The Science of Everything Podcast - Episode 35: DNA Structure and Function Part 2

Episode Date: July 3, 2012

Continuing on from episode 34, I discuss in detail the processes of DNA replication, transcription from DNA to RNA, and the translation of RNA to proteins. In doing so I examine the molecules and structures involved, the mechanisms of their operation, and how all the processes work together to facilitate the production of proteins from DNA.

You're listening to The Science of Everything podcast, episode 35, DNA structure and function, part two. So in this episode, we're going to continue directly from episode 34, so pretty good idea to listen to that first, where I talked about the structure of DNA, including nucleotides, how they connected together, the different types of nitrogenous bases that are connected to the nucleotides, a part of the nucleotides and form the double-stranded structure of the DNA double helix. We also talked about the genetic code, including the central dogma of molecular biology, the one gene-one-protein hypothesis, we talked about codons and the reading frame. In this episode, what we're going to do is look at the details of how the central dogma works. We're going to look at how we get from DNA to RNA and how we get from RNA to proteins.

Specifically, we're going to look at the processes of replication, transcription, and translation, including how they start, or how they activated, how they are continued, how they're terminated, and how all that fits together in the structures that. carry these processes out. Let's get into it. We'll start with replication. So replication is actually not exactly part of the central dogma because this is just about how DNA replicates itself or how we go from one DNA strand to two DNA strands, containing essentially the same information. So DNA replication is the process by which a cell's entire DNA is copied or replicated. This process occurs during the synthesis phase of the eukaryotic cell cycle. So we haven't actually talked about the cell cycle before. That's a topic I need to cover actually. But there are different Cell cycle is basically the cycle of life for cells, and there are different phases to that cycle.

One of them is called the synthesis phase, and it basically refers to the time when DNA is copying itself. And that's important because if you're going to have a cell that divides up into two cells, you know, that replicates itself, obviously each of those copy cells or daughter cells needs to have a copy of the DNA that made up the cell, otherwise it doesn't know what proteins to make. And so the synthesis phase is when you copy the DNA so that you've now got two copies, one for each of the daughter cells. In prokaryotic cells, these are the simple cells like bacteria and archaea, replication of the DNA strand occurs at a single site, or I should say it begins at a single site around the DNA strand called the terminus, and then proceeds in one direction and going around

the strand, because in prokaryotes, the DNA is, well, for the most part, there are additional insertions called plasmids, but we won't worry about those. For the most part, DNA in prokaryotes is just one big long circular strand. I mean, it's still a double-hirt. helix structure, but the DNA is just one long circle of that double helix. And so when that replicates, you just start at one spot and go around, replicating the whole thing. And by the time you finish, you're separating out and you've got two rings of DNA. In eukaryotes, it's more complicated, largely because they have a lot more DNA, and it would be difficult to do it in one go because you get tangled and other problems.

So eukaryotic cells have multiple origins of replication. So you don't have a single term, and you have multiple ones where the replication is occurring in both directions. and essentially you can imagine you've got two points where you start replicating and those replication occurs until the two points link up, kind of like a railway. A railway, you imagine you start building a railway at one spot, and you build to east, and you also start a different spot, you build to the west, and eventually the eastern west lines link up,

and you've got one railway line. That's kind of what happens in Eukaryotic Cell replication, that Eukaryotic Cell DNA replication. Okay, but that's some background, but how does the process actually work? One thing that you need to know is, in eukaryotic cells, and this is mostly what we'll talk about from now on, the DNA is not just in a single circular strand like it is in prokaryotes. It's arranged in a very complicated structure that has multiple levels of folding and curling and layering and it's exceptionally complicated,

we still actually don't fully understand all of the details. Normally, in most phases of the cell cycle, the DNA in eukaryotic cells is tightly curled and wound and bound up. During replication, all of the DNA has to unwind, at least the parts that are replicating, in order for the replication to occur. So that's the first thing that happens in a sense. The DNA, or the chromosomes, unwind and uncurl and unravel, so that you can actually get to the actual DNA strands and start doing the replication. Once that's occurred, the first stage sort of after that is called initiation.

Initiation is when you have a particular protein that binds to a particular series of nucleotides in the terminus, you know, the place where we start the replication process. So particular protein bias to this spot and starts to unzip the DNA. So when I say unzip, this is sort of a euphemism, because remember, we've got two strands of nucleotides, which are connected to each other via the hydrogen bonds between their nitrogenous bases. If you want to split up the DNA strand into two nucleotide strands, you need to unzip or break those hydrogen bonds. And that's what is begun by the initiation process, but that's really carried out in the next stage,

which is the unwinding phase, which is when an enzyme called helicase, or DNA healer case, I should say, enzymes, it's basically just a protein. This helicase unwinds the two strands. It's kind of like a zipper. It just moves through breaking all of the bonds, the hydrogen bonds, connecting the two nitrogenous bases together. And so it sort of looks like a fork structure where you've got the helicase sort of pushing into the unbroken section of the DNA

and leaving behind it in its wake two separate, now separate strands of nucleotides separated from each other, kind of like a zipper going down a jacket. So that site that the helicase has moved through is called the replication fork. So that's the unwinding phase where you have to split up the two sides to the DNA. Now there's a problem with that

when we have these bare single-stranded DNAs it tends to fall back on itself and form secondary structures kind of like the folding I talked about before, and that will interfere with replication. So we can't have that to happen. In order to avoid this in this third stabilization phase, what happens is special single-strand proteins bind onto the DNA,

basically just to stop it from curling up and interacting with itself. This is really important. You can imagine that if it was just left to itself, the DNA, the single-stranded DNA would curl up into loops, because remember, there will be parameters and purines, both at various different locations on the single strand, and if two of those get close enough to each other, they'll form a new lot of hydrogen bonds and bind together,

and that will put a loop into the single strand, will affect the replication process and screw things up. So you can't have that happen. To avoid it happening, you have special proteins coming on and binding to the DNA, the single-strand DNA, both of the sides that are left, in order to prevent that curling up from happening. So that's called the stabilization phase, and that happens.

Now we've got two strands stabilized, that have been unzipped by the helicase and stabilized by these special proteins. What happens next? Well, in this phase, another enzyme, so another protein called DNA polymerase, catalyzes the formation of phosphodiaster bonds between nucleotides that are being added to the new DNA strands.

Remember, we're unzipping the DNA strand, exposing the nitrogenous bases on each of the two strands, and those bases will naturally tend to pair with their complementary base pairs. And of course, we've got a whole bunch of these separate individual nucleotides sort of floating around it in the cytoplasm, and just sort of randomly, basically, some of these will happen to be in the area where the DNA is replicating, and some of them will bond to their corresponding,

complementary base on the naked DNA strand, because that's energetically favorable for them to do. And what the DNA polymerase does is just basically runs along the naked strand and joins up all of these new base pairs to each other, that is, joins up the sugar backbone sections of these nucleotides by forming phosphodice bonds. So the DNA polymerase does not actually provide the extra nucleotides. It just connects them together via the catalization of phosphorylase. deist bonds, which link these new nucleotides. And the DNA polymerase just moves along from the 3 prime to the 5 prime end of the leading strand of DNA, making all of these, catalyzing all of these reactions to link all the nucleotides up into a new chain. Now, you notice I use

the term leading strand there. This is because you unzip the DNA, the original DNA, and it's now in two sections, two single strands. One of these is called the leading strand, and that once nice and easy because the DNA polymerase can just go from the 3 prime to the 5 prime amend. Once again, don't worry about the terminology. It's just a way of referring to the direction of the DNA. It can go from one into the other and just catalyze all of the phosphodestabonds and it's all good. However, the lagging strand, which is the other strand of DNA, the other single strand now, from the original, goes in the opposite direction because the DNA is sort of like a road. On one side you drive in one direction, on the other side you turn around and you drive

in the opposite direction. But you always have to drive on the same side of the road, whether it's left or right, depending on what country you're in, where I live, you drive it on the left side of the road. So the DNA's kind of like that. You have to stay on the left side of the road. Or in this case, the polymerase has to run from the 3 prime to the 5 prime end. However, the complementary strands of both sides of the DNA can't be catalyzed from 3 prime to 5 prime ends. Because, basically, if you imagine the original DNA molecule is a zip that's being opened up, on one side of the, on one of the two strands, is the leading strand, you can just go from the 3 prime to the 5 prime, and the DNA, the DNA polymerase can just go from the 3 prime to the 5 prime end straight, no problems, because it's

moving in the direction of the replication fork. Remember, that's the bit where the DNA is opening up and it's splitting it to the two sections. The DNA polymerase is moving towards it. So as the DNA opens up, the DNA polymerase just moves on and goes in the same direction and it's all good. But for the lagging strand, the DNA polymerase, because it has to sort of go in the same direction, relative to the strand, would have to move away, or does have to move away from the replication fork, which is a problem because it means it can't just sort of start and keep going as the DNA keeps unfolding, because it's moving in the opposite direction to which the DNA is unfolding. Very hard to describe this without a diagram, but hopefully you can kind of get what I'm saying.

Basically, you've got kind of like a zip that's being unwound, and on one side, the DNA polymerase is fine because it can just go, it can just keep moving along, catalyzing their reactions in the direction of the zip itself as the zip moves down. But on the other side of the DNA, the other side of the zip in our analogy, the DNA polymerase has to move in the opposite direction away from the zip. And the only way you can do this is in lots of small little segments. So you do one little bit and then you do another little bit as extra portions of the lagging strand are opened up as the zip continues to unwind. Or in other words, as the as the HILA case continues to open up more of the DNA. So this is why the replication process

This is different on the leading and the lagging strands. So on the leading strand, remember that's the easy one, the DNA polymerase just go straight along, catalyzes the phosphory diastobons between the sugar backbones of the corresponding nucleotides, and then you've got new domicesterate of DNA is formed, and it's all good. However, on the lagging strand, the DNA polymerase has to move in the opposite direction away

from the healer case, which is unwinding the DNA. And so the only way that can work is it has to start with small sections of R&Ns, primers, which is like a bunch of RNA nucleotides, so not DNA in this case, a short segments of which bond to the lagging strand, which has been opened up, and provide a sort of starting point for the DNA polymerase to catalyze the bonds with. And then basically the DNA polymerase bonds to that RNA primer and then moves along in the three prime to the five prime direction, as it normally does, as it has to actually, because it doesn't work any other way, catalyzing phosphodastobons in the same way as it does on the leading strand.

In this case, though, remember, because we're looking at the opposing single-stranded DNA, when the DNA polymerase moves in three-prime to five-prime direction, because it's sort of on the other side of the road now, it's now moving away from the helicase and the splitting open of the double helix. So you can imagine, the helicase has just opened up a portion of the DNA, and on the leaning strand, yeah, we're fine, the polymerase goes straight down. On the lagging strand, a couple of those nucleotides that have just been, opened up, are bonded to by the DNA, sorry, the RNA primer, and then the DNA polymerase bonds

to that primer and starts moving along, catalyzing phosphodiaster bonds in the same way as on the leaning strand, and moves in the opposite direction to which the helicase is moving, opening up the two strands. And that keeps going for a short while until it's sort of finished it, until it's finished its stretch. But as that's been occurring, the DNA has continued to unwind, and now there's a bunch more naked, exposed, that is, non-paired nucleotides, that are on the other side of the RNA primer and the bunch of nucleotides that we just put in with that DNA polymerase. And so now the DNA polymerase sort of has to go back again and start again doing another one of those fragments, starting with an RNA primer and then moving along and catalyzing once again until it meets up.

It joins up those two fragments. The first one I did with the second one it just did, they meet up and they're joined by a similar enzyme. but then the whole process has to start again because once again the hila cases open up even more of the DNA and so we have to go back again with a new RNA primer and the and the DNA polymerase keeps catalyzing again so basically the DNA polymerase is constantly moving backwards and forwards catalyzing the phosphoderosobons in these short segments rather than doing it in one whole stretch as you can on the leading strand now these short segments are called Okazaki fragments and basically they're just sections of you nucleotides that are whose phosphodiceabonds are catalyzed together in short chunks by the DNA polymerase. And remember I mentioned that you have to start each of these Okazaki fragments, each of these little chunks, with an RNA primer. Well, once that little fragment has been done, has been put in, another enzyme comes along and removes that RNA fragment and replaces it with DNA, because obviously you need DNA and they're not RNA ultimately. The enzyme that does this is called DNA ligase. It rips out those RNA-Pragments. primers because they're not needed anymore and replaces them with proper DNA nucleotides

and catalyzes the phosphodeaster bonds as necessary around the edges. Now, this requirement to have a primer sort of just to the left of your position when you start catalyzing the bonds of the complementary strand on the lagging strand is a problem. And this problem becomes manifest in the phenomenon of telomeres and telomere shortening. So telomeres are basically just the nucleotides at the end of a chromosome, or at the end of a DNA molecule. Now, you can imagine, once we get to the very end of replication on the lagging strand, imagine that we're unzipping a zip from right to left. So we start with it all done up, and we pull the zip to the left,

and the two strands come apart, DNA strands here, we're thinking about them, they come apart, and then we keep zipping to the left. For the top, which we'll call the leading strand, the DNA polymerase can just come along and catalyzed all the phosphodiaster bonds of the new strand, no problem, and it goes along the whole way and it's finished. On the bottom, the bottom strand, which we'll call the lagging strand, remember, we have to get the DNA polymerase to go in short segments, making all the Okazaki fragments moving in the opposite direction each time from the way the zip is actually moving. So the DNA polymerase on the lagging strand is actually moving left to right, as opposed to the zip, which moves right to left. However, to start each of those Okazaki fragments, you need the RNA primer to bond just to the left,

of where you're going to start. So you put the RNA primer to the left, then the DNA polymer response to that, and then moves and starts catalyzing to the right until it reaches the end of that little fragment there, and then picks up and moves and does the next fragment. But when you get to the very end of our zip or of our lagging strand,

there's nowhere to put the primer. You need to put the primer just to the left of where you're about to start catalyzing bonds. But for those last few nucleotides, there's nowhere to put the primer. I mean, you could bind the primer to those bonds, to those free nucleotides themselves, but then you can only catalyze

phosphodestibons to the right of that. There's no way to actually catalyze phosphodias bonds for nucleotides actually on those last few exposed positions. And so there's no way the DNA is able to copy the nucleotides at the very end of the lagging strand. Now there are actually ways around this,

which are used in gamete cells, but most cells, those are sex cells, by the way, like sperm and eggs, but most cells in adult animal and bodies and plant bodies and so on, don't have the ability to fix that. And so basically the telomeres, or the very ends of the DNA molecules, get shorter and shorter every time it replicates because you lose those last few nucleotides, and that happens every time. And for a while, that's not a problem,

because the telomeres or the last few nucleotines usually don't really do anything anyway. They don't code for any proteins, and so you don't really need them. but eventually if you lose enough of that information, it can start eating into genes, and obviously if you lose that information, you lose the ability to make vital proteins, and you can lead to problems. So this depletion or shortening of telomeres is thought to be one of the contributions to aging. Basically, that is you lose these telomeres, or they shorten over time, you start to lose genetic information, which means you lose the ability to make certain proteins,

or you don't make enough of them, or something like that. Now, as I said, gametes or sex cells have ways of fix. this problem, which would be essential, otherwise essentially the whole species would go extinct because its entire genome would be lost if there was no way of replenishing these telomeres. But that's an interesting application of that knowledge of the difference in replication between leading and lagging strands of DNA. So hopefully that was reasonably clear. It's a bit complicated, but remember the basic concept is that helicase unwinds the DNA,

the naked strands are stabilised by proteins, And then DNA polymerase comes along and catalyzes the phosphodester bonds of the corresponding base pairs that have now bonded to the naked DNA strand. And that happens separately and slightly differently on both of the naked strands of DNA. And once we're done, we get two strands of DNA, which then, once the whole process is finished, and the helicase and disassociate and unbide from each other, they sort of just drift apart. Now we've got two separate strands of DNA, both of them double-stranded, and both of them pretty much identical copies of the original. Also, each of the two copies has half of the original in it. So we've got two double strands, two double-stranded DNA molecules now.

Each of the two strands has one original side, or single strand of DNA, and one copy. This is called a semi-conservative, replicative process. That's opposed to, for example, a fully conservative process where the original DNA molecule, double strand, both strands of which would remain completely the same, and you'd make a copy of that, which would be kind of like cloning the original DNA strand, or a non-conservative version where you just take bits and pieces and mix them all up together. This version where each daughter DNA molecule in the sense has the exact same molecules as we're in one of the parents, plus half new molecules, is called semi-conservative. Also, this DNA replication process has to be

very precise, because if there's too many mistakes, genetic information is lost, and usually that's a bad thing. That basically leads to mutations, which are usually detrimental to the species and hurts survival. So there's been substantial evolutionary pressures to evolve ways of maximizing the efficiency of DNA replication. So that means that the cell has a whole bunch of different ways of proofreading the DNA after replication

to essentially check for any errors or problems or mistakes that have been made and fix them. And I'll only talk about one here because many of them are quite complicated. and they operate at various stages and so on. But this one is basically, after it's finished, so we've got two daughter strands, two double strand, door to DNA strands. The polymerase, or termed DNA polymerase a lot,

they're actually a bunch of different types of DNA polymerases, but they're all just enzymes that aid in this process, basically, of replication and transcription. So anyway, we've got a DNA polymerase which runs along the daughter strand and essentially checks for any mistakes. Any nucleotides have been placed in an incorrect spot. Remember, I said previously in the previous episode,

that every nucleotide, or every base pair, I should say, phosphide, sorry, every nitrogenous base can only bond properly with one other nitrogenous base. If you pair it with the wrong nitrogenous base, so you've got an incorrect base pairing, the bond sort of bends or is out of shape in some way, and the DNA polymerase can detect this, remove the incorrect nucleotide,

and replace it with the correct one, while being added with other enzymes, of course, too. to catalyze these reactions. And how does it know which nucleotide to put in? Well, it replaces the incorrect nucleotide with the correct one using the parent strand, the original DNA molecule, as the template. Because obviously the original would have been correct, and it's the copy that would be wrong.

Okay, so that's the process of DNA replication. Remember, that only occurs basically just prior to cell division. Next, we're going to look at transcription, which can occur really at any time in the cell's life, or much more, at many other occasions at least. So transcription is the process of taking the information we have stored in the DNA and making a copy of it in a messenger RNA. And this copy of the information is then taken outside of the nucleus

and used to make the actual protein. That process is called translation, which we'll look at shortly. But transcription is the process of making this copy first. Now, the process of transcription is reasonably similar, conceptually, to the process of replication, except it's actually simpler. So once again, transcription begins with helicase unwinding the DNA by moving along between the two strands and breaking a hydrogen bonds connecting the nucleotides. So that's the same as with replication. Next, what happens is the RNA nucleotides are paired or naturally will bond to their complementary DNA basis.

Once again, this is the same thing that happens in replication. Third step is that the RNA sugar phosphate backbone is formed by RNA polymerase in this. case it's RNA polymerase because we're dealing with RNA nucleotides as opposed to DNA polymerase with the DNA nucleotides in the replication version of this. But RNA polymerase catalyzes the phosphodiaster bonds between these nucleotides that have been added or that have bonded to their complementary DNA basis, thereby forming one long RNA molecule. So once again, that's basically the same as happens in replication. And finally, once the molecule has been formed, once the RNA molecule has been formed, the hydrogen bonds connecting the RNA to the DNA helix break,

and that frees the newly synthesized RNA strands to move and exit the nucleus. So this, by the way, replication and transcription both happen inside the nucleus. Translation does not, and so we'll look at that in a second, but this transcription process does happen inside the nucleus, obviously for a eukaryotic cell, procurates don't have nucleuses. There are some differences between replication and transcription, though. For one thing, replication, well, pretty much always just happens once, because you just want at least once at a time. You make a cell divides once, so you need one copy of the DNA,

and then maybe later or divide again, but at least on that initial occasion, it just divided once. But in the case of transcription, you might want multiple MRI or RNA copies of the DNA information, because, for example, you might want to make a bunch of proteins, and so you want more than one copy.

And so what can happen is that the same gene is transcribed many times, in a sense, in the same instance. That is that the helicase unwinds the DNA, and then RNA polymer, polymerase catalyzes the formation of multiple RNA strands, one after the other, from that same gene, without the DNA winding up again. So that's essentially an efficiency measure to get more bang for you buck really, to get more MRNA molecules out from a given transcription process. Also, another difference between transcription and replication is that only one of the two strands in the DNA is copied. The other one is not.

So you don't need to have the whole leading and lagging strand thing in transcription. It's not necessary. have the leading strand version and it's simplified by that process because you only need to copy the gene. You don't need to copy the complement of the gene. So that simplifies things. And of course another difference is that in replication you basically make a copy of the entire DNA molecule whereas in transcription you just copy a little portion of it into RNA which is basically the gene that you want to extract the information from the particular sequence of nucleotides that

codes for the amino acid that you're interested in. How does a cell know or how How does an RNA polymerase or Helicase know when to start transcribing a particular gene? Well, basically, this is possible because there are certain regions of DNA, basically sequences of nucleotines, that are called promoters. And these generally sit right near the genes that they regulate upstream to the 5 prime end, which allows easy movement of the RNA polymerase and therefore avoids the complications of the whole lagging strand thing, because they always sit to the 5 prime end of the DNA. molecule. So some promoters are more efficient than others, which means that they could essentially

have differing rates of production of RNA copies of the DNA information and therefore differing rates of gene expression, different amounts of protein produced. But the basic idea is still the same that this segment of DNA, this segment of nucleotides, binds to or is bonded to by the RNA polymerase or the RNA polymerase complex. And that initiates the whole process of transcribing the gene, which as I said, lies downstream to the three prime end of the particular section of DNA that we're talking about. Now, in eukaryotes, it's slightly more complicated. The polymerase doesn't bind directly to the promoter. What actually happens is a whole bunch of other proteins called transcription factors first bind to the promoter, and then that attracts other transcription

factors, which forms an initiation complex, and then finally the polymerase itself bonds to the initiation complex and then you can actually start the process of transcription. But still basically you can think of it as if you have a sequence of DNA which is right near the gene called a promoter. The polymerase bonds to the promoter directly or indirectly in a sense. And that starts the process of transcription. Moving along, opening up the, unwinding the DNA strand, moving along, catalyzing the bonds between the new RNA nucleotides and then closing up and rewinding the DNA strand after you're done. Very similar to replication in that sense. Once we've made our RNA copy, one or more copies of the gene,

it usually undergoes a variety of post-transcriptional modifications, which is basically processes by which the primary RNA transcript is modified and converted into a mature RNA transcript before it leaves the nucleus. So these modifications happen inside the nucleus. Remember, transcription occurs inside the nucleus. We haven't left the nucleus yet. And we're talking about eukaryotic organisms here. So the primary RNA transcript is just the one that is produced by just simple copying straight out of the DNA sequence near your promoter.

Copying straight out of the gene of the sequence of nucleotides that appeared on your DNA. But you might not actually want all of that information. Only some sections of it may be relevant to the protein you're actually trying to produce. And so this is sort of the idea behind the process called splicing. Splicing is the process by which some regions of RNA don't code for protein are removed from the preliminary MRNA, and the remaining sections are connected together to form one continuous molecule. So the sections that are removed are called introns, and the sections that remain are called exons. So the way I like to think about that is that the introns, the sections of RNA, the introns go out,

and the exons are the ones that remain. Introns go out of the RNA transcript. it. The way that this happens is essentially you just have a bunch of proteins together forming a spliceosomes, that's a complex of enzymes, which then pinch out the intron and catalyzes the bonding of the two exons near it. So you can imagine a length of string which you sort of, and you take your two fingers, grab one little bit and pinch so that you've got the string, which now curls into a little sort of circle and then continues on. If you would have cut out that little circle bit and join the two ends of the string, the bit that

you just cut out is the intron and the remaining bits of the exons. And that can happen multiple times along a single gene. Now, this might seem a little redundant. I mean, why have that information at all if it's just going to be cut out? I don't think it's fully understood exactly why this occurs, but one interesting factor is it's believed that these introns may play some role in regulating gene expression, like how often this particular gene is produced, or how often it's copied into RNA and made into proteins and so on, or to what degree, how many copies are made. But the details of that I don't think are as yet fully understood. Another thing that happens in at least some organisms is a phenomenon known as alternative splicing,

which means that pending upon what protein you want, you will cut out different introns. So, you know, if you're making protein A, you cut out this bit and the other bit, and those are your introns that go away. But if you're making protein B, you cut out different sections of the same gene, but cut out different sections forming a different mature RNA. So in both cases, you start with the same gene in the DNA, and you start with the same pre-MRNA molecule, just after you've done transcription, but after your modifications, after the splicing, you get different mature mRNA molecules, which then go on to make different proteins. So that's called alternative splicing, and it's very interesting,

and it's another sort of blow to the one gene, one polypeptine hypothesis, which I mentioned in the previous episode, because this is another way, remember we had overlapping genes in the previous episode, but this is the second way that we can get different genes from the, or different proteins from the same sequence of nucleotides in the DNA. There are also two other main modifications, post-transcriptional modifications that occur before the MRNA leaves the nucleus. One is capping.

Basically, a special altered guany nucleotide is added on the five prime end of the messenger RNA. The messenger RNA, I should have already said, is just what we call this segment of RNA that is a copy of the information in the DNA. So basically the cap, we just, on the 5 prime end of the RNA, we stick on a special altered guine nucleotide. The second modification is called polyadenolation, which basically means adding a whole bunch of adenine, which basically means adding a whole bunch of adenosine monophosphate nucleotides to the end, to the opposite end, pre-MRNA. So basically, we've got the pre-Messinger RNA, we remove the introns, snip those. out, we add a cap to one end, which is just a single nucleotide, or slightly modified form,

and we add a tail to the other end, which is a whole bunch of A's, dendocines, and those are our modifications, those are all our postscription modification, so the cap, the tail, and the splicing. And now that we've got our mature mRNA, we spit that out the, that is ejected from the nucleus, and goes into the cytoplasm, and is ready for translation. So, moving on to translation, this is the process by which we take a mature messenger RNA and use it as a blueprint to make a protein. Because remember, what we're ultimately interested in is taking the genetic information stored in the DNA

and using it to make a protein, which can do the stuff that we want. The messenger RNA itself is just a means to do that. The messenger RNA is not the final goal. So before we explain translation, how that works, there's just a couple of other concepts we need to understand. So previously I've been talking about messenger RNA, which is that copy of the DNA molecule made out of RNA nucleotides. There are two other main types of RNA as well.

well, there's some minor types, but two other main ones called ribosomal RNA and transfer RNA. These are also called R RNA for ribosomal RNA and T RNA for transfer RNA. The ribosomal RNA is, so both of these, all of these three types of RNA are made of nucleic acids, that's why they're called RNA. So they're made of sort of the same thing, but they're different shapes and they're different lengths and they do different things, hence why they're given different names. That's why they're given different letters to start off with. Now, ribosomal RNA is an important component of the ribosome.

If you remember back to Tour of the Cell episode, we talked about ribosomes as being the organelles that are used to manufacture proteins from messenger RNA. Well, part of them are made from ribonucleic acid or RNA nucleotides. I say part of it because the ribosome itself is a complex, which is comprised of two ribosomal RNA units and a whole bunch of proteins. So these two subunits are important. We'll talk about these a bit later on.

One is called a large subunit and the other one is the small subunit. So the way I like to visualize this is the small ribosomal subunit sits on the bottom and the big ribosol or the large ribosomal subunit sits on the top. And the proteins are just sort of studded in here and there and connect them together and do various other things. That whole complex of the two subunits made of RNA and the bunch of proteins is called the ribosome. and we'll come back to that because it plays a crucial role in the translation process.

The other type of RNA, remember, is the transfer RNA. Now these are also very important. The transfer RNA is much smaller than the ribosomal RNA. Even the small subunit of the ribosomal RNA is pretty big. It's just obviously not as big as the large subunit, but TRNA is quite small, only like 80 nucleotides long. So they're small, and there's single-stranded RNA molecules, which sort of curve back on themselves several times.

So they're sort of loopy in that they, it's a single strand, but it curves back on itself and forms hydrogen bonds with earlier sections of itself. So it forms sort of a complex, tangled, three-dimensional structure, which we don't need to worry about too much, except that the three-dimensional structure has two important properties. It's sort of got two ends to it. The whole molecule sort of looks vaguely like a key. At least that's the way I like to think about it.

But the T-R-N molecule is sort of long, lengthwise, and it's got two ends. On one end, on one end of the molecule is what is called an anticodon, and at the other end is an amino acid that corresponds to that anticoadone. So what's an anticoatone? So you remember before, we talked about codons in the previous podcast, codons are a sequence of three nucleotides in a row, which code for or translate into a single amino acid.

An anticoadone, therefore, is just the same as a codon, except it's comprised of each of the three complementary base pairs to the original codon. So, for example, if we had, in the case of RNA, the codon for lysine is A-A, so three adenosines. The antichotone for lysine is therefore U-U-U-U-U-U-U, or three urosils. It's just the three nucleotides that correspond to the complementary base pairs to the original codon. The reason we need that will become clear shortly. So that's what we have at one end of the molecule, this antichotone,

three nucleotides that correspond to the original codon. On the other end, we have the amino acid that corresponds to the codon that corresponds to the antichron. So basically, think of it this way. We've got a short sequence of ribonucleic acid, so RNA. On one end we have a particular amino acids, there are 20 of them, so whichever one it is. And on the other end, we have the codon for that amino acid that corresponds to it. And there can be several different codons, remember, that correspond to the same amino acid, because there's a fair bit of redundancy in the genetic code.

Except it's not actually the codon that corresponds to that amino acid. It's the complementary codon, essentially, which is called the anti-codon. So it's just like the reverse of that codon. So that is what... That is transfer RNA or the T-R-NA. Anticodon at one end, corresponding amino acid at the other end. Okay, so now we've got all our pieces, our messenger RNA, our ribosomal RNA, and our transfer RNA.

We can put them together and explain the process of translation. Now, conceptually, the translation process, once we've got all our parts, once we understand all the parts that are involved, It's actually fairly simple. Basically, the small ribosomal subunit binds to a particular region of the messenger RNA. And it bonds to a specific or it bonds to a specific codon of the RNAs, which basically represents the start codon. So it's starting the whole process.

So we've got our small ribosomal subunit sitting on the bottom and the mRNA spread along the top. Then what happens is a special initiated TRNA comes in and binds to its corresponding codon on the MRNA, which is the same as the start code on. Okay, so the translation process is conceptually reasonably simple once we've got all the component ingredients in place. It all starts with a start codon. I'm simplifying this a little bit, but basically the start codon is just, you know, a codon, which doesn't actually correspond to any event. amino acid, but just tells the whole process to get started. Now, this start codon will be placed, you know, will be located somewhere along our MRNA transcript, and wherever it is, two things will bind to it. First of all, its corresponding TRNA, which is called the

initiated TRNA, will bind to it via its anticoadone, because remember, the TRNA that corresponds to a given codon will have, on one of its two ends, the anticoadone pair, or the complementary bases of the codon we're interested in. And so it can naturally bind to it because, of course, if it's got the complementary base pairs, then they'll bind nicely together via the hydrogen bonds, which they do if it was just a normal DNA molecule. And so that just will happen naturally. The other thing that binds to this start codon is the small ribosomal subunit, which binds sort of underneath the MRNA.

So if you can imagine the MRNA lying sort of flat as if it was along a table with the unpaired bases sticking upwards. and we've got our TRNA sitting on top of that, with its anti-codon pair pointing downwards, binding to its start codon, then the small ribosomal subunit will be sitting underneath the MRNA. Once that has happened, so we've got our small subunit, our MRNA, and our TRNA, the large ribosomal subunit comes along and binds to the whole lot. Now, the large ribosomal subunit has three binding. spots for TRNAs sort of, well, embedded in it or at various places within the molecule.

These sites are called E, P&A, so I think of that as the Environmental Protection Agency, EPA, going from left to right if you're sort of looking at it that way, but that doesn't matter too much. I'm not terribly concerned with what they're called. Just remember that there are three sites, which means it can, though ribosome as a whole, the large and the small subunits, can fit three TRNAs in it at once, although it generally doesn't have three at any given time, but it can fit three in. There are three spots for TRNAs. Now, the way that the large ribosomal subunit bonds to the whole thing is such that the initial, the initiator TRNA, remember the first one that comes and binds there to the start codon, is in the middle spot. So that's

what we start with. The small ribosomal subunit lying sort of on top of that with its unbonded base pairs sticking upwards is the MRNA, bonded to the start codon of the MRNA, I should say, the initiator t rna, which like any t rna has an amino acid attached to the opposite side. The opposite side then is bonded to the start codon. And sitting around the tRNA is the large ribosomal subunit. Okay, so given that setup, we're now ready to begin the actual translation process. The translation process is pretty simple. To one side, we'll think of it as the right side of the start tRNA,

is located a codon, obviously, because the MRNA is just a long sequence of codons. And this codon will have some corresponding TRNA that has the corresponding anti-codon that will bind to this codon on the MRNA because they have complementary base pairs. So whenever this TRNA comes along, because the TRNAs are all sort of swimming around in the cytoplasm, it won't take too long, the TRNA will come in. The complementary base pairs will form hydrogen bonds and bind with each other, and now we'll have a second TRNA TRNA sitting next to the original TRNA on one side of it.

So we've got two TRNAs sitting next to each other. And both of these TRNAs have amino acids attached to the opposite side, so like the top end, that is the opposite side to the anticoatone. What the ribosome does, specifically the large ribosomal subunit, is it catalyzes the formation of a peptide bond between these two amino acids. That is the two amino acids carried by the two separate TRNA, which have bonded to the ribosome.

The peptide bond is just the bond that joins amino acids together to form a protein, analogous to the phosphodiaster bond in DNA or RNA. Once that bond has been catalyzed, that prompts a change in the shape of the ribosome as a whole, and what happens is it moves along the mRNA. Specifically, it moves three nucleotides down. Now, because the TRNAs are stuck in place,

because they're attached to their particular codon, depending on whatever anticoadone they're carrying. The TRNA don't move, and the MRNA doesn't really move either, but the ribosome moves along. That means that the ribosome moves in relation to the TRNA. So remember I said there were three spots, three binding spots for TRNA in the large ribosomal subunit. And starting off, we had the first one taken up by the start,

the initiator TRNA, and then the one to the right of that was taken up by the next one to come along. Well, now, instead of having the middle and the rightmost spots taken up, the whole thing's been moved along by one. So now the leftmost and the middle spots are taken up, and the right one is free again. So another way of thinking about that is... So remember we had EPA, the three slots. Originally, P was full.

It had the initiated TRNA, and A was full with the next one that came along. But now the whole thing's moved along one, and so now E is full and P is full, but A is free. But because the initiated TRNA, that first TRNA, doesn't have an amino acid anymore because the amino acid's been bonded on to the other amino acid that was on the second TRNA. So the first TRNA doesn't have any amino acid. It's just sitting there in the E-spot, and so it disassociates and floats back into the cytoplasm, basically. And now we're back at the original situation. Now we've just got one TRNA sitting in the P spot, so that's the middle spot, on the MRNA, bonded to its antipsum, corresponding anticoadone. And then another TRNA comes along, which then binds to the complementary base pairs that correspond to its anticoadone, and it brings along its corresponding amino acid. The large ribosomal subunit catalyzes the peptide bond between those, between the two amino acids.

Then the large ribosomal subunit moves along three nucleotides to the right, and we repeat the whole process. And that keeps going. The TRNAs keep coming in, bringing along new amino acids, and we keep building up this longer and longer chain of amino acids. And literally, the amino acid chain grows and grows and comes to stick out of the ribosome, like a long sort of weird tail. And as the amino acid is forming, excuse me, as the polypeptide is forming, or the protein is forming, it begins to fold in accordance with, you know, entering its lowest energy state, as all molecules will do. And folding is very important for a protein because it needs to adopt the three-dimensional shape, a specific three-dimensional shape in order to carry out its biological function properly.

So that folding process is vital. And so this process continues, elongation it's called, when you just keep any more TRNAs, until we reach the termination phase. Basically, this occurs when we reach one of the three stop codons. These are three codons. Remember, there are 64 codons in total. Three of them don't code for any amino acid, which means there aren't any TRNAs which bind to them. So there's no TRNAs with the, the korens.

anti-codon to bind to these stop codons. So whenever we have one of them in our in our MRNA sequence, instead something different, a protein called a release factor binds to the stop codon. A release factor doesn't carry an amino acid, unlike all of the other TRNAs that have been coming in during the elongation phase. And so now since there's no more amino acids, the job is done, the protein is finished basically. The large ribosomal subunit snips off the final amino acid and everything, and so the completed polypeptide chain now floats off and everything dissociates and the job's done. The protein has been formed or at least the polypeptide chain has been formed.

Now once again, just like with transcription, often we want to make more than one copy or we want to make more than one protein from a given MRNA transcript. And so you'll often have multiple ribosomes working to produce proteins from a single given MRNA transcript. And so what it will look like is you'll have a big long RNA transcript, and all along it, you'll see ribosomes working at different stages of completion producing the same protein. And also similar to the transcription process, once a protein has been made in the translation process, it's often modified by, for example, adding carbohydrates or other small molecules, or cleaving it at a particular point, or removing some amino acids

and stuff like that, and these are done by additional enzymes. Let's just quickly review. the translation process as a whole. It begins with initiation where the small ribosomal subunit and the initiator TRNA both bond to the start codon and also then after that the large ribosomal subunit comes along and binds to the lot of it, such that the initiator or TRNA is in the P, the middle position. That's the initiation phase. The second phase is the elongation phase where a whole bunch of new TRNAs come in, bringing their corresponding amino acids, bonding to their antichodon, their antichodons bonding to the original codons on the RNA template and the large ribosomal subunit catalyzing the bonds between amino acids on the growing chain. That's called

the elongation phase. And finally, termination phase, which occurs when the ribosome reaches a stop codon, which doesn't correspond to any amino acid or doesn't have a TRNA which corresponds to it. Instead, protein called a release factor binds to the stop codon, which then leads to basically the ribosome and the whole complex disassembling, disassociating, and leaving the protein to go free. The way I like to think about this whole process in a sort of a stylized model is that the ribosome is a three-seater couch, and at all times you have one person sitting in the middle of the couch. People in this case are analogous to the TRNA. Now, during the elongation phase, a new person comes along and sits to the right-hand side of the person on the couch from our

perspective. Imagine we're standing in front of the couch, and someone comes along and sits to the right of the person there. But the person sitting in the middle of the couch is wearing a whole bunch of hats stacked on top of each other. And the new person coming in is just wearing a single hat. The hats here are analogous to the amino acids. Now, the person in the middle is wearing many hats because they have a, in a sense, polypeptide chain growing out of their head, all with each of the amino acids bonded to each other. The new person coming to sit down, however, only has a single amino acid because they just have whichever one corresponds to their anticoat. Once the new person sits down, the person who's on the centre of the couch takes off all their hats and puts them on top of the hat that the person to their right is wearing.

Then once that's done, both people move one seat to the left on the couch. This is analogous to the whole ribosome moving along three nucleotides to the right, and thereby the TRNA moving into the different binding positions in the large ribosomal subunit. Once that's occurred, and the person who's wearing all the hats now wearing one extra hat than before because they brought their own hat plus they got all the old ones. They are sitting in the middle and the person who previously had all the hats is sitting to their left. They don't have any hats anymore so they get up and leave. And a new person wearing a single hat comes along and sits to the right of the person in the center and the whole process continues. So each time a person brings in one new hat and the pile of hats keeps getting bigger and bigger until basically one person comes along who doesn't

wear, who isn't wearing any hat and the whole process stops and the pile of hats is now finished. The pile of hats being analogous to our polypeptide chain. So hopefully that analogy was somewhat useful. On that note, we're basically done. We've gone through the processes of replication, transcription, and translation. Remember, replication and transcription are fairly similar to each other involving unwinding the DNA, the two strands of DNA by helicase, and then DNA or RNA polymerase coming along and catalyzing the phosphodiaster bonds between the new lot of nucleosines that are being added. Translation is quite different because it involves, it doesn't involve any DNA directly. Instead, it involves a messenger RNA, transfer RNA, and ribosomal.

RNA, all coming together to form the initial complex, and then new transfer RNAs continually bringing their amino acids to sort of add onto the lengthening chain of polypeptides, which then finally form the protein. So this is the process, replication, transcription and translation, by which the central dogma is manifested, whereby DNA makes RNA makes proteins, and this, and it's through this process by which the cell is able to express the genetic information that's contained in its DNA, and use it to actually produce proteins. do real things in. Hopefully the explanation I provided were reasonably clear. It's very hard to describe these things without using visual aids, so maybe I'm foolish who even attempted. But you can let me know, send me an email at Fods12 at gmail.com, where you can comment about the podcast, even suggest potential future episodes that I can, topics that I can look at in future episodes. Also, be sure to check out our Facebook page, which I've just set up for the podcast. Go to Facebook.com slash The Science of Everything podcast, all one word, and there you can have a look at

extra materials and links that I'll post up. For this episode, for example, I'll post up a few links to some good diagrams that will help explain the process that I'm talking about of transcription and so on. I'll also on the Facebook page put up previews of what I'm working on and when you can expect the next episode and so on. So check that out. Thanks for listening, and I'll talk to you next time.