Biochemistry (Nucleotide Polymerization)

In summary, the conversation discusses two statements related to RNA and nucleotides. The first statement, "In RNA, the sugar is present in the 2'-endo conformation," is false. The correct conformation for RNA is the C3'-endo pucker, which is also seen in A-form DNA. The second statement, "When two nucleotides polymerize, pyrophosphate is released," is correct. This is because the triphosphate bonds where the hydroxyl group is located, turning it into a pyrophosphate. The reason for using triphosphates in these reactions is still unknown. The conversation ends with the individual realizing their previous fallacy.
  • #1
physicisttobe
56
13
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)?
 
Last edited:
Biology news on Phys.org
  • #2
physicisttobe said:
"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.

physicisttobe said:
"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.
 
  • Like
Likes TeethWhitener
  • #3
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.
 
  • #4
physicisttobe said:
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"?
 
  • Like
Likes TeethWhitener
  • #5
physicisttobe said:
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.
 
Last edited:
  • Like
Likes BillTre
  • #6
Okay, I got it! I had a fallacy.
Thanks for your response!
 

Related to Biochemistry (Nucleotide Polymerization)

1. What is nucleotide polymerization?

Nucleotide polymerization is the process by which nucleotides, the building blocks of DNA and RNA, are joined together to form long chains called polynucleotides. This process is crucial for the synthesis of genetic material and the transmission of genetic information.

2. How does nucleotide polymerization occur?

Nucleotide polymerization occurs through a series of chemical reactions that involve the formation of phosphodiester bonds between the phosphate group of one nucleotide and the sugar group of another. This results in a chain of nucleotides connected by a sugar-phosphate backbone.

3. What is the role of enzymes in nucleotide polymerization?

Enzymes play a crucial role in nucleotide polymerization by catalyzing the chemical reactions that join nucleotides together. These enzymes, such as DNA polymerase and RNA polymerase, are specialized proteins that ensure the accuracy and efficiency of nucleotide polymerization.

4. What is the difference between DNA and RNA polymerization?

The main difference between DNA and RNA polymerization is the type of sugar present in their nucleotides. DNA contains deoxyribose sugar, while RNA contains ribose sugar. This difference results in slightly different chemical reactions and structures of the polynucleotide chains.

5. How does nucleotide polymerization contribute to genetic diversity?

Nucleotide polymerization is a key process in the replication of genetic material, which allows for the transmission of genetic information from one generation to the next. Additionally, the occasional errors in nucleotide polymerization can lead to genetic mutations, which contribute to genetic diversity and evolution.

Similar threads

  • Engineering and Comp Sci Homework Help
Replies
1
Views
2K
  • Biology and Chemistry Homework Help
Replies
4
Views
3K
  • Biology and Chemistry Homework Help
Replies
1
Views
49K
  • Biology and Medical
Replies
4
Views
6K
  • Biology and Chemistry Homework Help
Replies
11
Views
19K
  • High Energy, Nuclear, Particle Physics
Replies
15
Views
3K
  • Beyond the Standard Models
Replies
34
Views
921
Replies
3
Views
1K
  • Biology and Chemistry Homework Help
Replies
1
Views
3K
  • Biology and Chemistry Homework Help
Replies
1
Views
950
Back
Top