- DNA questions
- Eukaryotic gene transcription: Going from DNA to mRNA
- Molecular structure of DNA
- Antiparallel structure of DNA strands
- Telomeres and single copy DNA vs repetitive DNA
- Leading and lagging strands in DNA replication
- Transcription and mRNA processing
- Speed and precision of DNA replication
- Translation (mRNA to protein)
- Differences in translation between prokaryotes and eukaryotes
- DNA repair 1
- DNA repair 2
- Semi conservative replication
- Protein modifications
- Jacob Monod lac operon
- DNA structure and function
Translation (mRNA to protein)
Translation is the process whereby mRNA is converted into proteins by ribosomes. Ribosomes are cellular structures made of proteins and ribosomal RNA (rRNA). They act as the site for translation, facilitating the process of matching codons with amino acids and forming peptide bonds between amino acids.
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- How does it know whether to form a secondary or tertiary structure?(8 votes)
- After translation, the primary structure determines how the protein will fold. Both secondary and tertiary will result after translation, and are aided by chaperones.(12 votes)
- How does one change mRNA into tRNA(7 votes)
- They do not directly interconvert.
mRNAs and tRNAs are transcribed separately from different genes (and in eukaryotes this is even done by different RNA polymerases).
These two molecules do interact during during translation — aminoacyl-tRNAs (that is tRNA bound to the appropriate amino acid) bind to codons on an mRNA that is loaded onto a ribosome. This results in the amino acid being added to the growing polypeptide.
Does that help?(12 votes)
- Which one of the two actually moves in translation? I know at12:50he says the ribosome moves but I've seen many conflicting opinions on other sites and resources I've viewed.(6 votes)
- That's a good question, I've been wondering that myself. Most of what I've seen is that the ribosome moves. And that makes sense since more than one ribosome can be translating one mRNA at the same time. It would probably be messy if each ribosome moved the mRNA (the mRNA definitely doesn't move by itself) along while the other ribosomes are working on a different part. That is for cytosol, but some mRNA are translated directly into the ER, and in that case, the ribosome itself won't be able to move, so I presume it is moving the mRNA in that case.(9 votes)
- If AUG is the start codon, and it also codes for methionine, does that mean every polypeptide starts with methionine as the first amino acid?(6 votes)
- Many do, but not all.
Those that don't (usually) occur due to removal or modification of the amino-terminal (start) methionine. For example, enzymes called "methionine amino-peptidases" cut off this amino acid from the beginning of some proteins — this is an example of what is known as a "post-translational modification".
It is also quite common for the first part of a protein (including the starting methionine) to be removed during processing — an example is secreted proteins that have their signal sequences removed during secretion or membrane insertion.
Methionines can also be oxidized to form chemically related residues.(6 votes)
- According to this video, the cap on mRNA is added after transcription. However, I have also learned that the cap is added to the mRNA while it is still being transcribed. Which is correct? Thank you.(5 votes)
- According to "The Cell" by Alberts (p.317, sixth edition) it happens while RNA-polymerase is busy doing it's job.(5 votes)
- At the end of the video, when Sal talks about antibiotics, he says that bacteria ribosomes or different enough than eukaryotic ribosomes so we can hurt the bacteria ribosomes functions. But does that mean that we will also hurt the good bacteria?(3 votes)
- Most antibiotics hurt "good" bacteria as well, yes.(5 votes)
- I think one thing Sal didn't mention in this video was that methionine amino acid is often subsequently removed from newly synthesized proteins. Does that mean Methionine, goes to E-site(exit) or does it remove after the polypeptides are formed?(3 votes)
- After polypeptides re made, cleavage of Methionine takes place. Either by Methionine aminopeptidase or by N terminal signal peptide.
In bacteria and yeast, knockout or inhibition of MAP is lethal. In humans, MAP’s are overexpressed in cancer cells and their inhibition is targeted for drug development.
- What happens to the tRNA once it reaches the "E" site? Is it simply discarded since it no longer has an amino acid attached, or does it attach to another amino acid corresponding to its anticodon? Hopefully the latter is true so we could think of our bodies as recycling centers.(3 votes)
- After tRNA reaches the E site and is moved out of the ribosome it is recruited in the cytoplasm floating around looking for amino acid to grab corresponding to the codon. Then it comes back to ribosome once the amino acid is captured by aminoacyl(1 vote)
- Why does the ribosome require the bases to include Urasil instead of Thymine? Can it not read thymine? If so, why not?(2 votes)
- It all depends what is the goal of each nucleic acid (it has nothign to dow ith the riboome but with the DNA or RNA itself).
Uracil is also pyrimideine, like Thymine.
Uracil is energetically less expensive to produce than thymine - that's why it is used in RNA. RNA has to be fast produced and has short life-time.
In DNA, however, uracil is readily produced by chemical degradation of cytosine, so having thymine as the normal base makes detection and repair of such incipient mutations more efficient.
Uracil is appropriate for RNA, where quantity is important but lifespan is not, whereas thymine is appropriate for DNA where maintaining sequence with high fidelity is more important.
- Why is AP a thing?(1 vote)
- So that you have the ability to gain college credits.(4 votes)
- [Voiceover] So we already know that chromosomes are made up of really long strands of DNA all wound up into themselves, so something like, well I'm just kind of drawing it as a random long strand of DNA all wound up in itself. And on that strand, you have sequences which we call genes, so that might be one gene right over there, this might be another gene, that might be a gene right over there. And each of those genes can code for specific polypeptides or specific proteins. And the key question is, is how do you go from the information encoded in these genes, encoded as sequences of DNA, how do you go from that? How do you go from the gene, which is encoded in DNA, how do you go from that to protein? Which is made up of polypeptides, which are made up of amino acids. And this is often called the central dogma of biology, but we already saw in the video of transcription, that the first step is to go from the gene to messenger RNA, that the RNA, the messenger RNA, you can use as a transcript, we have rewritten the information now as RNA. And then the next step which we're gonna dive into in this video is going from that message RNA to protein, and this process is called translation, because we're literally translating that information into a polypeptide sequence. And you can see a little bit visually here, this is all review, we covered a lot of this in the video on transcription and the overview video on transcription and translation, is if you look at a eukaryotic cell and the bacteria in a prokaryotic cell, it's analogous, you just don't have the nuclear membrane, and you're not gonna do the processing step that I'm gonna talk about in a little bit and we went in detail on the video on transcription. But you start with the DNA, you have your RNA polymerase as the main actor that's able to transcribe the RNA from that. If we're talking about a eukaryotic cell, what you end up with we wouldn't call mRNA we would call pre-mRNA, pre-mRNA, which then needs to be processed, the introns need to be taken out, we add a cap and a tail here, and if we're talking about a eukaryotic cell, we then formally call that mRNA, and then it can travel, and this is where we get into the translation step. It can travel to a ribosome, which is where it will be translated into a polypeptide sequence. And you see the analogous thing happening here in this bacterial, or this prokaryotic cell right over here, except you don't see the nuclear membrane, because it's prokaryotic, and you don't see that processing step, so you could just consider this straight, this is mRNA right over there. So the questions are well how does this thing happen? And what even is a ribosome? So let's zoom in a little bit on a ribosome right over here, and there's a couple of interesting actors. One, as you can imagine, is the ribosome itself, and it is made up of proteins, proteins plus ribosomal RNA. So in the video on transcription, we're already familiar with messenger RNA and we often view RNA like DNA as primarily encoding information, it's acting as a transcript for a gene, but it doesn't have to only encode information. It can also, so it's proteins plus, it's not a 'T' there, this is a plus. It can also provide a functional structural role, which it does in ribosomal RNA. And this big, you know, this looks like a an oversized hamburger bun or something right over here, this is super oversimplification of what a ribosome looks like and I encourage you to do a web search for image searches for ribosomes, and then you can get more appreciation of how how beautiful these structures are, and how intricate they actually are. So this is the site, and you can broadly think of the ribosome as having this, you know, this is the top bun, and the bottom bun. And it's going to travel along the mRNA from the five prime end, to the three prime end, reading it, and taking that information, and turning it into a sequence of amino acids. So how does that actually happen? Well, each, each of these three, every three nucleotides, every three nucleotides there, we call that a codon, so that's a codon, this is, let me do this in a color that is visible on both white and black. So these next three nucleotides is a codon, this is a codon, this is a codon, and what's actually the information is actually encoded in the nitrogenous bases. So this first codon right over here, we see it's AUG, so the nitrogenous bases are adenine, uracil and guanine. And this has, this codon, it codes for the amino acid methionine, but this is also, this is a good one to know, AUG, let me write it over here. AUG is know as the start codon. Start codon. This is where the ribosome will initially attach to start translating that messenger RNA, and so we, the way this drawing is, that we are just starting to translate this messenger RNA. So how does that actually happen? How do we get from these three letter sequences to specific amino acids? Well let's think about it, how many, how many possible three letter sequences are there? Well, there are, there are four possible nitrogenous bases there, so there's four possible, so if you, if you have a codon, and it has three places, there's four possible things that could be in the first place. There's four possible things that could be in the second place, and there's four possible things that could be in the third place. So there are 64 possible permutations. 4 times 4 times 4. Permutations, so you can think of it, there's 64 different codons, different ways of arranging the A, the U and the G. And that's good, because there are many amino acids, and this is actually overkill, because there's actually 22 standard amino acids, 22 standard, amino, amino acids, and 21 that are typically found in eukaryotic cells. So we have more than enough, more than enough permutations to cover the different amino acids. And it's not hard to find tables that will actually show us what the different sequences, what they actually code for. So you can see here, you can take the first letter, the second letter and the third letter, figure, look at the different sequences, and you can say, okay, look at that. AUG, adenine, uracil, guanine. That codes for methanine. Right over here. You could do that with any of them, you could say cytosine, uracil, uracil, that codes for leucine. And you can see that it's not just one amino acid per codon, but here you have four codons all code for, all code for leucine. And so it turns out that 61 of the codons, let me write this down. So 61 of the codons, of the possible 64, code for amino acids, amino acids, and three play a role that essentially tells the the ribosome to stop, three codons, three codons are stop codons, and you can see them right over here. UAA, UAG, UGA, that's how the ribosome knows to stop translating. So AUG, that's a start codon, and it codes for methionine. So that lets you know that these polypeptide chains are going to start with methionine, and then these characters tell it where to stop. But how do, how does the amino acid actually get, how do they all get tied up together to form this polypeptide? And how do they get matched up, how do they actually get matched up with the appropriate codon? And that's where we have another RNA based actor, and this is tRNA. So tRNA, the t stands for transfer, transfer RNA. There's a bunch of different tRNAs that each combined to specific amino acids, and on parts of those tRNA, they have what are called anti-codons. That pair with the appropriate codon. So this tRNA, and that's not what it looks like, I'll show you in a second what it looks like. That's a tRNA molecule, tRNA, at one end of the molecule, it's binding to the appropriate amino acid, methionine, right over here. And then at the other end of the molecule, though that's in the middle of the tRNA actual chain, you have your anticodon. And your anticodon matches up to the appropriate codon. And so this is how they bump into each other the right way and the ribosomes going to facilitate it, that the AUG is going to be associated with the methionine. And if we look at what tRNA actually looks like, and this is still just a visualization. So this is a strand of tRNA, you get a sense of, okay, it's a sequence of RNA right over here, this it's, I guess you could say, you could think of it, it's two dimensional structure. But then it wraps around itself to form this fairly complex molecule. And the anticodon, which is right here, it's kind of in the middle of the sequence, it forms the basis for this end of the molecule, that's the part that's gonna pair with the codon on the mRNA, and then at the other end of the molecule, at the other end of the molecule is where you actually bind to the appropriate amino acid. So I know what you're thinking, alright, I see that the ribosome, it knows where to start, it starts at the start codon. I see how the appropriate tRNA can bring the appropriate amino acid, but how does the chain actually form? And you can view this in three steps, and associated with those three steps are three sites on the ribosome. And the three sites, we call this the A-site, you're not gonna be able to see it if I write it in black. A, or yellow, alright, let me write it in blue. So that is the A-site. This is the P-site, and this is the E-site. And I'll talk in a second why we call them A, P and E. So the A-site is where the appropriate tRNA initially bounds, the tRNA that's bound to an amino acid. And so you can see, we're starting the translation process, the next thing that's going to happen is another tRNA, the one that is, that matches, that has an anticodon that matches the UAU, that's going to bond over here on the A-site, and it's bringing the appropriate amino acid with it, it's bringing the tyrosine with it. So why is that called the A-site? Well A stands for aminoacyl. An easy way to remember it it's the tRNA, it's the place where the tRNA that's bound to the amino acid, just one amino acid is going to bind on the ribosome. And so once that happens, once this character comes here, let me draw that. Once this character comes right over here, it's gonna be AUA, and it's bound to the tyrosine. Well then you could have a peptide bond form between the two amino acids, and the ribosome, and the ribosome itself can move to the right. So this, this tRNA will then be in the E-site. This tRNA will then be in the P-site, and then the A-site will be open for another amino acid carrying tRNA. So what this, what do the P and E sites stand for? Well you can see a little bit more clearly right over here. So the P-site is where you have the polypeptide chain actually forming, and, so the P-site is often, well, one way to remember it is is that's where you have the polypeptide chain, and now you have a new, you have a new A-site where you can bring in a new amino acid. And then the ribosome is going to shift, once this is bound, the ribosome, the peptide bond forms, and then the ribosome can shift to the right, when the ribosome shifts to the right, we're gonna be in this position, where the thing that was here, that was in the A-site, now the polypeptide is attached to it, it is now going to be in the P-site, and the thing that was in the P-site is now going to be in the E-site. It is now ready to exit, and that's why it's called the E-site. Because that's the site from which you exit. And so this is going to keep happening until we get to one of the stop codons. And when you get to one of the stop codons, then the appropriate polypeptide is going to be released, and we will have created this thing that could either be a protein, or part of a protein, so this is very exciting, because this is happening in your cells as we speak. This is, and in fact if you think about things like antibiotics, the way that they work are, is that, or the way that antibiotics work is that ribosomes and prokaryotes are different enough than ribosomes in plants and animals or in eukaryotes, that we can find molecules that hurt the function of ribosomes in prokaryotes, but don't do it to eukaryots. And so if you have bacteria in your blood stream, and if you take the appropriate antibiotic, it could disrupt this translation process in the bacteria, but not in your cells that you want to keep.