tRNA, rRNA and the Codon Code: Study with Video Lessons, Practice Problems & Examples

Translation is the process of converting mRNA into proteins, utilizing codons, tRNA, and ribosomes. Codons, groups of three nucleotides, correspond to specific amino acids, with start codon AUG initiating translation and stop codons signaling termination. tRNA molecules, shaped like cloverleaves, carry amino acids to ribosomes, where rRNA facilitates the assembly of amino acids into polypeptides. The wobble hypothesis allows flexibility in codon-anticodon pairing, enhancing translation efficiency. Ribosomes, composed of rRNA and proteins, are essential for synthesizing proteins, making them crucial in cellular function.

Codon Code

Hi. In this video, we're going to be talking about tRNA, rRNA, and the codon code. So even though the codon code is mentioned last in the title, we're actually going to talk about it first. And so, the reason we need to talk about the codon code is because of translation. And so, what is translation again? Translation is the process of going from DNA to protein. And so, how do we do that and what are the terms that we use to describe this process and what's needed for translation to occur? So in order to explain these terms to you, I'm going to keep coming back to this example. And the example is this: if I was trying to translate a set of texts, say a paragraph, for instance, from English to Spanish, what would I need to know? Well, I would need to know words. Right? I would need to know characters. Does Spanish use the same alphabet as English, or is it a different alphabet? And what kind of rules are there so that I know how to take one English word and what the meaning of that is in Spanish? We need a dictionary. We need to know something about grammar, how the sentences are formed, how the paragraph is formed. And the same thing, all of this is also needed for translation from DNA to protein. But instead of talking about it in terms of paragraphs and sentences and words and characters, we're going to introduce the terms that we have to talk about translation from DNA to protein. And so the first thing is that translation, yes, it goes from DNA to protein, but what is it actually doing? What it actually is doing is taking combinations of nucleotides, so A, T, C, and G, and changing them to amino acids, translating nucleotides and amino acids are not similar at all. It's much more diverse languages. And so, we can kind of think of nucleotides and amino acids as our alphabets. Okay? And so that's translation. Translation is the process of converting this alphabet, these nucleotides, into this amino acid alphabet. And so, in terms of alphabet, how are they similar? So we know that there are 4 nucleotides. Right? We have A, T, C, and G, but we have 20 amino acids. So there are a lot more amino acids than there are nucleotides, and so that means that translation is not one to one. It's not that nucleotide A encodes for amino acid 1, and that G encodes for amino acid 2, right? That's not how this works because there are not 4 amino acids. If there were 4 nucleotides and 4 amino acids, we would think, okay, well, 1 nucleotide equals 1 amino acid. That's not the case. And so because it's not the case, we have to decode exactly how to translate these 4 nucleotides into amino acids. And how we do that, how we decode that process is through a codon. So what is a codon? A codon is a group of 3 nucleotides that represent 1 single amino acid. So it takes 3 nucleotides to create a codon and 3 nucleotides encode for an amino acid. So we're starting to get our rules here, how the alphabet of DNA can be translated into the alphabet of amino acids, and in order to do that, we have to take at least three letters of nucleotides to be encoded for 1 amino acid. So knowing that, the next thing that we need to do is say, okay, well we're looking to translate this paragraph, for instance, in English to Spanish. Well, we know where the start of the paragraph is, right? So usually there's an indent if we're looking at it on a piece of paper, we can easily tell where the start of a paragraph is. But for DNA, that's not necessarily the easiest thing to identify, right? Because unlike written word where we can see the structure of a paragraph, we can see where it starts. DNA is just a combination of nucleotides, right? It's just like one long line of these random four nucleotides repeated at different combinations again and again and again for thousands and thousands of letters. So where do we start? So, in order to identify where we start, where that start of that paragraph is, we look for a start codon, which in this case is AUG. So here's these 3 nucleotides that encode for the start codon. So, we have 3 nucleotides A, U, G, and it encodes for 1 amino acid. So what's that amino acid? It's going to be a methionine. And this is actually going to be a special methionine, so this is the amino acid, it's named methionine, and usually it's a special type of methionine that's used to only start the paragraph, for instance, start the translation of the gene there. And it's always the starting amino acid. So, we want to know where to start the paragraph, we look for AUG. But we also need to know where to end the paragraph, and so that's when we look for stop codons. Now, there's more than one stop codon, UAA, UAG, and UGA, but these do not actually code for amino acids. So, this is kind of unusual because the rest of the different nucleotide combinations encode for amino acid, but stop codons don't. They're the only exception, and what they do is they just say stop here. It's kind of like a period at the end of the paragraph, so that they know that this is where you need to press enter on your Word doc and start a new paragraph. So we have a start codon that says here it starts the paragraph, we have a stop codon, which is the period, you press enter and then you can start something new. So that is a codon. That's how we decode the dictionary of knowing, you know, what three nucleotide combinations equal a single amino acid. So the next thing we need to know is that the genetic code is redundant. You may also see this as degenerate. So what does this mean? Well, the scientific definition means that multiple combinations of nucleotide encode for a single amino acid. But in terms of just going back to our example that we've been talking about translating English to Spanish, for instance, we know that English has multiple synonyms. Right? It has words that are different, they're spelled differently, but they mean the same thing. And the genetic code is also like that, where you can have multiple combinations of nucleotides that mean the same thing, meaning that they all 3, even though the nucleotides are different, can encode for the same amino acid. So, there are actually 64 total nucleotide combinations. How I know that is that we have 3 spots, right, for codons, that's 3 nucleotides, and there are 4 possibilities for each spot. Each one of these can be A, T, C, or G. Each one of these can be A, T, C, or G, and each one of these can be A, T, C, or G. And so, if we multiply 4 by 4 by 4, we get 64 different combinations that can occur for each, for codons. Right? There are 64 nucleotide combinations with 3 nucleotides. But we only have 20 amino acids. So it's clear that not every single one of these combinations, each one of these 64 unique combinations, can encode for the same amino acid. Just like synonyms have looked different, they're spelled differently, right, but they have the same meaning, the exact same way. And this is actually really important in terms of evolution. I'm only going to mention this here because we're not talking about evolution right now, but you can imagine, having this redundancy, having synonyms in the genetic code means that if you have a mutation, right, if you spell a word wrong, it lessens the effect because you still have all of these synonyms that could be similar and sort of lessen the effect of a single mutation. So but I'm only going to mention that here briefly because we're not talking about evolution. We're talking about understanding how to translate things. So the next thing we need to do, and that this is a little bit different than our traditional example, and that is reading frames. And there are, 3 reading frames, each beginning with the nucleotide within the first codon. Okay. So remember, we talked about where to start the paragraph, right, we looked for the starting codon, and when we're writing a paragraph in English, translating that to Spanish,

tRNA Processing

Okay, so now let's talk about tRNA processing. tRNAs are the RNA molecules responsible for matching amino acids to the proper codons. Before we discussed vocab, understanding, and where to start and end a paragraph in terms of translating, but tRNAs are actually the ones doing the translation. If we wanted a paragraph translated from English to Spanish, we would need to go to someone who can read both languages and translate it. tRNAs are those translators. So, what does a tRNA look like? tRNA is an RNA molecule, as mentioned, but it has 75 to 90 nucleotides in length. When RNA comes together, it forms a double helix which slightly alters its shape to resemble an "L." Here is an example of that, showing the "L" that was kind of upside down. Sometimes people also describe it as looking like a cloverleaf; you can see the three leaves here. The colors represent different structures of the tRNA.

Now, speak about the different structures. Each color represents a different structure, but you only need to know a couple of them. You need to know about the anticodon region — the part that would equate to reading English in terms of translation. Let's discuss each part individually. The anticodon region is made up of nucleotides that are complementary to the codon. So if the codon is AUG, then the tRNA will contain RNA that's complementary, which will be TAC. Thus the anticodon is a region of these three nucleotides complementary to the codon it binds to. The 'Spanish region', or the amino acid binding region, is at the 3' prime end of the tRNA. It's a single-stranded area where an amino acid binds. This region here is the amino acid binding region - an amino acid will bind here, and the anticodon region will be here in gray recognizing the corresponding codon.

When RNA is transcribed from DNA encoding for tRNAs, it's not immediately perfect for function. tRNAs need to be processed, which includes addition of certain chemical groups, replacement of uracils with a CCA sequence, and other modifications. Unlike mRNAs, tRNAs do not require a 5' cap or a 3' poly tail but do undergo some splicing. There are approximately 50 nucleotide modifications found in tRNAs. After all processing steps, the tRNAs are ready for translation.

Synonymous codons can correspond to the same amino acid due to the wobble hypothesis. This hypothesis allows flexibility at the 3rd position of the codon where the nucleotide can "wobble," meaning it can be different nucleotides yet still code for the same amino acid. This flexibility helps in the translation accuracy even if a slight variation occurs at the 3rd position of the codon.

Regarding aminoacyl tRNA synthetase, it's crucial as it attaches the correct amino acid to its corresponding tRNA. There is one synthetase per amino acid, and these enzymes ensure that tRNAs are charged correctly—when a tRNA is charged with its amino acid, it is said to be active. The proofreading function of these enzymes ensures that the amino acid bound to the tRNA is unique and specific, minimising any error in protein synthesis.

tRNAs are essential as they translate RNA sequences into proteins through their interaction with mRNA and ribosomes. Instead of translating multiple codons, a tRNA can typically translate one perhaps two codons, making multiple tRNAs necessary for translating an entire RNA sequence. Although individual tRNAs are not as versatile as human translators, the collective activity of tRNAs ensures precise protein synthesis.

In conclusion, tRNAs are crucial in translating RNA into proteins. Their specific binding and interaction with the correct amino acids and codons ensure the accuracy of the proteins synthesized. With this understanding of tRNA structure, processing, and function, let's move on.

rRNA Processing

Okay, so we've talked about codons, we've talked about tRNA's, now we're going to talk about rRNA's and the ribosome. So in our example of translating English to Spanish, we have gone through codons, how that fits into this example, how we need to know the dictionary, we need to know the vocabulary, we need to know the alphabet, we need to know the reading frame to figure out what order things are read in, the start and stop codon to figure out where the paragraph or the gene starts and stops. In terms of tRNA, we need people who can actually translate translators, right? And tRNA is to act like that, and we know that there's a specificity to it. But now, we need to focus on ribosomes. And so, in this example of English to Spanish translation, a ribosome would kind of be like the pencil. So, if you wanted to have somebody translate a paragraph of English and write down the paragraph of Spanish, you need a tool to be able to do that. It could be a pencil, it could be a word document, whatever tool you want to use. The ribosome is the tool to actually combine everything together, the knowledge from the tRNAs, this codon code, and actually turn it into or translate it into protein. So ribosomes are made up of ribosomal RNAs, and ribosomes form the majority of the ribosome. So our rRNAs, ribosomal RNAs, that are responsible for translating RNA to protein. Remember, they kind of act like the pencil to do this. Now it says the majority of the rib of the ribosome because the ribosome is made up of both rRNAs and proteins, but rRNAs are the real important part of this. And so in prokaryotic cells, there are 3 different types, 16S, 23S, and 5S. You probably don't need to know the differences between these, but there are 3 different rRNAs. And in prokaryotes, in order to create the rRNA, there's actually just one transcript that encodes for all 3 of these. And, the processing separates them and then forms them into the prokaryotic ribosome. In eukaryotes, there's an extra 4 rRNAs, here are their names. And in eukaryotes, 3 of them, the 5S, the 5.8S, and the 28S, are also encoded in the same transcript, and then once they're transcribed processing allows them to be separated and then put into the ribosome. So, because if you're going to encode multiple genes on the same transcript, obviously there needs to be processing. So, our RNAs must be processed and cleaved, meaning that these are separated, right, into the individual rRNAs before they can form the ribosome. So what are the examples of processing things that can happen to RNAs? Now when we talk about processing RNAs, we're typically thinking we're thinking about the processing of mRNAs, the addition of a 5' cap, the poly A tail splicing. But rRNAs, again like tRNAs, are processed differently than mRNAs. And so, oftentimes, what happens to rRNAs for processing is that individual nucleotides are slightly altered chemically. So an example of this would be adding a methyl group onto an individual nucleotide, onto a uracil, for instance, or cytosine, whichever it wants to. And then in addition to these nucleotide modifications, there can also be conformational changes in the structure. So remember, our RNAs have the ability to fold into these complex structures, and that gives them the ability to act almost like enzymes. And in the ribosome, they do act like enzymes. They exert some type of to allow for translation. And so rRNAs have to be folded in a certain way to allow that, and changing that structure of the RNA and the changing the conformation can change its function and help process it into its final ribosome form. And our RNAs are there are actually a ton of them. Right? Because ribosomes are necessary for all types of translation, and we constantly need to be producing more proteins. So actually, the total amount of RNA in the cell, if you think about how much is in there, tRNAs, mRNAs, the things that are making proteins, but ribosomal RNAs make up nearly 80% of that total. So the other 20% is made up of the stuff that creates proteins and tRNAs and other small RNAs as well. But nearly 80% of all the RNA in the cell is ribosomal RNA. So it's obviously a lot and all of it's used to create ribosomes. So there's a ton of ribosomes in the cell. So here's an example of the 5S rRNA, and you can see that I mean it's RNA, but it forms this complex structure here. And that structure then is incorporated with other rRNAs, other proteins, and that creates the ribosome. So now that we've talked about the rRNA, let's actually talk about the ribosome itself. And the ribosome consists of 2 subunits, a small and a large. And this, the names of the small and large just depend on how many rRNAs are included. So in prokaryotes, the small subunit has the 16S and the large subunit has the 23S and 5S. And in eukaryotes, the small subunit has the 18S with the large containing all 3 of these. And so, yeah, so those are just good things to, you know, memorize. I know I just read that off the thing, but there's nothing really else to say about that other than it's good to know which rRNAs are responsible for each, subunit for small and large for both prokaryotes and eukaryotes. So small nuclear RNA, this is a different type of RNA. And, what it does is it helps, it can bind to the pre-rRNA. So, what is the pre-rRNA? That's going to be the unprocessed RNA transcript. So, we have DNA here, right, and it's going to undergo transcription to create the pre rRNA. And then, it'll undergo processing to become the final rRNA transcript. And so how does this happen? Well, snoRNA binds to the pre-rRNA right here. And then when the small RNA, the snoRNA here, binds to the pre-rRNA, it allows for proteins to come in. And whenever we have this complex of the pre-rRNA, the snoRNA, and the protein, we call those snoRNPs. So, we get a little bit confused about what we're talking about, but you notice here that all the RNAs have RNAs in them. If it says RNPs, there's some type of protein incorporated into that. And so these snoRNPs help to position the rRNAs, which are being processed, right, for processing. So, we have to connect so in order for the RNAs to be processed, we have to connect them with these different types of RNAs, these different proteins so that they can be processed. And these snoRNAs really help with that process. And so, the summary of this though, the really important crucial part that you need to know is that the ribosome is formed by these processed RNAs and proteins, and the rRNAs are the most important because they are the ones with the functions. They're the ones that are sort of helping this translation process along. The proteins don't really do much other than just provide a little bit of support and structure to the ribosome. So here we have a ribosome looks like. The, we have the large subunit here and the small subunit here. And what happens is that the mRNA is fed through this way, right, and tRNAs can come into this area and that allows for the connection of the codon in the RNA and the anticodon in the tRNA, and then that connects the amino acid. And that is how translation occurs. So, we'll go over this process, this one here, much more, but that's just a very brief overview. So that is the ribosome and rRNAs. So with that, let's move on.

Which of the following is not true about the codon code?

• A. One sequence (AUG) initiates translation
• B. The number of codons is more than the number of amino acids
• C. Out of three possibilities there is only one correct start site (frame) for each gene
• D. Anticodons are encoded in the DNA of the gene

Aminoacyl tRNA synthetase is an ezyme that is responsible for doing what?

• A. Forming the tRNA into its cloverleaf structure
• B. . Binding the tRNA anticodon and mRNA codon together
• C. Attaching the amino acid onto the tRNA
• D. Attaching the amino acid onto the growing polypeptide chain

Which of the following rRNAs make up the small subunit of the eukaryotic ribosome?

• A. 18S
• B. 5S
• C. 16S
• D. 28S

Here’s what students ask on this topic:

What is the role of tRNA in translation?

tRNA (transfer RNA) plays a crucial role in translation by matching amino acids to their corresponding codons on the mRNA strand. Each tRNA molecule has an anticodon region that is complementary to a specific mRNA codon and an amino acid binding site at the 3' end. When the anticodon pairs with the codon on the mRNA, the tRNA delivers the appropriate amino acid to the ribosome, where rRNA facilitates the assembly of amino acids into a polypeptide chain. This process ensures that the genetic code is accurately translated into functional proteins.

What is the wobble hypothesis in translation?

The wobble hypothesis explains the flexibility in codon-anticodon pairing during translation. According to this hypothesis, the first two nucleotides of a codon must pair precisely with the corresponding nucleotides of the tRNA anticodon, but the third nucleotide can 'wobble' or vary. This flexibility allows a single tRNA to recognize multiple codons that code for the same amino acid, enhancing the efficiency of protein synthesis. The wobble hypothesis helps explain why there are fewer tRNAs than codons, as some tRNAs can pair with more than one codon due to this wobble effect.

How do ribosomes facilitate protein synthesis?

Ribosomes are essential for protein synthesis, acting as the site where translation occurs. Composed of rRNA and proteins, ribosomes have two subunits: a small subunit that binds to the mRNA and a large subunit that facilitates the formation of peptide bonds between amino acids. During translation, tRNAs bring amino acids to the ribosome, where the rRNA helps align the tRNA anticodon with the mRNA codon. The ribosome then catalyzes the formation of peptide bonds, linking the amino acids into a growing polypeptide chain, which eventually folds into a functional protein.

What are start and stop codons, and what are their roles in translation?

Start and stop codons are essential signals in the translation process. The start codon, AUG, signals the beginning of translation and codes for the amino acid methionine. It ensures that the ribosome begins translating the mRNA at the correct location. Stop codons, such as UAA, UAG, and UGA, signal the termination of translation. These codons do not code for any amino acids but instead instruct the ribosome to release the newly synthesized polypeptide chain. Together, start and stop codons define the boundaries of the protein-coding region on the mRNA.

What is the significance of reading frames in translation?

Reading frames are crucial in translation as they determine how the nucleotide sequence of mRNA is divided into codons. There are three possible reading frames for any mRNA sequence, but only one is correct for producing the intended protein. The correct reading frame is established by the start codon (AUG) and continues in sets of three nucleotides until a stop codon is reached. If the reading frame is shifted due to mutations like insertions or deletions, it can result in a completely different and often nonfunctional protein, highlighting the importance of maintaining the correct reading frame.