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DNA structure questions (simple)

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DNA structure questions (simple)

Postby doctobe » Sat Feb 20, 2010 6:52 pm

I had some DNA questions. kind of straightfoward I posted what I believe to be the right answers. I wanted to make sure I was reading the questions properly.

The twist of a DNA double helix corresponds to the angular rotation that is needed to get from one base pair to the next. In an idealized DNA molecule the twist is 36 degrees, meaning that if you rotate one base pair by 36 degrees and move it up the helix by 0.34 nm, you will occupy the position of the next base pair. Thus, the distance or rise along the axis of the double helix is 0.34 nm between 2 consecutive base pairs.
1) Based on the values of twist and rise of an idealized DNA molecule, calculate the number of base pairs per complete turn in a double helix, and the pitch (the width of one complete helix turn measured along the helix axis) of the double helix. Show your calculation (5 pts)

1 twist = 36 degrees
10 twists =360 degrees = one complete helix turn
1 base per twist =.34nm =length of twist.
.34nm=36 degrees
34nm x10=360 degrees
1.10 base pairs per turn
2. each base pair is 0.34 nm thick
3. 10 base pairs would be 0.34 nm X 10 = 3.4 nm length


2) What is the length of a double stranded piece of DNA coding for a 200 amino acid long protein? Show your calculation. (5 pts)

1 amino acid = 1 codon= 3 base bairs
200 amino acids= 600 base pairs.
From question 1.
.34nm=1base pair.
Answer: .34nm x 600 bp.= 204nm (length of DNA)
(isn’t the mRNA what codes?)


3) A known protein recognizes a specific DNA sequence and binds to one side of the DNA double helix that contains that sequence. It was shown that two -helices separated by a distance of 34 Å in the protein interact with the major groove of the DNA molecule. Each helix “recognizes” a short sequence and both sequences are separated by a fixed number of nucleotides. Would the binding affinity of the protein for the DNA increase (or decrease) when number of nucleotides separating the two protein binding sites is increased (or decreased)? Explain (5pts)

The binding affinity of the protein for the DNA would decrease. Any change in the distance of the binding sites whether greater or smaller would decrease the affinity.

I know this answer is correct but it hard to put into words. Any help?
What concept is this question testing. I went to the section on recognition helix and there was no one sentence that kind of answered this question although it is relatively straightforward.
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Postby JackBean » Sat Feb 20, 2010 7:53 pm

I think, that the length should be 603 bp, because you have also STOP codon ;)

3) yes, the protein would be able to bind only with one helix.
Imagine, that you insert only one nt, only one! What does it cause? Shift by 0.34 nm, that's not so bad, but you have also the twist by 36° and that's more serious, because the helix in the same position would bind to brand new sequence. Depends, how much flexible the protein is...
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re:

Postby doctobe » Sat Feb 20, 2010 8:48 pm

JackBean wrote:I think, that the length should be 603 bp, because you have also STOP codon ;)

3) yes, the protein would be able to bind only with one helix.
Imagine, that you insert only one nt, only one! What does it cause? Shift by 0.34 nm, that's not so bad, but you have also the twist by 36° and that's more serious, because the helix in the same position would bind to brand new sequence. Depends, how much flexible the protein is...


I never thought about the stop codon. I am missing the little things.

So for question 3. I succinct answer could read, if once changes the number of nucleotides that could alter the twist and angle of the helix. This could change the size and shapes of the major and minor grooves which are important in protein-Dna binding.
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