Biochemistry (Nucleotide Polymerization)

[physicisttobe]

Hi everyone!

I did some multiple choice tasks and got stuck on two statements:

"In RNA, the sugar is present in the 2'-endo conformation". This statement is false, but why? What conformation does the sugar molecule have? How do I recognize the conformation?

"When two nucleotides polymerize, pyrophosphate is released". This statement is correct, but why? Why is pyrophosphate released here? Do we simply not have a single phosphate group here that binds to the C3 atom, i.e., where the hydroxyl group is located? What does this have to do with the release of pyrophosphate? I thought there is no release. I can't imagine anything about it. Could you explain me these things ( graphically and with simple words)?

 

[Drakkith]

"In RNA, the sugar is present in the 2'-endo conformation". This statement is false, but why? What conformation does the sugar molecule have? How do I recognize the conformation?

I'm not an expert in this area, but I did find this source:https://casegroup.rutgers.edu/lnotes/dnab.pdf
See slide 23 where it says:
The two types of sugar pucker most commonly found in nucleic acids. The C3′-endo pucker is prevalent in RNA and A-form DNA, whereas the C2′-endo pucker is characteristic of B-form DNA. It is seen that the C3′-endo pucker produces a significantly shorter phosphate-phosphate distance in the backbone, resulting in a more compact helical conformation.

I wish I could help you more.

"When two nucleotides polymerize, pyrophosphate is released". This statement is correct, but why? Why is pyrophosphate released here? Do we simply not have a single phosphate group here that binds to the C3 atom, i.e., where the hydroxyl group is located? What does this have to do with the release of pyrophosphate? I thought there is no release. I can't imagine anything about it. Could you explain me these things ( graphically and with simple words)?

I believe the hydroxyl is located on the 3' end of the DNA or RNA molecule. The triphosphate bonds where the hydroxyl is, turning it into a pyrophosphate since one of the phosphates stays bound between the two nucleotides while the other two are freed.

 

[physicisttobe]

Thank you for your effort. I really appreciate your reply!

In the solution this statment is false, but when I compare it with your source, then the statment should be correct.

 

[Drakkith]

In the solution this statment is false, but when I compare it with your source, then the statment should be correct.

What do you mean? Doesn't the source say "The C3′-endo pucker is prevalent in RNA", while your test says "In RNA, the sugar is present in the 2'-endo conformation"?

 

[epenguin]

I did some multiple choice tasks and got stuck on two statements:

"When two nucleotides polymerize, pyrophosphate is released". This statement is correct, but why? Why is pyrophosphate released here? Do we simply not have a single phosphate group here that binds to the C3 atom, i.e., where the hydroxyl group is located? What does this have to do with the release of pyrophosphate? I thought there is no release. I can't imagine anything about it. Could you explain me these things ( graphically and with simple words)?

Surely it is unreasonable to ask us to write out for you the formula for the reaction which you can't imagine but which must be in your textbook?

To why life has evolved to make so much use of triphosphates (We can imagine using diphosphate mostly) I am not aware that we have at present an answer. But for RNA, DNA and protein synthesis, producing pyrophosphate from triphosphates (rather than phosphate from diphosphates) makes the RNA, DNA and protein synthesis reactions "more irreversible": the inorganic pyrophosphate that is produced is then hydrolysed by a pyrophosphatase.

 

[physicisttobe]

Okay, I got it! I had a fallacy.
Thanks for your response!