacks an oxygen at the 2' carbon)	Ribose (has an oxygen at the 2' carbon
Pyrimidine bases	Cytosine, thymine	Cytosine, uracil
Purine bases	Adenine, guanine	Adenine, guanine

Key Concepts

DNA and RNA comprise the two types of nucleic acids found in cells. DNA provides the code for a cell's activities, while RNA is involved in translating that code into proteins that carry out these activities.

Some important concepts to remember:

• Both DNA and RNA are made from nucleotides
• Nucleotides contain a five-carbon sugar backbone, one to three phosphate groups, and a nitrogenous base.
• Nucleotides are joined to one another by a phosphodiester bond.
• Phosphodiester bonds form in the 5' to 3' direction.
• The bases of nucleic acids are adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U).
• The bases of DNA are A, G, C, and T; the bases of RNA are A, G, C, U.
• Bases are classified as purines (A, G) or pyrimidines (C, T, U)
• The nitrogen bases A pairs with its complementary base T (or U in RNA); the base C pairs with its complement G
• DNA is found as a double-stranded helix, made of two "anti-parallel" DNA strands
• Most RNA is single-stranded

Glossary

Adenine (A) - a nitrogenous base found in DNA and RNA; pairs with thymine (T) in DNA and uracil (U) in RNA.

Anti-parallel - the orientation of the two strands of DNA in opposite directions, one running 5' to 3' and the other 3' to 5'.

Complementary base pairing - the specific hydrogen bonding between complementary nitrogenous bases in nucleic acids (A-T/U, C-G).

Cytosine (C) - a nitrogenous base found in DNA and RNA; pairs with guanine (G).

Deoxyribonucleic Acid (DNA) - a double-stranded nucleic acid that carries genetic information and directs cellular functions.

Deoxyribose - the five-carbon sugar found in DNA; lacks an oxygen atom at the 2' carbon.

Double helix - the spiral-shaped structure of DNA, consisting of two complementary strands.

Guanine (G) - a nitrogenous base found in DNA and RNA; pairs with cytosine (C).

Hydrogen bond - a weak bond found between the positively-charged hydrogen of one molecule and a negatively-charge atom of another molecule (usually O or N); holds complementary nitrogenous bases together in DNA and RNA.

Nitrogenous base - an organic molecule found bound to the pentose sugar of a nucleic acid.

Nucleic Acid - a macromolecule composed of nucleotides, essential for storing and transmitting genetic information (DNA and RNA).

Nucleotide - the basic building block of nucleic acids, consisting of a nitrogenous base, a sugar, and a phosphate group.

Pentose sugar - a 5-carbon sugar.

Phosphate group - a functional group that links nucleotides together in the sugar-phosphate backbone of nucleic acids.

Polymer - a large molecule made up of repeating units called monomers

Purines - a category of nitrogenous bases with a double-ring structure; adenine (A) and guanine (G).

Pyrimidines - a category of nitrogenous bases with a single-ring structure; cytosine (C), thymine (T), and uracil (U).

Ribonucleic Acid (RNA) - a single-stranded nucleic acid involved in protein synthesis and gene expression.

Ribose - the five-carbon sugar found in RNA; has an oxygen atom at the 2' carbon.

Sugar-Phosphate backbone - the repeating structure of sugar and phosphate groups that forms the framework of DNA and RNA strands.

Thymine (T) - a nitrogenous base found in DNA; pairs with adenine (A); replaced by uracil (U) in RNA.

Uracil (U) - a nitrogenous base found only in RNA; pairs with adenine (A) instead of thymine.