Naked Science Forum
Non Life Sciences => Chemistry => Topic started by: tuhin on 04/09/2003 06:17:25
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Hello,
I am searching for answers to 1. why are DNA strnds are antiparallel and 2.the circular DNA being a closed structure , how to determine their 5' and 3' ends of a particular strand ( this becomes specially relevant during the replication of the circular DNA).
Let me explain-
A 5' end of a strand means , to the fifth carbon atom of the pentose sugar of that nucleotide only a phosphate is attached .There is no nucleotide beyond that & hence diester bond formation does not take place.3' end of a strand means the third carbon atom of the pentose sugar of the terminal nucleotide ( the other or opposite end of the 5' end ) bears -OH group. Being terminal, the -OH grou is free & is not involved in diester bond formation.DNA replication by Pol3 proceeds in 5'-->3'direction. Pol3 actually catalyses the diester bond formation between 3'-OH of the growing end of the nucleotides & the incoming 5'-PPP of the deoxynucleoside triphosphate. Now if a DNA strand reads 5'-ATATAT-3' , replication of the complimentary strand actually starts from 3' end of the template strand. It does not start from the 5' end of the template strand. Since DNA replication can proceed only 5'-->3', theoretically it could start from the 5' end of the template strand but it does not happen that way.
Why do two strands of the DNA need to be oppositely oriented? One is head to tail & the other is tail to head ?! Does it something to do with the nitrogen base pairing of the opposite strands? Is it because of the fact that hydrogen bond formation between complimentary nitrogen bases can not occur if they are not oriented that way?!
My second question is , for any circular DNA ( as in E.coli or any prokaryotes), being a closed structure ( and there are free ends)how do I designate a particular nucleotide of a strand as the first (5'-P) & the last nucleotide (3'-OH). In other words how do I designate the 5' and the 3' ends of the strands?
tuhin
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Ok, good question.
5' and 3' ends of DNA are relative terms. Mostly we speak in terms of in the 5' to 3' direction meaning that in the case of a circular piece of DNA the polymerase always works 5' to 3', no matter where it starts. When it copies the complementary (3 to 5) strand, at low resolution it looks as though synthesis is progressing the wrong way (3 to 5) but if you look closely the DNA is actually being copied in short 200bp segments each in the 5 to 3 direction. These are called Okazaki fragments after the guy who first described them
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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Thanks Chris for your quick reply ! But I made a small typing mistake in the second part of my question. Circular DNA does not have any free ends. We normally mean 5' end of a strand when to the fifth carbon atom of the sugar only P is attached and there are no nucleotides beyond that point. Similarly, 3' end of the strand means to the third carbon atom of the pentose sugar only -OH is attached and there are no nucleotides beyond that.
Both the leading( continuously replicating) and the lagging( discontinuously replicating) strands are copied in the 5'-->3' direction.
It would be good if you elaborate your answer slightly.
What do you think of the first question?
Thanks
tuhin
quote:
Originally posted by chris
Ok, good question.
5' and 3' ends of DNA are relative terms. Mostly we speak in terms of in the 5' to 3' direction meaning that in the case of a circular piece of DNA the polymerase always works 5' to 3', no matter where it starts. When it copies the complementary (3 to 5) strand, at low resolution it looks as though synthesis is progressing the wrong way (3 to 5) but if you look closely the DNA is actually being copied in short 200bp segments each in the 5 to 3 direction. These are called Okazaki fragments after the guy who first described them
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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tuhin, I'm not sure if this answers your questions, but the sense and antisense strands are not limited to a particular DNA strand. TATA box recognition can occur on both strands, therefore only the antiparallel nature of DNA would permit this to occur.
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Absolutely right. The strands are antiparallel and either can contain coding regions. In some viruses the strands are co-linear (overlapping) so some genes contain antisense bits of others. But transcription always occurs in the 5' to 3' direction, no matter what strand it originates from.
In a plasmid you don't need free ends to define the 5' and 3' direction - it's arbitrary depending upon where you start and merely refers to the direction you are moving in along the strand relative to where you started; that is, what base you called 1.
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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Hello
If you heat DNA, composed of only adenine in one and thymine in other strand, well above melting temperature, and then slowly cool, strands reanneal in antiparallel fashion. Only in this orientation proper H-bonds between bases could be formed.
Tom
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Dear Tom
not quite sure where you are coming from with this - can you explain please ?
Chris
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx
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Any piece of DNA separates in two complementary strands upon heating and these two strands reanneal in antiparallel fashion, one can say, because of COMPLEMENTARITY, not because only in antiparallel orientation H-bonds could be formed. Example:
5'-TTACGGCAT-3'
3'-AATGCCGTA-5'
is the only possible orientation and not:
5'-TTACGGCAT-3'
5'-ATGCCGTAA-3'.
"Theoretically", polyA and polyT (or palindromic structures) could fit together in two ways:
5'-TTTTTTTTTTTTTTTTT-3'
5'-AAAAAAAAAAAAAAAAA-3'
I hope this will help.
Tom
and
5'-TTTTTTTTTTTTTTTTT-3'
3'-AAAAAAAAAAAAAAAAA-5'
Only in the second model H-bonds could be formed, but to see why, you need 3-D model in your hand.
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Interesting point. Thanks.
"I never forget a face, but in your case I'll make an exception"
- Groucho Marx