Question

Draw a structural formula for the \(\beta\) - \(N\)-glycoside formed between 2 -deoxyD-ribofuranose and adenine.

Short answer

Question: Draw the structural formula of the β-N-glycoside formed between 2-deoxy-D-ribofuranose and adenine. Answer: The structural formula for the β-N-glycoside formed between 2-deoxy-D-ribofuranose and adenine is: ``` O || 1-C--N--C N | ||\ // 4-C--H N-C N--C-H | |\ || C C N | \ H \ C--H (2-deoxy group) | O1 (anomeric carbon in β-configuration) ```

Step-by-step solution

Understand the structure of 2-deoxy-D-ribofuranose

2-deoxy-D-ribofuranose is a sugar molecule and the structural difference between it and ribofuranose is the absence of a hydroxyl group (-OH) at carbon 2. The structure of 2-deoxy-D-ribofuranose is: ``` O || 1-C--H | 4-C--H | C | \ H C--H | O1 (anomeric carbon) ``` In D configuration, hydroxyl group on carbon 4 points to the right in a Fischer projection.

Understand the structure of adenine

Adenine is a purine nucleobase. Its structure is as follows: ``` N N || \\ || C C N-C-H || | || C --C N \\ N ``` The nitrogen atom N9 is the one that forms a N-glycosidic bond with a sugar molecule (in this case, 2-deoxy-D-ribofuranose).

Formation of the β-N-glycosidic bond between 2-deoxy-D-ribofuranose and adenine

The β-N-glycosidic bond forms between the anomeric carbon (O1) of the sugar 2-deoxy-D-ribofuranose and the nitrogen atom (N9) of adenine. The bond is formed through the nucleophilic attack of the nitrogen (N9) on the anomeric carbon (C1) of the sugar, leading to the loss of a hydroxyl group at C1. ``` O || 1-C--N9--C N | ||\ // 4-C--H N-C N--C-H | |\ || C C N | \ H \ C--H | O1 ``` In β-N-glycoside, the orientation of the N-glycosidic bond is such that N9 of adenine and hydroxyl group of carbon 4 are on the opposite side of the sugar ring in a Fischer projection.

Drawing the final structural formula

The final structural formula for the β-N-glycoside formed between 2-deoxy-D-ribofuranose and adenine is: ``` O || 1-C--N--C N | ||\ // 4-C--H N-C N--C-H | |\ || C C N | \ H \ C--H (2-deoxy group) | O1 (anomeric carbon in β-configuration) ```

Key concepts

2-deoxy-D-ribofuranose Structure

2-deoxy-D-ribofuranose is an essential component in the structure of DNA. Unlike its close relative, ribofuranose, 2-deoxy-D-ribofuranose lacks an oxygen atom on its second carbon atom, hence the '2-deoxy' designation. The sugar ring structure of 2-deoxy-D-ribofuranose is termed a 'furanose' due to its resemblance to the furan ring, comprising four carbons and one oxygen in the ring.

Visualizing the structure:

• Carbon 1 (C1) is known as the anomeric carbon and is vital for forming the N-glycosidic bond.
• The 'D' in 2-deoxy-D-ribofuranose indicates the orientation of the hydroxyl group attached to carbon 4 (C4), which is positioned to the right in a Fischer projection.
• The absence of the hydroxyl (-OH) group on the second carbon (C2) is crucial as this modification makes DNA more chemically stable than RNA, which contains ribofuranose.

In a 3-dimensional space, this seemingly simple sugar adopts a puckered conformation, allowing it to interact with other molecules, such as nucleobases, to form the backbone of DNA.

Adenine Nucleobase Structure

Adenine is one of the four nucleobases found in DNA and plays a critical role in encoding genetic information. As a purine nucleobase, it has a two-ring structure composed of a six-membered and a five-membered nitrogen-containing ring fused together.

• The structure of adenine includes several nitrogen atoms; however, the nitrogen at position 9 (N9) is the attachment point for the N-glycosidic bond formation with a sugar molecule.
• The intricate arrangement of double bonds in adenine's rings allows it to form hydrogen bonds with its complementary nucleobase, thymine, in DNA.
• The planar characteristic of adenine enables it to stack efficiently with other nucleobases, contributing to DNA's double-helical structure.

Understanding how adenine is structured is vital when exploring how it forms connections within DNA, such as the N-glycosidic bond, enabling the creation of intricate structures like the double helix.

Beta-N-glycoside Formation

Beta-N-glycoside formation involves a specific type of bond known as the N-glycosidic bond, which connects a nucleobase to a sugar molecule. Here are the critical features of beta-N-glycoside formation:

• The bond forms between the anomeric carbon of the sugar (carbon 1 in 2-deoxy-D-ribofuranose) and the N9 atom of the adenine molecule.
• The 'beta' designation refers to the spatial orientation of the glycosidic bond. In the beta-N-glycoside, the adenine base is above the plane of the sugar ring when drawn in a conventional Haworth projection.
• This bond is essential for crafting the nucleoside structure, which further joins with phosphate groups to form nucleotides—the basic building blocks of DNA.

The formation is the result of a nucleophilic attack where the lone pair of electrons on the nitrogen atom (N9) of adenine attacks the anomeric carbon (C1) of 2-deoxy-D-ribofuranose. This reaction signifies a pivotal step in the assembly of DNA's structure; each nucleotide is formed when a nucleobase, such as adenine, is linked to a sugar molecule through this essential bond.