Chapter 17, Problem 17.29UKC

Consider the given dinucleotide.

1. a. Identify the bases present in the dinucleotide.
2. b. Label the 5ˈ and 3ˈ ends.
3. c. Give the three- or four-letter abbreviations for the two nucleotides.
4. d. Is this dinucleotide a ribonucleotide or a deoxyribonucleotide? Explain your choice.
5. e. Name the dinucleotide.

Interpretation Introduction

Interpretation:

Bases present in the below dinucleotide has to be identified.

Concept Introduction:

The skeleton structure of base in nucleic acid generally consists of a nitrogen atom in it. There are two types of bases that are pyrimidine base and purine base.

(a) Pyrimidine base consists of one ring and is present in uracil (U), cytosine (C), and thymine (T).

(b) Purine base consists of two rings and is present in adenine (A) and guanine (G).

Explanation of Solution

The given structure contains two nucleotides that are nucleotide 1 and nucleotide 2 and is drawn as follows:

Nucleotide 1 contains a base with one ring in it thus is a pyrimidine base. Therefore, the base is uracil. Whereas nucleotide 2 contains a base with two rings in it thus is a purine base. Therefore, the base is adenine.

Interpretation Introduction

Interpretation:

The $5^{\prime }$ end and $3^{\prime }$ end of below dinucleotide have to be labeled.

Concept Introduction:

Nucleotide is defined as basic unit for formation of nucleic acid that is essential for completion of metabolic reactions in body. The three basic components of nucleotide are as follows:

1 Nitrogen-containing base

2 Pentose sugar

3 Phosphate group

Dinucleotide is a polymer that is composed of two nucleotide unit either of DNA or RNA that is bonded to each other through a covalent bond.

Explanation of Solution

Phosphate group is attached to $5^{\prime }$ end of the nucleotide. Hence it is a phosphate end. While $\text{OH}$ group is bonded to $3^{\prime }$ end of the nucleotide. The two nucleotides are joined together through $5^{\prime }$ and $3^{\prime }$ linkage. Thus, $5^{\prime }$ end and $3^{\prime }$ end in below dinucleotide is labeled as follows:

Interpretation Introduction

Interpretation:

Three or four letter abbreviation of below dinucleotide has to be identified.

Concept Introduction:

Nucleotides are named accordingly as follows:

1 Identify the type of sugar unit attached is ribose or deoxyribose. If in the structure of nucleoside there is $\text{OH}$ group at $\text{C}{\text{2}}^{\prime }$ then the sugar is ribose sugar and if there is no $\text{OH}$ group at $\text{C}{\text{2}}^{\prime }$ then it is deoxyribose sugar and prefix deoxy is used.

2 Identify the name of the different nitrogen bases present in the molecule. There are two types of bases that are pyrimidine base and purine base.

(a) Pyrimidine base consists of one ring and is present in uracil, cytosine, and thymine.

(b) Purine base consists of two rings and is present in adenine and guanine.

3 Nucleosides with pyrimidine bases end with the suffix $\text{-idine}$ and purine bases end with $\text{-osine}$.

4 Identify the number of carbon atom to which phosphate group is attached. The prefix is added as mono, di or tri for numbers of phosphate groups present in the nucleotide.

Abbreviation is assigned with respect to the type of sugar. For ribose sugar, 3 letter abbreviation is used and for deoxyribose sugar, 4 letter abbreviation is used followed by d as a prefix.

Explanation of Solution

In the below structure of dinucleotide, base, phosphate group and monosaccharide are labeled as follows:

For nucleotide 1:

Name of nucleotide is assigned as follows:

1 There is $\text{OH}$ group at $\text{C}{\text{2}}^{\prime }$ therefore, it is ribose sugar.

2 It contains one ring, therefore, it is a pyrimidine base called uracil and suffix used is $\text{-idine}$.

3. Phosphate group is attached to $5^{\prime }$ carbon of sugar and only one phosphate group is present. Therefore mono is added before phosphate group.

Hence, the name of the given nucleotide is $\text{uridine }{5}^{\prime }\text{-monophosphate}$ and abbreviation used is UMP.

For nucleotide 2:

Name of nucleotide is assigned as follows:

1 There is an $\text{OH}$ group at $\text{C}{\text{2}}^{\prime }$ therefore, it is a ribose sugar.

2 It contains two rings, therefore, it is a purine base called adenine and suffix used is $\text{-osine}$.

3. Phosphate group is attached to $5^{\prime }$ carbon of sugar and only one phosphate group is present. Therefore mono is added before phosphate group.

Hence, the name of the given nucleotide is $\text{adenosine }{5}^{\prime }\text{-monophosphate}$ and abbreviation used is AMP.

Interpretation Introduction

Interpretation:

Whether the below nucleotide is ribonucleotide or deoxyribonucleotide has to be explained.

Concept Introduction:

Refer to part (c).

Explanation of Solution

Since in the structure of dinucleotide both the nucleotide contains an $\text{OH}$ group at $\text{C}{\text{2}}^{\prime }$, therefore, the sugar is ribose sugar. Hence, the given nucleotide is ribonucleotide. The structure of dinucleotide is as follows:

Interpretation Introduction

Interpretation:

Name of the below dinucleotide has to be identified.

Concept Introduction:

Refer to part (c).

Explanation of Solution

The given structure contains two nucleotides that are nucleotide 1 and nucleotide 2 and is drawn as follows:

For nucleotide 1:

Name of nucleotide is assigned as follows:

1 There is an $\text{OH}$ group at $\text{C}{\text{2}}^{\prime }$ therefore, it is ribose sugar.

2 It contains one ring, therefore, it is a pyrimidine base called uracil and suffix used is $\text{-idine}$.

3. Phosphate group is attached to $5^{\prime }$ carbon of sugar and only one phosphate group is present. Therefore mono is added before phosphate group.

Hence, the name of the given nucleotide is $\text{uridine }{5}^{\prime }\text{-monophosphate}$ and abbreviation used is UMP.

For nucleotide 2:

Name of nucleotide is assigned as follows:

1 There is $\text{OH}$ group at $\text{C}{\text{2}}^{\prime }$ therefore, it is ribose sugar.

2 It contains two rings, therefore, it is a purine base called adenine and suffix used is $\text{-osine}$.

Since phosphate group is attached to $5^{\prime }$ carbon of sugar and only one phosphate group is present. Therefore mono is added before phosphate group.

Hence, the name of the given nucleotide is $\text{adenosine }{5}^{\prime }\text{-monophosphate}$ and abbreviation used is AMP. Therefore, the name for the dinucleotide is UA.