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How many nucleotides are in a base pair?

davcro

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The solution for question 38 in BR bio part 2, ch 9 (pg 341) says DNA is replicated at 1,666 bp / sec. However there are two replication forks, so each fork replicates 833 bp / sec. The question asks how many nucleotides are added at each fork in one second. Since there are 2 nucleotides in a base pair, the answer shoud be 1,666 nucleotides per second. Instead the answer is 833. How can this be?

Click the image below to see the full solution

http://min.us/lKduD4GBDSRi9
 

chiddler

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A nucleotide is a nucleoside linked to one phosphate group, according to wiki. So all the components of a nucleotide are a phosphate group, a ribose sugar, and the nucleoside/nitrogenous base/pyrimidine or purine. Why do you think there are two nucleotides in a base pair?
 
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davcro

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One of the nucleotides in the base pair is already there. Each replicated base pair contains one old and one new nucleotide, so the number of added nucleotides in each fork is the same as the number of replicated base pairs there.

But there are two strands being replicated. It takes 20 nucleotides to replicate 10 base pairs.
 

davcro

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Yes, 10 of them go to one of the forks and 10 to the other. The question asks how many nucleotides are added at each fork in one second.

A fork replicates two strands of DNA: the leading strand and the lagging strand. One nucleotide goes to the leading strand, one goes to the lagging. If what you say is true, than only one strand is being replicated.

For my example, assume there is only one replication fork. That one fork would add 2 nucleotides for every base pair.
 
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Whe they say a fork replicates at 833bp/sec, does that mean that it produces a net of 833bp/sec, or that it rips apart and processes 833bp/sec from the original strand (and creates 1666bp/sec at that fork)?

I think we all know what we are talking about, and the wording of the question needs to be examined very carefully.
 

davcro

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Whe they say a fork replicates at 833bp/sec, does that mean that it produces a net of 833bp/sec, or that it rips apart and processes 833bp/sec from the original strand (and creates 1666bp/sec at that fork)?

I think we all know what we are talking about, and the wording of the question needs to be examined very carefully.

I attached an image with the full explanation from the answer key in the first post. Anyway here is the exact question:

38. The rate of nucleotide incorporation at each growing replication fork would be roughly:

A. 225 nucleotides per second
B. 425 nucleotides per second
C. 850 nucleotides per second
D. 1700 nucleotides per second

The passage tells you the full chromosome has 4000kbp and that it replicates in 40 minutes. Basically its a unit conversion from 4,000 kpb / 40 min to nucleotides per second.

I'm going to go out on a limb here and say the solution key is wrong. People rave about the passages in BR Bio, but I think they could use another round of editing. I've encountered several questions with grammar / editing errors. Bio is my biggest weakness. Sometimes I cannot tell if the question has vague wording, or if I don't fully understand the vocabulary.
 

milski

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I attached an image with the full explanation from the answer key in the first post. Anyway here is the exact question:

38. The rate of nucleotide incorporation at each growing replication fork would be roughly:

A. 225 nucleotides per second
B. 425 nucleotides per second
C. 850 nucleotides per second
D. 1700 nucleotides per second

The passage tells you the full chromosome has 4000kbp and that it replicates in 40 minutes. Basically its a unit conversion from 4,000 kpb / 40 min to nucleotides per second.

I'm going to go out on a limb here and say the solution key is wrong. People rave about the passages in BR Bio, but I think they could use another round of editing. I've encountered several questions with grammar / editing errors. Bio is my biggest weakness. Sometimes I cannot tell if the question has vague wording, or if I don't fully understand the vocabulary.

Ok, the important information that's missing here is that it is an e.coli chromosome. Bacteria have circular chromosomes that always have two forks working simultaneously (you did mention the two forks in the first post). You are correct that after conversion you end up with 1700 nucl/sec. But since there are two forks working simultaneously and the question asks for nucleotides per fork, the answer is 1700/2 nucl/sec.
 
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teh Big Sky!
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Ok, the important information that's missing here is that it is an e.coli chromosome. Bacteria have circular chromosomes that always have two forks working simultaneously (you did mention the two forks in the first post). You are correct that after conversion you end up with 1700 nucl/sec. But since there are two forks working simultaneously and the question asks for nucleotides per fork, the answer is 1700/2 nucl/sec.

But the conversion doesn't give you 1700 nucl/sec. It gives you 1700 bp/sec. The next conversion is (2 nucl/bp) and the next conversion is (1 chromosome/2 forks).

Each fork is adding 1700 nucl/sec.
 
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MedPR

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The solution for question 38 in BR bio part 2, ch 9 (pg 341) says DNA is replicated at 1,666 bp / sec. However there are two replication forks, so each fork replicates 833 bp / sec. The question asks how many nucleotides are added at each fork in one second. Since there are 2 nucleotides in a base pair, the answer shoud be 1,666 nucleotides per second. Instead the answer is 833. How can this be?

Click the image below to see the full solution

http://min.us/lKduD4GBDSRi9


Either I'm completely confused, or I'm the only one seeing that the question wants to know how many are added at each fork, not at both forks combined.

If DNA is replicated at 1,666 bp/second, then each fork is doing 833 bp/sec. One BP is 2 nucleotides, but one of the nucleotides is already there, so each fork is only adding 833 nucleotides per second..
 

milski

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Either I'm completely confused, or I'm the only one seeing that the question wants to know how many are added at each fork, not at both forks combined.

If DNA is replicated at 1,666 bp/second, then each fork is doing 833 bp/sec. One BP is 2 nucleotides, but one of the nucleotides is already there, so each fork is only adding 833 nucleotides per second..

By 1666 bp/s they mean 1666 full new base pairs, not just completing them. If you read the question, they say that it takes 40 minutes to replicate 400 kbp. That is 400k new base pairs.
 
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teh Big Sky!
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Either I'm completely confused, or I'm the only one seeing that the question wants to know how many are added at each fork, not at both forks combined.

If DNA is replicated at 1,666 bp/second, then each fork is doing 833 bp/sec. One BP is 2 nucleotides, but one of the nucleotides is already there, so each fork is only adding 833 nucleotides per second..

One base pair is 2 nucleotides. You rip them apart, and how many more nucleotides do you need to add to duplicate the base pair? Two more nucleotides. One on one strand, and one on the other strand. In order to duplicate 833bp/sec, you will need to add 1666 nucleotides per second. 833 nucleotides will go on one of the original strands, and 833 nucleotides will go to the other half of the original strand.
 

davcro

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Are we sure the question isn't asking about how many nucleotides are added to each strand by each fork? In that case it would be 833, right? 833nucleotides per second at each of the parent strands, or 1,666 total.

The rate of replication for the entire chromosome is 1,666 bp / second (4000bp/40min). There are two replication forks. Each fork must replicate at 833 bp / second. There are 2 nucleotides in 1 base pair. So each fork must replicate at 1,666 nucleotides / second.
 

MedPR

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The rate of replication for the entire chromosome is 1,666 bp / second (4000bp/40min). There are two replication forks. Each fork must replicate at 833 bp / second. There are 2 nucleotides in 1 base pair. So each fork must replicate at 1,666 nucleotides / second.


If your parent strand is AB, then your daughter strands will be Ab and aB.

If AB has two forks, each one moves in opposite directions around the circular DNA and replicates A and B (forming b and a). If each fork is replicating 833 bp/second, that means 833bp/second on the copy of A as well as the copy of B, for a total of 1,666 bp/second. However, if the question is asking for how many nucleotides/second per fork per parent strand, then it would be 833, no?

I'm just trying to figure out what they might mean in their answer.

"...(1,666bp/sec)/2 or about 833 nucleotides per second." is definitely not right. 833 nucleotides = 1,666/4 bp.
 

gettheleadout

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If your parent strand is AB, then your daughter strands will be Ab and aB.

If AB has two forks, each one moves in opposite directions around the circular DNA and replicates A and B (forming b and a). If each fork is replicating 833 bp/second, that means 833bp/second on the copy of A as well as the copy of B, for a total of 1,666 bp/second. However, if the question is asking for how many nucleotides/second per fork per parent strand, then it would be 833, no?

I'm just trying to figure out what they might mean in their answer.

"...(1,666bp/sec)/2 or about 833 nucleotides per second." is definitely not right. 833 nucleotides = 1,666/4 bp.
This sounds correct to me.
 

theseeker4

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If your parent strand is AB, then your daughter strands will be Ab and aB.

If AB has two forks, each one moves in opposite directions around the circular DNA and replicates A and B (forming b and a). If each fork is replicating 833 bp/second, that means 833bp/second on the copy of A as well as the copy of B, for a total of 1,666 bp/second. However, if the question is asking for how many nucleotides/second per fork per parent strand, then it would be 833, no?

I'm just trying to figure out what they might mean in their answer.

"...(1,666bp/sec)/2 or about 833 nucleotides per second." is definitely not right. 833 nucleotides = 1,666/4 bp.
I think the above is right. They are asking how many nucleotides are being added per second. There are 2 nucleotides per base pair, but only ONE is being ADDED per base pair. The key here is that when you are forming a base pair, you are adding one nucleotide, since one is already present on the parent strand, therefore you don't have to ADD 2 nucleotides per base pair you are creating. For this reason, the number of base pairs created is equal to the number of nucleotides added.

That is the only way it makes sense to me.
 
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Except the exact wording of the question (post 10) specifically asks how many nucleotides are being added per fork-second, not nucleotides per strand-second. A fork contains two strands.

Here is the solution using the factor-label method:

(4000 kbp original/40 min-replication)(1 min/60s)(1000/k)(2 new nt/original bp)(1 replication/2 forks) = 1666 new nt/fork-second

Correct number. Correct units. Correct solution.
 

gettheleadout

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Except the exact wording of the question (post 10) specifically asks how many nucleotides are being added per fork-second, not nucleotides per strand-second. A fork contains two strands.

Here is the solution using the factor-label method:

(4000 kbp original/40 min-replication)(1 min/60s)(1000/k)(2 new nt/original bp)(1 replication/2 forks) = 1666 new nt/fork-second

Correct number. Correct units. Correct solution.

Your calculation assumes each fork is replicating the same base pair as the other at the same time, meaning each fork replicates 1,666 bp/sec and thus adds 1,666 nuc/sec. However, if a circular genome has replication forks going in opposite directions from opposite start points as MedPR said, then at any given second each fork is replicating a different bp than the other. Each can replicate 833 different bp/sec, totaling 1,666 bp/sec for the whole original strand, but since each fork is responsible for only half of those 1,666 unique bp, each fork adds 1,666/2 nuc/sec = 833.
 

theseeker4

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Except the exact wording of the question (post 10) specifically asks how many nucleotides are being added per fork-second, not nucleotides per strand-second. A fork contains two strands.

Here is the solution using the factor-label method:

(4000 kbp original/40 min-replication)(1 min/60s)(1000/k)(2 new nt/original bp)(1 replication/2 forks) = 1666 new nt/fork-second

Correct number. Correct units. Correct solution.
This has to be right. I worked backward from 1666 new nt/fork-second * 60 sec/min * 40min * 2forks = 8,000,000 new nt, which is what is necessary for a 4,000,000bp chromosome to be completely replicated (4,000,000 new nt for each strand). The question must be missing some type of qualifier, or they simply screwed up. I don't see how the book can be right, as hard as I try....
 
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teh Big Sky!
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Your calculation assumes each fork is replicating the same base pair as the other at the same time, meaning each fork replicates 1,666 bp/sec and thus adds 1,666 nuc/sec. However, if a circular genome has replication forks going in opposite directions from opposite start points as MedPR said, then at any given second each fork is replicating a different bp than the other. Each can replicate 833 different bp/sec, totaling 1,666 bp/sec for the whole original strand, but since each fork is responsible for only half of those 1,666 unique bp, each fork adds 1,666/2 nuc/sec = 833.

If a fork replicates 1666 original bp/sec, it adds 3332 new nt/sec, not 1666 new nt/sec as you assert. 1666 original bp = 3332 original nt. After duplication you have to end up with 3332 total bp = 6664 total nt.

A replication fork is defined as one fork, i.e. one master strand being split and made into two daughter strands. It looks like a tuning fork, or a Y. One replication origin creates two forks, each one running away from the other.

http://en.wikipedia.org/wiki/Replication_fork

If there is some outside information that suggests that this particular organism has exactly two origins of replication and therefore four replication forks, that would change the calculations. No such outside information has been presented to us yet, and if this organism is indeed an E. coli going through one replication event, E. coli only has one origin of replication per duplication.

http://en.wikipedia.org/wiki/Origin_of_replication#Prokaryotic
 

gettheleadout

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If a fork replicates 1666 original bp/sec, it adds 3332 new nt/sec, not 1666 new nt/sec as you assert. 1666 original bp = 3332 original nt. After duplication you have to end up with 3332 total bp = 6664 total nt.
That's not what I'm asserting though, I'm saying that as the entire original strand is replicated by the two forks, each fork is positioned at a different point on the original strand (see MedPR's description of circular genome replication) and thus each fork is replicating different base pairs. If each fork replicates 833 unique base pairs of the original strand per second, then the entire genome is replicated at 1,666 bp/sec. However in such a situation, since each fork is individually replicating 833 bp/sec, only 833 nucleotides are added per second at each fork.

A replication fork is defined as one fork, i.e. one master strand being split and made into two daughter strands. It looks like a tuning fork, or a Y. One replication origin creates two forks, each one running away from the other.

http://en.wikipedia.org/wiki/Replication_fork

If there is some outside information that suggests that this particular organism has exactly two origins of replication and therefore four replication forks, that would change the calculations. No such outside information has been presented to us yet, and if this organism is indeed an E. coli going through one replication event, E. coli only has one origin of replication per duplication.

http://en.wikipedia.org/wiki/Origin_of_replication#Prokaryotic
Sorry, I misstated the point about the separate forks. In bacterial genome replication there is a single origin at which the forks begin, but they proceed in opposite directions. (See 13.2.1 here: http://www.ncbi.nlm.nih.gov/books/NBK21113/) All I'm seeing at that Wiki link is that E. coli does indeed have a single origin of replication, which is consistent with the corrected (from my misstated version) description of bidirectional genome replication.

Edit: To further clarify, the forks in this case are not comprised of two individual strands of nucleotides acting as templates. In each fork, one strand is used to add new nucleotides, while the other is only added to at the opposite fork (semi-conservative replication.)

[YOUTUBE]HMMq2uH4iUk[/YOUTUBE]
 
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since each fork is individually replicating 833 bp/sec, only 833 nucleotides are added per second at each fork.

If you have 833 original bp, you have to add 1666 nucleotides at that fork in order to duplicate the 833 original bp. If you only add 833 nucleotides, as you suggest in the sentence I quoted above, you have not duplicated 833 original bp. Your job is only half done. You have 833 new bp (consisting of 833 original nucleotides and 833 of the new nucleotides), and you still have another 833 unmatched original nucleotides wondering why they have not been duplicated yet.

833 original base pairs
1666 original nucleotides
...requires...
1666 new nucleotides to perform a duplication of the original 833 original base pairs

833 new nucleotides isn't gonna get the job done
 

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This question sucks, period. If the answer in the book wasn't 833, I would have no problem accepting what MT Headed is saying.

Problem is, you would think this error would've been caught before considering how many people here use TBR Bio. No offense to MT, or to TBR, but I can see how both arguments are right (and wrong) depending on the context and exact wording of the question.
 

gettheleadout

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If you have 833 original bp, you have to add 1666 nucleotides at that fork in order to duplicate the 833 original bp. If you only add 833 nucleotides, as you suggest in the sentence I quoted above, you have not duplicated 833 original bp. Your job is only half done. You have 833 new bp (consisting of 833 original nucleotides and 833 of the new nucleotides), and you still have another 833 unmatched original nucleotides wondering why they have not been duplicated yet.

833 original base pairs
1666 original nucleotides
...requires...
1666 new nucleotides to perform a duplication of the original 833 original base pairs

833 new nucleotides isn't gonna get the job done

Each fork is only duplicating one of the single strands present in the fork.
 

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Each fork is only duplicating one of the single strands present in the fork.

Good heavens, no!

Single stranded DNA is SCARY :eek: It binds to itself in hairpin turns, making a real tangled mess of things, and it is easily broken. Once the DNA is broken, it's highly likely the cell will die.

During DNA replication, single strand binding proteins are attached to the temporarily single stranded DNA (http://en.wikipedia.org/wiki/Replisome#Single-strand_binding_proteins - good pic at the top of the article) but it would be utterly impractical to bind two million nucleotides to SSBP's from each fork until the replisome from the other side wraps around to start duplicating the other strand.
 

gettheleadout

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http://en.wikipedia.org/wiki/File:DNA_replication_en.svg
In this image, there are 2 strands being replicated in 1 fork. The question has two forks in the circular chromosome, so a total of 4 strands, each adding 833 nucleotides per second, so 1666 nucleotides per fork per second.

No, both strands are simultaneously being replicated at each fork.
I've been imagining each of the two original strands being added to separately at only one fork each. I realize that in linear DNA the two strands split completely and, as there are free ends, both strands are added to. My inference with circular DNA was that only one strand would be added to in each of the two directions.

See 0:15-0:16 here: http://www.youtube.com/watch?v=6EAI4_NGNTM

I'm only seeing nucleotides being added moving in one direction on each strand. As the gap shown there gets larger, the forks are apparent, but each one is adding to only one strand in the fork in only one direction. Am I misinterpreting this?
Good heavens, no!

Single stranded DNA is SCARY :eek: It binds to itself in hairpin turns, making a real tangled mess of things, and it is easily broken. Once the DNA is broken, it's highly likely the cell will die.

During DNA replication, single strand binding proteins are attached to the temporarily single stranded DNA (http://en.wikipedia.org/wiki/Replisome#Single-strand_binding_proteins - good pic at the top of the article) but it would be utterly impractical to bind two million nucleotides to SSBP's from each fork until the replisome from the other side wraps around to start duplicating the other strand.
I didn't mean to imply that the DNA was single-stranded, I was referring to the two strands present at each fork individually as "single strands."

Edit: I see I was leaving out the addition of Okazaki fragments to the opposite strand in the fork, which does indeed still result in semiconservative replication. Okay, that makes sense.

I concede the point; there have to be 833 base pairs added to each fork, which means there must be 1,666 nuc's added per fork.
 
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Whiteshoes

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I've been imagining each of the two original strands being added to separately at only one fork each. I realize that in linear DNA the two strands split completely and, as there are free ends, both strands are added to. My inference with circular DNA was that only one strand would be added to in each of the two directions.

See 0:15-0:16 here: http://www.youtube.com/watch?v=6EAI4_NGNTM

I'm only seeing nucleotides being added moving in one direction on each strand. As the gap shown there gets larger, the forks are apparent, but each one is adding to only one strand in the fork in only one direction. Am I misinterpreting this?

I didn't mean to imply that the DNA was single-stranded, I was referring to the two strands present at each fork individually as "single strands."

Edit: I see I was leaving out the addition of Okazaki fragments to the opposite strand in the fork, which does indeed still result in semiconservative replication. Okay, that makes sense.

I concede the point; there have to be 833 base pairs added to each fork, which means there must be 1,666 nuc's added per fork.

I think i still may agree with you. If each replication fork yields 833bp doesn't that mean ~416.5 nucleotides were added complementary to the leading strand and ~416.5 nucleotides were added on the opposite lagging strand. So total should still be roughly 850 right?
 

gettheleadout

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I think i still may agree with you. If each replication fork yields 833bp doesn't that mean ~416.5 nucleotides were added complementary to the leading strand and ~416.5 nucleotides were added on the opposite lagging strand. So total should still be roughly 850 right?
833bp means 1666 nucleotides added over both strands. That means 833 nucleotides added per strand, not 416.5
 
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