Question

Draw a structural formula for each nucleotide. (a) \(2^{\prime}\)-Deoxythymidine \(5^{\prime}\)-monophosphate (b) \(2^{\prime}\)-Deoxythymidine \(3^{\prime}\)-monophosphate

Short answer

Answer: The main difference between the structural formulas of 2'-deoxythymidine 5'-monophosphate and 2'-deoxythymidine 3'-monophosphate is the position of the phosphate group. In 2'-deoxythymidine 5'-monophosphate, the phosphate group is attached to the 5'-carbon of the sugar, while in 2'-deoxythymidine 3'-monophosphate, the phosphate group is attached to the 3'-carbon of the sugar. Both structures contain a 2'-deoxyribose sugar and a thymine base.

Step-by-step solution

Draw the 2'-Deoxyribose Sugar

To draw the 2'-deoxyribose sugar, you need a 5-membered ring with one oxygen atom and four carbon atoms. Number the carbons starting from the carbon adjacent to the oxygen atom in a clockwise direction. The 2'-carbon will have H instead of OH group, while the other carbons have the OH group attached (except for 5'-carbon).

Draw the Thymine Base

Thymine is a pyrimidine base, which means it has a six-membered ring containing two nitrogen atoms and four carbon atoms. Add a carbonyl group at the 2nd and 4th carbon and an amino group at the 5th carbon. Add double bonds between the nitrogen atom at position 1 and carbon atom at position 6, and between the nitrogen atom at position 3 and carbon atom at position 4.

Connect Thymine to Deoxyribose Sugar

Attach the 1st nitrogen atom in thymine to the 1'-carbon of the 2'-deoxyribose sugar to form N-glycosidic bond.

Add Phosphate Group for 5'-Monophosphate

Add a phosphate group at the 5'-carbon of the sugar, which has a double bond with an oxygen atom and two single bonds with O^– groups (one of them represents the monophosphate).

Add Phosphate Group for 3'-Monophosphate

Add a phosphate group at the 3'-carbon of the sugar, which has a double bond with an oxygen atom and two single bonds with O^– groups (one of them represents the monophosphate). Now, we have the structural formulas for both nucleotides: (a) 2'-Deoxythymidine 5'-monophosphate - Is the structure containing 2'-deoxyribose sugar, thymine base, and phosphate group at the 5'-carbon of the sugar. (b) 2'-Deoxythymidine 3'-monophosphate - Is the structure containing 2'-deoxyribose sugar, thymine base, and phosphate group at the 3'-carbon of the sugar.