Learning Objectives:

After completing this chapter, you will be able to:

• • Identify and describe the three components of a nucleotide.
  • Distinguish between the structures of deoxyribose and ribose.
  • List the nitrogenous bases found in DNA and RNA and identify them as purines or pyrimidines.
  • Explain the formation of a phosphodiester bond and the resulting 5′ to 3′ directionality of a nucleic acid strand.
  • Describe the key features of the DNA double helix, including anti-parallel strands, complementary base pairing, and hydrogen bonding.

Nucleic Acid Structure: The Building Blocks of Life

Welcome to this review of nucleotide structure and how these fundamental units assemble into deoxyribonucleic acid, or DNA, a molecule essential for life as we know it. This information builds upon concepts typically introduced in introductory biology courses.

Nucleic acids are one of the four major classes of biological macromolecules crucial for constructing all living things, from single cells to complex organisms. The other three macromolecules are carbohydrates (sugars), lipids (fats), and proteins. Our focus here is on nucleic acids.

Nucleic acids are polymers, meaning they are large molecules built from repeating smaller units called nucleotides. Each nucleotide comprises three key components:

• A Pentose (5-carbon) Sugar: Located at the center of the nucleotide molecule.
• A Nitrogenous Base (or Base): Attached to one side of the sugar.
• A Phosphate Group: Linked to the other side of the sugar. A nucleotide can have one, two, or three phosphate groups, depending on its specific role.

As mentioned, nucleotides serve as the building blocks for nucleic acids. The two primary types of nucleic acids you’ve likely encountered are DNA and RNA (ribonucleic acid). While both are constructed from nucleotides, the specific structure of the nucleotides used, and how they are arranged, differs.

Key Differences in Nucleotides for DNA and RNA

The nucleotides that make up DNA and RNA exhibit two main differences: the sugar component and the nitrogenous bases they contain.

1. The Sugar:

• The sugar in DNA nucleotides is called deoxyribose. The prefix “deoxy-” indicates that it lacks one oxygen atom compared to the sugar found in RNA.
• The sugar in RNA nucleotides is ribose.

2. The Nitrogenous Bases:

There are five primary nitrogenous bases found in nucleic acids. Four of these are present in DNA, and four are present in RNA, with one difference between the two. These bases are categorized into two groups:

• Purines: Adenine (A) and Guanine (G) – these have a double-ring structure.
• Pyrimidines: Cytosine (C), Thymine (T), and Uracil (U) – these have a single-ring structure.
• Mnemonic device for remembering: purines (“Pure As Gold” – Purines are Adenine and Guanine) or pyrimidines (“CUT the Pie” – Cytosine, Uracil, Thymine are Pyrimidines)

The specific bases found in DNA and RNA are:

• DNA: Contains the bases Adenine (A), Guanine (G), Cytosine (C), and Thymine (T).
• RNA: Contains the bases Adenine (A), Guanine (G), Cytosine (C), and Uracil (U). Notice that RNA uses uracil instead of thymine.

Therefore, the nucleotides that form DNA contain a deoxyribose sugar and one of the four bases: adenine, guanine, cytosine, or thymine. Conversely, RNA nucleotides contain a ribose sugar and one of the four bases: adenine, guanine, cytosine, or uracil.

From Nucleotides to Nucleic Acid Strands: Phosphodiester Bonds

Individual nucleotides are linked together to form long chains, or strands, of nucleic acids through a specific type of covalent bond called a phosphodiester bond. This bond forms between the phosphate group of one nucleotide and the sugar of the next nucleotide in the chain. This creates a continuous sugar-phosphate backbone with the nitrogenous bases projecting outwards.

As nucleotides are linked, a nucleic acid strand develops a directionality. One end of the strand has a free phosphate group attached to the 5′ (five prime) carbon of the sugar, and this end is designated the 5′ end. The other end has a free hydroxyl group (-OH) attached to the 3′ (three prime) carbon of the sugar, and this end is designated the 3′ end. This 5′ to 3′ directionality is crucial for understanding many processes involving nucleic acids.

The Double Helix of DNA: Anti-Parallel Strands and Base Pairing

While RNA typically exists as a single strand, DNA most often occurs as a double helix. This iconic structure consists of two nucleic acid strands that interact with each other. These two strands are not oriented in the same direction; instead, they run in anti-parallel directions. This means that one strand runs in the 5′ to 3′ direction, while the complementary strand runs in the 3′ to 5′ direction.

The two strands of DNA are held together by interactions between their nitrogenous bases. These interactions follow specific pairing rules known as base pairing:

• Adenine (A) always pairs with Thymine (T).
• Guanine (G) always pairs with Cytosine (C).

This complementary base pairing ensures that the sequence of bases on one strand dictates the sequence of bases on the other strand. For example, if one strand has the sequence 5′-ATG-3′, the complementary strand will have the sequence 3′-TAC-5′ (or written in the conventional 5′ to 3′ direction, 5′-CAT-3′).

The bases are held together by hydrogen bonds, which are relatively weak individually but collectively provide significant stability to the DNA double helix. Adenine and thymine form two hydrogen bonds, while guanine and cytosine form three hydrogen bonds.

In summary, DNA’s structure is characterized by two anti-parallel strands wound around each other in a double helix. The sugar-phosphate backbone forms the structural framework on the outside, while the nitrogenous bases pair in the interior, linked by hydrogen bonds. The specific base pairing (A with T, and G with C) is fundamental to DNA’s role in storing and transmitting genetic information.

Understanding the structure of nucleotides and how they assemble into DNA is crucial for comprehending the many biological processes that rely on this remarkable molecule, which we will explore in future discussions.

Key Takeaways:

• Nucleic acids (DNA and RNA) are polymers of nucleotides.
• Each nucleotide consists of a pentose sugar, a phosphate group, and a nitrogenous base.
• DNA contains deoxyribose, phosphate, and bases A, T, G, C.
• RNA contains ribose, phosphate, and bases A, U, G, C.
• Nucleotides are linked by phosphodiester bonds, forming a strand with 5′ and 3′ ends.
• DNA is a double helix with anti-parallel strands, complementary base pairing (A-T, G-C), and hydrogen bonds holding the strands together.”