3.3 Nucleic Acid Structure and Function

Melissa Hardy; Christelle Sabatier

3.3 Nucleic Acid Structure and Function

Melissa Hardy and Christelle Sabatier

Learning Objectives

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

Describe nucleic acids’ structure
Define the two types of nucleic acids (DNA and RNA)

DNA and RNA

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell’s genetic blueprint and carry instructions for its functioning.

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes, and in the chloroplasts and mitochondria, two membrane-bound organelles. In prokaryotes, the DNA is not enclosed in a membrane-bound organelle.

The other type of nucleic acid, RNA, has many roles in the cell. One type of RNA, called messenger RNA (mRNA) carries information from DNA to ribosomes. Other types of RNA—like ribosomal RNA (rRNA), transfer RNA (tRNA), and microRNA (miRNA) — are involved in protein synthesis and its regulation.

Video 3.4. Central Dogma of Biology by BioCASTS

Nucleotides

DNA and RNA are comprised of monomers called nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Three components comprise each nucleotide: a nitrogenous base, a pentose (five-carbon) sugar, and one or more phosphate groups. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

Figure 3.7. Three components comprise a nucleotide: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbon residues in the pentose are numbered 1′ through 5′ (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the ribose’s 1′ position, and the phosphate is attached to the 5′ position. When a polynucleotide forms, the incoming nucleotide’s 5′ phosphate attaches to the 3′ hydroxyl group at the end of the growing chain. Two types of pentose are in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an H instead of an OH at the 2′ position. We can divide nitrogenous bases into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring. (Figure by OpenStax is used under a Creative Commons Attribution license). [Image Description]

The nitrogenous bases are organic molecules that contain nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen and thus decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).

Scientists classify adenine and guanine as purines. The purine’s primary structure is two carbon-nitrogen rings. Scientists classify cytosine, thymine, and uracil as pyrimidines which have a single carbon-nitrogen ring as their primary structure. Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, we use the symbols A, T, G, C, and U for the nitrogenous bases. DNA contains A, T, G, and C; whereas, RNA contains A, U, G, and C.

Nucleotide structures of DNA and RNA nucleotides (linked Image Description available)

Figure 3.8. The nucleotides that make up DNA and RNA. Notice that each has a phosphate group and a pentose sugar. In deoxyribonucleotides, this sugar is deoxyribose. In ribonucleotides, this sugar is ribose. Each nucleotide has a nitrogen-containing base — A, C, G, or T for monomers of DNA, and A, C, G, or U for monomers of RNA. (Nucleotides by Melissa Hardy is in the public domain). [Image Description]

The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose’s second carbon and hydrogen on the deoxyribose’s second carbon. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”).

Polynucleotides

A phosphate residue connects the 5′ carbon of one sugar to the 3′ carbon of the sugar of the next nucleotide, which forms a 5′–3′ phosphodiester linkage. A polynucleotide may have thousands or even millions of phosphodiester linkages.

In a polynucleotide, one end of the chain has a free 5′ phosphate, and the other end has a free 3′-OH. These are called the 5′ and 3′ ends of the chain.

DNA chemical structure (linked Image Description available)

Figure 3.9. The chemical structure of a four base pair fragment of DNA. Notice that adenine pairs with thymine via two hydrogen bonds, while cytosine pairs with guanine via three hydrogen bonds. The strands run antiparallel to one another. (DNA Chemical Structure by Thomas Shafee is used under a Creative Commons Attribution license). [Image Description]

The Double Helix

DNA has a double-helix structure. The sugar and phosphate lie on the outside of the helix, forming the DNA’s backbone. The nitrogenous bases are stacked in the interior, like a pair of staircase steps. Hydrogen bonds bind the pairs to each other. Every base pair in the double helix is separated from the next base pair by 0.34 nm. There are about 10 base pairs per turn of the double helix. The helix’s two strands are antiparallel, meaning that they run in opposite directions.

Figure 3.10. A fragment of double-stranded DNA rotates, showing the double-helix structure. The sugar-phosphate backbones are on the outside, and the base pairs are between them. (DNA animation by Brian 0918 is in the public domain). [Image Description]

Base pairing is specific. A can pair with T, and G can pair with C. This is the base complementary rule. In other words, the DNA strands are complementary to each other. If the sequence of one strand is 5′-AATTGGCC-3′, the complementary strand would have the sequence 3′-TTAACCGG-5′.

Video 3.5. The Structure of DNA by MITx Bio

Figure Descriptions

Figure 3.7. The image is a detailed schematic representation of nucleotide components and their structures. At the top, there are two sections labeled “Pyrimidines” and “Purines” with illustrations of their chemical structures. The pyrimidines section includes structures for Cytosine, Thymine, and Uracil, each labeled with their molecular structure. The purines section contains Adenine and Guanine, also showing their molecular structure. Below these sections is a central box labeled “Base” containing a generalized structure for a nitrogenous base linking it to a pentose sugar, labeled as “Deoxyribose or ribose sugar.” This sugar structure includes both deoxyribose and ribose configurations, highlighting differences at the 2′ position. To the left, a small box labeled “Phosphate” shows a phosphate group structure as part of the nucleotide. At the bottom, two separate boxes depict the structural differences between “Deoxyribose (in DNA)” and “Ribose (in RNA)” with emphasis on the 2′ carbon. On the right, there is a combination structure showing how the phosphate, sugar, and base are connected. It highlights the 5′, 3′, and 2′ carbon positions in red, with the sugar being a part of a larger nucleotide chain. [Return to Figure 3.7]

Figure 3.8. Left panel – “Nucleotides present in DNA.” Four deoxyribonucleotides are shown, each with a phosphate group on the left, a five-carbon deoxyribose sugar in the center (highlighted with thicker bond lines), and a nitrogenous base on the right. From top to bottom they are: Deoxyadenosine monophosphate (dAMP) – adenine base; Deoxycytidine monophosphate (dCMP) – cytosine base; Deoxyguanosine monophosphate (dGMP) – guanine base; Deoxythymidine monophosphate (dTMP) – thymine base. Each sugar lacks the 2′-hydroxyl group characteristic of ribose. Right panel – “Nucleotides present in RNA.” Four ribonucleotides are shown with the same general layout, but their sugars retain the 2′-hydroxyl group. From top to bottom they are: Adenosine monophosphate (AMP) – adenine base. Cytidine monophosphate (CMP) – cytosine base. Guanosine monophosphate (GMP) – guanine base. Uridine monophosphate (UMP) – uracil base (RNA’s substitute for thymine). Across both panels, the diagram highlights that every nucleotide consists of: one phosphate group (negatively charged), one pentose sugar (deoxyribose in DNA, ribose in RNA), and one nitrogen-containing base (A, C, G, T, or U). No color is used; structural details are conveyed with black lines and labels. [Return to Figure 3.8]

Figure 3.9. This diagram presents a four-base-pair fragment of double-stranded DNA displayed horizontally, with the antiparallel strands running left-to-right along the top and right-to-left along the bottom; each strand shows a repeating sugar-phosphate backbone (black pentagons and circles) and, extending inward, color-coded nitrogenous bases—adenine (red), thymine (pink), cytosine (dark blue), and guanine (light blue). Adenine on the upper strand forms two dashed hydrogen-bond lines with thymine on the lower strand, while cytosine forms three dashed hydrogen-bond lines with guanine, clearly illustrating the A–T and C–G pairing rules and the difference in hydrogen-bond number. Labels identify the 5′ and 3′ ends on both strands to emphasize their antiparallel orientation, and a small legend at the right matches each base’s color and shape to its name. [Return to Figure 3.9]

Figure 3.10. The looping GIF depicts a short fragment of double-stranded DNA rendered as a ball-and-stick model on a black background; as the molecule slowly rotates about its vertical axis, a right-handed double helix of roughly a dozen base pairs becomes visible, with two spiraling sugar-phosphate backbones on the outside—each alternating gray-and-white five-carbon sugar rings and orange-red phosphate groups—and flat, ladder-like rungs of complementary nitrogenous base pairs in blue and green tones spanning between them. The continuous rotation highlights the wider major groove and narrower minor groove, shows how the backbones shield the interior bases, and emphasizes the repeating twist along the molecule’s length, conveying the same instructional detail without narration or reliance on color alone. [Return to Figure 3.10]

Text adapted from OpenStax Biology 2e and used under a Creative Commons Attribution License 4.0.

Access for free at https://openstax.org/books/biology-2e/pages/1-introduction

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3.3 Nucleic Acid Structure and Function Copyright © by Melissa Hardy and Christelle Sabatier is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, except where otherwise noted.