Speed and precision of DNA replication
Sal reflects on the amazing speed and precision with which DNA replication takes place.
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- 1 mistake for every billion nucleotides. in the grand scheme of the body, will amount to a lot of mistakes, and an error in dna sounds pretty dangerous. can someone clarify about these "errors"? are they serious? what kind-of errors? how does our body react?(13 votes)
- The number may seem high. But there are large stretches of non-coding junk DNA which do not translate into anything, so an error does not affect anything.
Also the genetic code is called redundant, i.e. there are often more then 1 possible codons for an amino acid. So there is a good chance that a single wrong nucleotide doe not change the protein sequence at all.
If there is a wrong nucleotide in the newly synthesized DNA strand it cannot base-pair correctly with the older template strand. This mismatch then can activate the cell's DNA repair tools to remove the mismatch.(25 votes)
- What part is called as okazaki fragment? Does that include RNA primer too?(8 votes)
- Okazaki fragments are the unjoined fragments that make up the lagging strand. Okazaki fragments are joined by the enzyme ligase to form a continuous strand.(15 votes)
- How much time does it take to replicate a single DNA molecule?
1000 base pairs per second in itself sound fast. But looking at the broader context, of how many base pairs are needed for a single DNA molecule, then it seems kind of slow to me.
Khan mentions in this video that a DNA has billions of nucleotides, meaning a DNA has at least millions of base pairs.
Then replicating at 1000 base pairs per second, seems to make it take hours to replicate a single DNA molecule. Is this correctly understood?(5 votes)
- There is no single answer to this question because it depends on multiple factors including:
• the length of the DNA molecule — this can vary from very small (220 nt for the Grapevine yellow speckle viroid) to enormous (hundreds of billions of bp for some plant chromosomes)
• the speed of the DNA polymerase(s) — prokaryotic DNA polymerases are about 10x faster than the fastest eukaryotic DNA polymerase
• the number of origins of replication (ORIs) per DNA molecule
- bacteria typically only have one ORI (but they can initiate a new cycle of replication before the first one is is finished)
- eukaryotes typically have many ORIs, so they are duplicating different regions in parallel
So, DNA replication in eukaryotes is ~10x slower and the individual DNA molecules are usually much larger, but replication takes place from multiple sites.
The bacteria Escherichia coli (often abbreviated to E. coli) replicates its entire 4 million bp genome in ~30 minutes (depending on growth conditions like temperature).
Baker's yeast takes ~30 minutes to replicate its ~12 million bp genome, which means that each of its chromosomes (largest is ~1.5 million bp, smallest is ~230 thousand bp) takes about 30 min to replicate.
Human tissue culture cells take around 10 hours to replicate the ~6.4 billion bp of a diploid human genome. (Human chromosomes range from ~47 to ~250 million bp.)(9 votes)
- Dna polymerase begins replication from 3' to 5' end and so leading strand is replicated continuously without any problem but lagging strand is replicated in the form of okazaki fragments....is this not possible that replication fork is formed on both sides of dna and replication begins from both sides simultaneously and also dna polymerase begins replication from 3' to 5' on the lagging strand ...so both strands of dna will be replicated simultaneously and also the lagging strand can be replicated continuously without the formation of okazaki fragments.....can someone explain?(4 votes)
- No. It is not possible. It would be easier to show you with a diagram, but I'll try. First of all, understand that the 5'-3' numbering in DNA replication refers to the direction in which the new strand is being made - the DNA polymerase "makes" the new 5' end before the new 3' end, if that makes sense. Now, visualize a replication fork. The DNA polymerase making the leading strand can simply follow the progress of the fork's opening continuously, since there will always be room for it to proceed. If continuous replication were to happen on the opposite strand, since the new strands are synthesized 5'-3' relative to their complementary strands, and the original strands are antiparallel to each other, then the new strands are being synthesized in opposite directions. The DNA polymerase making the leading strand starts near the 3' end of the existing strand and follows the replication fork indefinitely, but where does the other DNA polymerase - the one making the lagging strand - start? If it starts at the literal fork in the two original strands and follows said strand indefinitely to the end, it will only replicate from that point to the end, and all of the DNA before that point in the fork won't get replicated. This is why Okazaki fragments are a thing - because the DNA polymerase has to keep "jumping" backwards along the original strand to replicate newly exposed segments of DNA. Sorry this is so long haha.(5 votes)
- A couple videos ago, Sal said that the human genome has around 6 billion base pairs. But in this video, he said that there is 1 mistake in every billion base pairs replicated. That means that there are around 6 mistakes in the human genome. I honestly think that's a lot, but we still function properly. What's going on?(4 votes)
- That's not really what he meant. In the human body, there are trillions of cells, and they are replicating their DNA if they need to divide to new cells. So the copying is happening all the time, and that probability means there are always some new errors in the newly formed cells' DNAs. Only an incredibly small portion of the errors has any effect at all. But as we age, the number of the errors tends to increase, and that will also increase the probability of different age-related diseases.(3 votes)
- What chemicals do you need to split DNA?(3 votes)
- DNA helix is unwound by Topoisomerase, which then allows the enzyme Helicase to separate the two strands of DNA.(2 votes)
- Why DNA plymerase which makes mistakes in every 10^4 bases in Vitro are so precise when functioning in Vivo(only one mistakes in every 10^10 bases)??(2 votes)
- Different polymerases have different error rates, so it is important to make sure you are comparing the same polymerases.
An error rate of 10⁻⁴ sounds very high, where did you get that number from? Was it for Taq polymerase used in PCR? (Taq has a very high error rate.)
In vivo error rates for replication will be lower than in vitro — the primary reason for this is that there are mechanisms for recognizing and correcting errors after replication.
KhanAcademy has material on this here:
- I realize the precision of DNA replication is crucial for the vitality of an organism. Is speed also an important factor? If so, why?(2 votes)
- Yes, it is. If the rate of polymerization was pretty low, it would take years to complete the process.
In our 23 chromosomes, there are approximately 3 billion base pairs. Think about every cell which holds chromosomes, and what about all those billions of base pairs in each.
If the rate was slow, nothing would have gone right.
We can't afford the process to be anything less than precise and fast.(1 vote)
- What exactly does the statement, "polymerase - as fast as 700t base pairs per second" describe?(1 vote)
- DNA polymerase can add as fast as 700 base pairs per second.
Each second, polymerase will add 700 base pairs to the segment.(2 votes)
- What are those little purple things hanging of the DNA (above and below the helicase) in the model? What do they do?(1 vote)
- I think these are the Single-strand binding proteins that keep the strands separated.(1 vote)
- [Voiceover] In the earlier video on DNA replication, we go into some detail about leading strands and lagging strands and all of the different actors, all of these different enzymatic actors. But I left out what is probably the most mind-boggling aspect of all of this, and that's the speed and the precision with which this is actually happening. As we talked about in that video, it feels pretty complex. You have this topoisomerase that's unwinding things, the helicase is unzipping it. Then you have the polymerase that can only go from the five prime to three prime direction, and needs a little primer to get started, but then it starts adding the, it starts adding the nucleotides. On the lagging strand, you have to have the R, you get the RNA primer, but then it's going from, once again, from five prime to three prime, so you have these Okazaki fragments. And all of this craziness that's happening, and remember, these things don't have brains. These aren't computers. They don't know exactly where to go. It's all because of the chemistry. They're all bumping into each other and reacting in just the right way to make this incredible thing happen. Now what I'm about to tell you is really going to boggle your mind. Because this is happening incredibly fast. DNA polymerase has been clocked, at least in E. coli, has clocked at approaching 1,000 base pairs per second. I think the number that I saw was 700-something base pairs per second. So polymerase, let me write this down. This is worth writing down, because it's mind-boggling. Gives you a sense of just how amazing what the machinery in your cells are. So it's been as high as, and it can change. It can speed up and slow down, and that's actually been observed. But polymerase as fast as, as fast as 700-plus base pairs per, per second. So if this, on this diagram, it, man, it's just zipping, it's just zipping along, at least from our perceptual frame of reference. A second seems like a very short amount of time to us, but on a molecular scale, these things are just bouncing around and just getting this stuff done. Now the second thing that you might be wondering, okay, this is happening fast, but surely it has a lot of errors. Well, the first thing you might say, well, if it had a lot of errors, that would really not be good for biology, because you always have, you have DNA replicating all throughout our lives. And at some point you just have so many errors that the cells wouldn't function any more. And so lucky for us that this is actually a fairly precise process. Even in the first pass of the polymerase, you have one mistake, you have one mistake, let me write this down, 'cause it's amazing. One mistake for every, for every approximately 10 to the seventh. So this is 10 million, 10 million in nucleotides. Nucleotides. And that might seem pretty accurate, but you gotta remember, we have billions of nucleotides in our DNA. So this would still introduce a lot of errors. But then there's proofreading that goes back and makes sure that those errors don't stick around. And so once all the proofreading takes place, it actually becomes one mistake, one mistake for every approximately 10 to the ninth nucleotides. So approximately, you can, it would do this at an incredibly fast pace, as fast as 700-plus approaching 1,000 base pairs per second. And you have one error every billion nucleotides, especially after you go through these proofreading steps. And so it's incredibly fast, and it's incredibly precise. So hopefully that gives you a better appreciation for just the magic that's literally, I would look at your hand, or just think about, this is happening in all of the cells or most of the cells of your body as we speak.