Question

(a) Draw the structural formula for the sugar \(\beta\) -p-2-deoxyribose. (b) Draw the structural formula for the nucleoside deoxyadenosine (it consists of \(\beta\) -D-2-deoxyribose and adenine). (c) Draw the structural formula for the nucleotide deoxyadenosine \(5^{\prime}\) -monophosphate.

Short answer

The sugar lacks oxygen at the 2' carbon. Deoxyadenosine adds adenine at the 1' position. Deoxyadenosine 5'-monophosphate has a phosphate at the 5' position.

Step-by-step solution

Understand the Sugar Structure

The sugar mentioned is \( \beta\)-2-deoxyribose, which is a 5-carbon sugar part of DNA. Unlike ribose, it lacks an oxygen atom at the 2' position. Draw a 5-membered ring with four carbon atoms and one oxygen atom in the ring, label the carbons as 1', 2', 3', 4', and 5'. Remove the OH group from the 2' position and make sure the OH group at the 1' position is shown in the \(\beta\)-configuration (above the plane for D-sugars).

Construct the Nucleoside

A nucleoside consists of a sugar and a nitrogenous base. In deoxyadenosine, adenine (a purine base) is attached to the 1' carbon of the \( \beta\)-D-2-deoxyribose. To draw this, connect the nitrogen base of adenine to the 1' carbon of the sugar, ensuring the \( \beta\)-linkage (adenine should be above the plane on a standard pyrimidine drawing).

Build the Nucleotide

Deoxyadenosine 5'-monophosphate is composed of a nucleoside linked to a phosphate group at the 5' carbon. First, ensure the structure from Step 2 is correct. Then, add a phosphate group (PO₄³⁻) to the 5' carbon of the sugar by replacing the hydrogen atom at the 5' position with the phosphate.

Key concepts

Nucleoside

At its heart, a nucleoside is a simple combination of two important molecules. It's formed when a nitrogenous base is linked to a sugar molecule. In the case of DNA, the sugar is deoxyribose, specifically 𝛽-D-2-deoxyribose. This type of interaction does not include any phosphate groups. Hence, nucleosides should not be confused with nucleotides, which do include phosphates.
This connection is significant because it determines how the bases are paired and organized within the DNA structure, crucial for genetic coding. The bond between the sugar and base is called a glycosidic bond.
For deoxyadenosine, a specific nucleoside, the nitrogenous base adenine pairs with the sugar. When these two components join, they form a stable structure, setting the stage for further complexity in genetic material. To visualize this, consider the atomic alignment: the 1' carbon of the deoxyribose sugar bonds with the nitrogen atom on adenine. This linkage is specifically a 𝛽-linkage, indicating spatial orientation.

Nucleotide

A nucleotide is a more complex molecule compared to a nucleoside, as it consists of three different components: a nitrogenous base, a sugar, and one or more phosphate groups. The addition of the phosphate(s) is the key factor that differentiates a nucleotide from a nucleoside.
In the solution, deoxyadenosine 5'-monophosphate is our nucleotide of interest. It starts with the nucleoside, deoxyadenosine, which contains the sugar deoxyribose and the base adenine. Then, a phosphate group (PO₄³⁻) is attached to the 5' carbon atom of the deoxyribose sugar. This addition gives the nucleotide its "mono-phosphate" naming.
This phosphate linkage endows nucleotides with the ability to store and transfer energy, an essential feature for cellular processes. The bonds between phosphates are high-energy and play crucial roles in metabolism. Nucleotides serve as the building blocks for nucleic acids such as DNA and RNA, forming the backbone of these molecules through phosphate-sugar linkages.

Adenine

Adenine is a fundamental component of DNA and RNA, both types of genetic material that convey genetic information. It is classified as a purine, one of the two categories of nitrogenous bases. Purines are bigger than the other category, pyrimidines, due to their double-ring structure.
The adenine structure includes two fused rings containing nitrogen, which participate in the formation of hydrogen bonds. These bonds are essential in pairing adenine with thymine (in DNA) or with uracil (in RNA) through complementary base pairing rules. This specific matching is critical for the stability of the DNA double helix.
In deoxyadenosine, adenine attaches to the deoxyribose sugar, creating a stable connection through the 1' carbon, as we've seen before. This connection is crucial for the encoding of genetic instructions and is regularly involved in numerous biological processes such as replication and transcription, where adenine's ability to form strong hydrogen bonds is leveraged.