Question

Draw the chemical structure of the three components of a nucleo- tide, and then link them together. What atoms are removed from the structures when the linkages are formed?

Short answer

Answer: The three components of a nucleotide are the nitrogenous base, the pentose sugar, and the phosphate group. During the formation of the linkages between these components, two water molecules are removed, resulting in a total of four hydrogen atoms and two oxygen atoms being removed from the structure.

Step-by-step solution

Drawing the Components of a Nucleotide

To begin, draw the three components of a nucleotide separately. These components are: 1. Nitrogenous base, which can be either a purine (adenine or guanine) or a pyrimidine (cytosine, thymine, or uracil) 2. The pentose sugar, which can be either ribose (in RNA) or deoxyribose (in DNA) 3. The phosphate group

Identifying the Linkages in a Nucleotide

In a nucleotide, the major linkages are: 1. The bond between the nitrogenous base and the sugar molecule (N-glycosidic bond) 2. The bond between the sugar and the phosphate group (phosphoester bond) Next, we will link these components together.

Forming the N-Glycosidic Bond

To form the N-glycosidic bond, attach the nitrogenous base to the C1' (carbon at position 1) of the pentose sugar. In this linkage, N1 of a pyrimidine or N9 of a purine is joined to the C1' of the sugar. A water molecule (composed of two hydrogen atoms and one oxygen atom) is removed from the structure during this process.

Forming the Phosphoester Bond

To form the phosphoester bond, attach the phosphate group to the C5' (carbon at position 5) of the pentose sugar. In this linkage, the phosphate group is joined to the sugar by replacing the hydroxyl group (-OH) at the C5' position. Another water molecule (composed of two hydrogen atoms and one oxygen atom) is removed from the structure during this bond formation. Now the nucleotide is complete with its nitrogenous base, sugar, and phosphate group linked together. The atoms removed in the process are from the two water molecules that were released during the formation of the N-glycosidic bond and the phosphoester bond, which consist of a total of four hydrogen atoms and two oxygen atoms.

Key concepts

Nitrogenous Bases

In any nucleotide, nitrogenous bases play a crucial role. They are organic molecules with a ring structure that contains nitrogen. There are two primary categories of nitrogenous bases: purines and pyrimidines.
Purines include adenine (A) and guanine (G), while pyrimidines consist of cytosine (C), thymine (T), and uracil (U). These bases are essential for encoding genetic information in nucleic acids such as DNA and RNA.

• Pyrimidines are characterized by a single ring structure.
• Purines, on the other hand, have a double-ring structure.

This difference in their structures accounts for the variations in their chemical properties and their specific pairing in nucleic acids. The bonding of these bases follows specific pairing rules: in DNA, adenine pairs with thymine, and cytosine pairs with guanine. In RNA, thymine is replaced by uracil, which pairs with adenine.
When a nitrogenous base attaches to a pentose sugar, forming a nucleoside, it establishes an N-glycosidic bond, further leading to the formation of nucleotides.

Pentose Sugar

A pivotal part of the nucleotide structure is the pentose sugar, which can be either ribose in RNA or deoxyribose in DNA. Both of these sugars are five-carbon sugars, hence the name "pentose."

• Ribose has a hydroxyl group (-OH) at the 2' and 3' positions.
• Deoxyribose lacks an oxygen atom in the 2' position, having only a hydrogen (-H) instead.

This slight variation between ribose and deoxyribose results in significant differences between DNA and RNA molecules. The pentose sugar forms the backbone of the nucleotide chain by connecting to both nitrogenous bases and phosphate groups.
The sugar serves as the foundation to which the nitrogenous base is attached at the C1' carbon, forming an N-glycosidic bond. Moreover, the phosphoester bond is created between the phosphate group and the C5' carbon of the sugar. These linkages are crucial for building the structure of nucleic acids.

Phosphate Group

The phosphate group is the third essential component in forming nucleotides. It consists of a phosphorus atom surrounded by four oxygen atoms, typically forming an ion at physiological pH.
This group is responsible for the acidic properties of nucleic acids. When attached to a nucleotide, it forms a phosphoester bond with the pentose sugar. This happens by linking the phosphate group's oxygen to the C5' hydroxyl group of the sugar.

• The phosphate group is critical for linking nucleotides together, forming the phosphodiester backbone of DNA and RNA.
• Each nucleotide in a chain shares a phosphate bridge, creating a strong chain of nucleotides, which is crucial for the stability and function of DNA and RNA molecules.

Notably, the release of a water molecule occurs when forming the phosphoester bond, highlighting how dehydration synthesis leads to forming larger biomolecules. Together with nitrogenous bases and pentose sugars, phosphate groups ensure the structural integrity essential for genetic function and information transfer.