Biochemistry : Sugar-Phosphate Groups and Phosphodiester Bonds

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #1 : Sugar Phosphate Groups And Phosphodiester Bonds

What type of bonds are found between the DNA sugar hydroxyl groups? What are their corresponding carbon numbers?

Possible Answers:

Phosphoester; 1', 5'

Phosphoester; 3', 5'

Phosphodiester; 1', 3'

Phosphodiester; 2', 4'

Phosphodiester; 3', 5'

Correct answer:

Phosphodiester; 3', 5'

Explanation:

The phosphodiester bonds in DNA occur between the 3' and 5' hydroxyl groups on deoxyribose. (This is related to DNA's 5' to 3' directionality as DNA polymerase can only synthesize DNA by adding nucleotides to the 3' hydroxyl group).

Example Question #2 : Nucleic Acid Structures

In DNA, the 5-carbon sugar is attached to the nitrogenous base by a __________.

Possible Answers:

ester

glycosidic bond

phosphodiester bond

phosphoester bond

deoxyribose

Correct answer:

glycosidic bond

Explanation:

The beta-N-glycosidic bond attaches the nitrogen on the purine or pyrimidine base to the 1' anomeric carbon on the deoxyribose sugar. Phosphodiester linkages connect the 3' and 5' sugar hydroxyl groups on adjacent nucleotides.

Example Question #2 : Sugar Phosphate Groups And Phosphodiester Bonds

Which of the following is not a reason that the anhydride linkage of pyrophosphate stores so much energy?

Possible Answers:

Pyrophosphate has less resonance forms than orthophosphate groups by themselves.

Phosphorus on pyrophosphate satisfies the octet rule, but does not on orthophosphate.

Orthophosphate by itself has more favorable interactions with water than two orthophosphates linked together (pyrophosphate).

All of the choices are true

The negative charges on the on the orthophosphates repel each other.

Correct answer:

Phosphorus on pyrophosphate satisfies the octet rule, but does not on orthophosphate.

Explanation:

Phosphorus on both orthophosphate and pyrophosphate is surrounded by 10 electrons. This does not satisfy the octet rule in either case, so that answer choice is false, and therefore the correct answer. With four negative charges close by, pyrophosphate is very unstable, and releases a lot of energy when cleaved. Finally, the two orthophosphates formed from a single pyrophosphate gain an additional resonance structure.

Example Question #3 : Sugar Phosphate Groups And Phosphodiester Bonds

What type of bond holds the phosphate group to the sugar group in DNA's backbone?

Possible Answers:

Hydrogen bond

Ionic bond

Glycosidic bond

Phosphodiester bond

Covalent bond

Correct answer:

Phosphodiester bond

Explanation:

The type of bond that holds the phosphate group to the sugar in DNA's backbone is called a phosphodiester bond. Hydrogen bonds connect bases to one another and glycosidic bonds occur between deoxyribose groups and the base groups.

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