Two Molecular Biology Doubts!

[Androide89]

5-3 or 3-5 direction?
I don't get this question: Which of the following is unique to DNA synthesis in the 3-5 direction? I thought DNA synthesis is ALWAYS 5-3 direction. The answer was okazaki fragments. Are okazaki fragments made in the 3-5 direction?

What makes the snRNA?
Also is snRNA made by RNA Polymerase 2 or 3 because in Kaplan it says its made by RNA Pol 2 and in UWorld it says its made by RNA Pol 3. Its not mentioned in FA.

Thanks

[inder]

1. That's a weird question... okazaki fragments are def. unique but i don't know what question is asking... could you post the exact question maybe?

2. both kaplan and UW are correct... both RNA pol II and III make snRNA. Lippincott biochem: page 422 and 424;

[Androide89]

Intestinal epithelial cells are rapidly dividing after diarrhea. Bidirectional DNA replication in these cells require building up two strands of DNA, both in the 5-3 and 3-5 directions. Which of the following is unique to the process of DNA synthesis in the 3-5 direction?

Ans: discontinuous dna synthesis with subsequent linking

[rasheed]

DNA polymerase I fills the gaps between the Okazaki fragments by laying DNA in the 3'-->5' direction. This is the only time when you have 3'--5' DNA replication, all other times are 5'---3'.

Another important difference which is related to the foregoing is that DNA Polymerase I remove the RNA primer of the okazaki fragment in the 5'---3' direction which is the opposite of the usual "proof reading" exonuclease activity of DNA polymerase III which is backward in 3'---5'.

Have a look at this animation

If you look carefully when the gaps between the okazaki fragments filled you'll see that they are filled in 3'--5' not 5'--3'

Update: I found out that there's no such thing of 3' to 5' DNA replication. Please disregard this post

[MagzMD]

Originally Posted by Androide89

5-3 or 3-5 direction?
I don't get this question: Which of the following is unique to DNA synthesis in the 3-5 direction? I thought DNA synthesis is ALWAYS 5-3 direction. The answer was okazaki fragments. Are okazaki fragments made in the 3-5 direction?

What makes the snRNA?
Also is snRNA made by RNA Polymerase 2 or 3 because in Kaplan it says its made by RNA Pol 2 and in UWorld it says its made by RNA Pol 3. Its not mentioned in FA.

Thanks

Okazaki fragments are synthesized on the lagging strand from the 3`-->5` direction...while the leading strand is replicated from the 5`---> 3` direction. Remember, both strands are replicated simultaneously in opposite directions.
From what I have learned in grad school, snRNAs are synthesized by RNA PolyII and in some cases RNA PolyIII...what specific cases, I am not sure...but both are true.
Good luck!

[khushboo]

RNA primers r removed by DNA polymerase 1 n this occurs in 5' to 3' direction....DNA polymerase 1 also fills in the resulting gap by synthesizing DNA beginning at 3' end of the neighboring Okazaki fragment..means in 5' to 3' direction....its given in Kaplan...
only exonuclease activity occurs in 3' to 5' direction,n that also only during proof reading...for removal of RNA primers also exonuclease activity is req...but it occurs in 5' to 3' direction....

[Androide89]

dna pol 1 also has 3-5 dna polymerase activity

[khushboo]

Originally Posted by rasheed

DNA polymerase I fills the gaps .... you'll see that they are filled in 3'--5' not 5'--3'

hey....where did u find this information regarding 3' to 5' direction in filling gaps between okazaki fragments..is it a reliable source??...as it is clearly written in kaplan that DNA polymerase 1 fills gap by synthesizing DNA at 3' end of neighboring okazaki fragment....means it must be in 5' to 3' direction....
any one with other options???

[rasheed]

Originally Posted by khushboo

hey....where did u find this information regarding 3' to 5' direction in filling gaps between okazaki fragments..is it a reliable source??...as it is clearly written in kaplan that DNA polymerase 1 fills gap by synthesizing DNA at 3' end of neighboring okazaki fragment....means it must be in 5' to 3' direction....
any one with other options???

After looking up several resources, I found out that you are right. DNA polymerases only lay down in 5' to 3' direction and never the reverse. In fact, that's why there's okazaki fragments.

I apologize for the error :sorry: You are right.

[Androide89]

then how do you explain the question? is it just a messed up question, cuz its from uworld

[khushboo]

Originally Posted by Androide89

then how do you explain the question? is it just a messed up question, cuz its from uworld

can u pls post that Q with all options....??

[im99]

I think this is the ques..
bidirectional DNA replication requires syntheses of 2 strands of DNA.. both in 5' to 3' and 3' to 5' direction. what is the main difference in these 2 strands?

ans is ligase activity is more in the strand which is made in 3' to 5' direction..which is the discontinuous strand/okazaki.

the answer is fine. but the stem of the question says... 3' to 5'.
I thought both the strands are made in 5' to 3' direction.
anybody?

[ALittleTeaPot]

I could be wrong but maybe:

A common mistake I make when reading questions about DNA synthesis is whether by 3'-5' or 5'-3' they mean the direction the synthesis of the new strand is occurring in or the direction in which the old strand is read.

The old strand is "read" from 3'-5' so that the new strand can be synthesised from 5'-3'. Maybe, just maybe the confusion lies in the wording not the validity of the content.

P.S. Yes you are right the both strands are made from 5'-3'. The Okazaki fragments are made in this manner too but obviously in fragments. Maybe the question is referring to the direction in which the replication fork is moving in.

[vikash]

it is all mixed up, whom to believe. plz clarify some one.

[googley]

Someone above already answered the question but i'll clarify.

In the 2010 Kaplan LN, pg 32 under RNA Polymerases it says that RNA II & RNA III both make snRNA.

Pg 23 of Kaplan LN, clearly shows that in the Lagging strand, the Primase synthesizes the Primer in the 5' to 3' direction. However, DNA polymerases alpha and delta extend the primer away from the replication fork in the 3'-5' direction.

Hope that helps