#17 Biochem Section Bank

[Haiba]

Hello! This question confused me and my friends.
So I know that palindromic sequences are the sequences that are the same on both strands when read from the 5' -> 3' direction. But what I'm confused on is whether or not there is a way to answer questions like these without having to memorize the palindromic sequences? (Like we need to know the AAGCTT sequence for HindIII) and If memorizing them is a must, which ones I should memorize because they are not in any of my review books?

Thank you! This question has been killing me for weeks

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[laczlacylaci]

You don't need to memorize any palindromic sequence. Like you said, a palindromic sequence is read exactly the same if you flip the 5'->3' to 3'->5'. The only thing I suggest memorizing is that you can have palindromic sequences with up to 4-6 bases, this is the range you will be searching for.
My thought process in getting to the answer would be something like this:
1) Southern blot->restriction site->palindromic sequence.
2) when I'm looking at choices A to D, I mentally highlight the one's where the mutant is different compared to the WT. for example in A, 8th position. You can work for that base to the left or right to find repeating letter that are read backwards.
3)when you figure that out, which takes time (I know) then you can choose the one that presents a mutation in the palindromic sequence.

 

[Haiba]

You don't need to memorize any palindromic sequence. Like you said, a palindromic sequence is read exactly the same if you flip the 5'->3' to 3'->5'. The only thing I suggest memorizing is that you can have palindromic sequences with up to 4-6 bases, this is the range you will be searching for.
My thought process in getting to the answer would be something like this:
1) Southern blot->restriction site->palindromic sequence.
2) when I'm looking at choices A to D, I mentally highlight the one's where the mutant is different compared to the WT. for example in A, 8th position. You can work for that base to the left or right to find repeating letter that are read backwards.
3)when you figure that out, which takes time (I know) then you can choose the one that presents a mutation in the palindromic sequence.

Thank you for your answer. I appreciate you trying to help me as this question is taking me sometime to understand.
But I still don't understand why A is the right answer? What tells us that the 8th position is in the palindromic seqience? All of the answer choices give 5' -> 3' sequences that are the same between the wild type and the mutant except on one location. So how do we know what is the palindromic sequence we look for?

I highlighted all the nucleotides that differs:


what tells us that the mutation is in the palindromic sequence AAGCTT without having to memorize it?
Why choice C can't work, for example, if we assume that the palindromic sequence is TAGTCG?

Again, thank you so much for trying to help me. I appreciate your time in doing so

 

[wizzed101]

You should look up what a palindromic sequence is.

 

[laczlacylaci]

Thank you for your answer. I appreciate you trying to help me as this question is taking me sometime to understand.
But I still don't understand why A is the right answer? What tells us that the 8th position is in the palindromic seqience? All of the answer choices give 5' -> 3' sequences that are the same between the wild type and the mutant except on one location. So how do we know what is the palindromic sequence we look for?

I highlighted all the nucleotides that differs:


what tells us that the mutation is in the palindromic sequence AAGCTT without having to memorize it?
Why choice C can't work, for example, if we assume that the palindromic sequence is TAGTCG?

Again, thank you so much for trying to help me. I appreciate your time in doing so

Palindromic sequence is a DNA/RNA sequence that is the same whether read 5'->3' or 3'->5' (ie. AACGTT the other way around would be TTGCAA)
For choice C, it doesn't work because TAGTC read backwards is GACTA which is completely different from what we first had.
For choice A, I would suggest you to start finding where the mutation happened. -> position 8.
And work forward and backwards to find the palindromic sequence. Let me know if you still need help understand this.

 

[Haiba]

Palindromic sequence is a DNA/RNA sequence that is the same whether read 5'->3' or 3'->5' (ie. AACGTT the other way around would be TTGCAA)
For choice C, it doesn't work because TAGTC read backwards is GACTA which is completely different from what we first had.
For choice A, I would suggest you to start finding where the mutation happened. -> position 8.
And work forward and backwards to find the palindromic sequence. Let me know if you still need help understand this.

Ohhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. I FINALLY GOT IT OMG! SO READY FOR NEXT WEEKEND haha
Sorry, I got really excited.
I got why I wasn't understanding it; bc I thought each choice represents the palindromic sequence not that we have a sequence and a mutation and we NEED to write down what the sequence is, but your answer cleared that up!
But I get it now! Thank you SO much
You made my night

 

[laczlacylaci]

Ohhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. I FINALLY GOT IT OMG! SO READY FOR NEXT WEEKEND haha
Sorry, I got really excited.
I got why I wasn't understanding it; bc I thought each choice represents the palindromic sequence not that we have a sequence and a mutation and we NEED to write down what the sequence is, but your answer cleared that up!
But I get it now! Thank you SO much
You made my night

Glad I could help!

 

[Mit Patel]

What about in Option C... could you not use the sequence TCGA as a palindromic sequence? It is four base pairs long and contains the mutation.

 

[avocadoc]

What about in Option C... could you not use the sequence TCGA as a palindromic sequence? It is four base pairs long and contains the mutation.

If that's the palindromic sequence, then option D is incorrect as well and we can't have two correct answers. This question is just demoralizing...

 

[deleted647690]

What about in Option C... could you not use the sequence TCGA as a palindromic sequence? It is four base pairs long and contains the mutation.

I'm a little confused by this, would a palindrome be defined as
GAAG (exactly same backwards and forwards)

Or

TCGA (complement backwards and forwards.....T with A, G with C)

 

[avocadoc]

I'm a little confused by this, would a palindrome be defined as
GAAG (exactly same backwards and forwards)

Or

TCGA (complement backwards and forwards.....T with A, G with C)

Sorry I'm not Mit Patel but I just saw your reply so I'm going to attempt to answer it. According to wikipedia, "A palindromic sequence is a nucleic acid sequence on double-stranded DNA or RNA wherein reading 5' (five-prime) to 3' (three prime) forward on one strand matches the sequence reading 5' to 3' on the complementary strand with which it forms a double helix."

In your example, the complementary to 5'-GAAG-3' will be 3'-CTTC-5' so it is NOT a palindromic sequence.
However, 5'-TCGA-3' will have a complementary reading 3'-AGCT-5' which reading from 5' to 3' is the exactly same as the template so it qualifies as a palindromic sequence (4-6 base pairs in length as well).

Let me know if it makes sense. It always helps me to write it out with the 5'- and 3'- so I know which direction I'm reading it from.