I recently came across this question in the MIT Open Learning Library Pre-7.01 Biology Course. It is question 2d in Problem Set 1 (archived link).

The question, as well as the correct answers and explanation from the answer key, is shown below:

The following is adenine base, which can covalently bond, through condensation reaction with ribose sugar to form a nucleotide (ATP).

Which carbon atom of the ribose sugar would covalently bond with the circled region of adenine to form Adenosine triphoshphate (ATP)?

🅐 C1' ← correct answer
Ⓑ C2'
Ⓒ C3'
Ⓓ C4'
Ⓔ C5'

Would you classify this base as purine or pyrimidine?

🅐 purine ← correct answer
Ⓑ pyrimidine


Bases bond to the 1' carbon (C1') in the formation of nucleotides. Other key carbons are the C5', which binds to the phosphate groups, and C3', where new bases are added in nucleic acid synthesis.
Purines have two rings, a hexagon and pentagon, while pyrimidines have only one (hexagonal) ring.

The question, answer, and explanation are confusing to me:

  1. It looks like the molecule shown in the picture (labeled adenine) is actually guanine. Is this a mistake in the question?
  2. I know that a nucleotide is formed when adenine bonds to (deoxy)ribose which bonds to a phosphate group, but the question says that adenine covalently bonds with ribose to form adenosine triphosphate, which it calls a nucleotide.
    1. Is ATP a nucleotide?
    2. Ribose ($\text{C}_5\text{H}_{10}\text{O}_5$) and adenine ($\text{C}_5\text{H}_{5}\text{N}_5$)—or ribose and guanine ($\text{C}_5\text{H}_{5}\text{N}_5\text{O}$)—do not contain any phosphorus atoms, so it doesn't make sense that they would be able to bond to form ATP ($\text{C}_{10}\text{H}_{16}\text{N}_5\text{O}_{13}\mathbf{\text{P}_3}$). Furthermore, the reactions would not balanced in either case without using multiple molecules. Am I missing something?

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1 Answer 1

  1. The structure shown is indeed of guanine, not adenine.

  2. A nucleotide is defined as being composed of a nitrogenous base, a pentose sugar and phosphate (see, e.g. the Wikipedia entry). So the simplest nucleotide based on adenine would be AMP. However ATP is also considered a nucleotide, as can be inferred from this IUPAC entry. Often we refer to it as a nucleoside triphosphate. (A nucleoside is just the base–sugar combination.)

  3. I think you misinterpret the wording as describing the formation of these compounds. The wording — which is poor — is meant to describe the components and bonds in the chemical structures, not laboratory chemical reactions or the mechanism of the formation of the compounds in the cell (which is different, complex, but well documented). The use of bond and bind as verbs is bad, as it implies an active process. If I were writing this (and I am an educator and an author), I would write something like “In this structure there is a covalent bond between…”

  4. If you paid for this course, I would ask for a refund. If it is free, “You get what you pay for.”

  • 4
    $\begingroup$ With all due respect, but if MIT out of all places is hosting this I think it's much more prudent to make them aware of the mistake so they can fix it instead of taking a "You get what you pay for" stance. $\endgroup$
    – Mast
    Commented Aug 30, 2023 at 13:39
  • $\begingroup$ @David Thank you for the excellent response! Can you please clarify your third point? Are you referring to the question "Which carbon atom … Adenosine triphosphate (ATP)?" If so, I'm afraid that I don't understand your explanation of how you interpret the question. $\endgroup$ Commented Aug 30, 2023 at 14:54
  • $\begingroup$ If only the synthesis pathways were as simple as that text you linked makes it sound... $\endgroup$ Commented Aug 30, 2023 at 16:59
  • $\begingroup$ @IanCampbell — Metabolism is not simple. However it can be understood if it broken up appropriately, and learned in an appropriate order. If one starts learning the central pathways of metabolism (as organized in a text book) one becomes familiar with the building blocks that are available. One will learn how ribose is made in the pentose phosphate shunt, and how phosphate is present in the cell and is introduced into sugars. Finally one can consult a text to see what constituents are used to assemble the more complex purines and pyrimidines. The overall balance between these follows. $\endgroup$
    – David
    Commented Aug 30, 2023 at 20:05
  • 1
    $\begingroup$ @Mast — I am judging the material as I see it. Anyone can copy and paste the structure of the wrong compound. However the ambiguous use of the verbs "bond" and "bind" indicate to me that the material is poor. If the poster wishes to make the producers of the course aware of this, that is his concern, not mine. $\endgroup$
    – David
    Commented Aug 30, 2023 at 20:17

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