tRNAs and ribosomes
Structure and roles of transfer RNAs and ribosomes. Codons, anticodons, and wobble. Aminoacyl-tRNA synthetases.
Translation requires some specialized equipment. Just as you wouldn't go to play tennis without your racket and ball, so a cell couldn't translate an mRNA into a protein without two pieces of molecular gear: ribosomes and tRNAs.
- Ribosomes provide a structure in which translation can take place. They also catalyze the reaction that links amino acids to make a new protein.
- tRNAs (transfer RNAs) carry amino acids to the ribosome. They act as "bridges," matching a codon in an mRNA with the amino acid it codes for.
Here, we’ll take a closer look at ribosomes and tRNAs. If you're not yet familiar with RNA (which stands for ribonucleic acid), I highly recommend checking out the nucleic acids section first so you can get the most out of this article!
Ribosomes: Where the translation happens
Translation takes place inside structures called ribosomes, which are made of RNA and protein. Ribosomes organize translation and catalyze the reaction that joins amino acids to make a protein chain.
Illustration of the molecules involved in protein translation. A ribosome is shown with mRNA and tRNA. Amino acids are emerging to form a protein chain.
Structure of the ribosome
A ribosome is made up of two basic pieces: a large and a small subunit. During translation, the two subunits come together around a mRNA molecule, forming a complete ribosome. The ribosome moves forward on the mRNA, codon by codon, as it is read and translated into a polypeptide (protein chain). Then, once translation is finished, the two pieces come apart again and can be reused.
Overall, the ribosome is about one-third protein and two-thirds ribosomal RNA (rRNA). The rRNAs seem to be responsible for most of the structure and function of the ribosome, while the proteins help the rRNAs change shape as they catalyze chemical reactions.
Below, you can see a 3D model of the ribosome. Proteins are colored in blue, while strands of rRNA are colored in tan and orange. The green spot marks the active site, which catalyzes the reaction that links amino acids to make a protein. It surprised me to see that the ribosome is wrinkly, kind of like the surface of a brain!
Model of the small and large subunits of the ribosome. Both subunits are made up of both ribosomal RNA and proteins. The large subunit contains the active site where peptide bond formation is catalyzed.
The ribosome has slots for tRNAs
As we saw briefly in the introduction, molecules called transfer RNAs (tRNAs) bring amino acids to the ribosome. We'll learn a lot more about tRNAs and how they work in the next section.
For now, just keep in mind that the ribosome has three slots for tRNAs: the A site, P site, and E site. tRNAs move through these sites (from A to P to E) as they deliver amino acids during translation.
The ribosome is composed of a small and large subunit. The small subunit binds to an mRNA transcript and both subunits come together to provide three locations for tRNAs to bind (the A site, P site, and E site). In the diagram, the A, P, and E sites appear in A-P-E order from right to left.
After the initial binding of the first tRNA at the P site, an incoming charged tRNA will then bind at the A site. Peptide bond formation will transfer the amino acid of the first tRNA (Met) to the amino acid of the second tRNA (in this case, Trp). This chain of two amino acids will be attached to the tRNA in the A site. The ribosome will then move along the mRNA template by one codon. The tRNA in the A site (with the polypeptide chain) will shift to the P site, and the empty tRNA previously in the P site will shift to the E site (where it will exit the ribosome). A new tRNA (in this case, one bearing Phe) will bind to the newly exposed codon in the A site, and the process can then repeat.
To learn more about each site's unique "job," check out the article on stages of translation.
What exactly is a tRNA?
A transfer RNA (tRNA) is a special kind of RNA molecule. Its job is to match an mRNA codon with the amino acid it codes for. You can think of it as a kind of molecular "bridge" between the two.
Each tRNA contains a set of three nucleotides called an anticodon. The anticodon of a given tRNA can bind to one or a few specific mRNA codons. The tRNA molecule also carries an amino acid: specifically, the one encoded by the codons that the tRNA binds.
Image showing a tRNA acting as an adapter connecting an mRNA codon to an amino acid. At one end, the tRNA has an anticodon of 3'-UAC-5', and it binds to a codon in an mRNA that has a sequence of 5'-AUG-3' through complementary base pairing. The other end of the tRNA carries the amino acid methionine (Met), which is the the amino acid specified by the mRNA codon AUG.
There are many different types of tRNAs floating around in a cell, each with its own anticodon and matching amino acid. In fact, there are usually to different types, depending on the species. tRNAs bind to codons inside of the ribosome, where they deliver amino acids for addition to the protein chain.
Some tRNAs bind to multiple codons ("wobble")
Some tRNAs can form base pairs with more than one codon. At first, this seems pretty weird: doesn't A base-pair with U, and G with C?
Well...not always. (Biology is full of surprises, isn't it?) Atypical base pairs—between nucleotides other than A-U and G-C—can form at the third position of the codon, a phenomenon known as wobble.
Wobble pairing doesn't follow normal rules, but it does have its own rules. For instance, a G in the anticodon can pair with a C or U (but not an A or G) in the third position of the codon, as shown below. Rules like this ensure codons are read correctly despite wobble.
Wobble pairing lets the same tRNA recognize multiple codons for the amino acid it carries. For example, the tRNA for phenylalanine has an anticodon of 3'-AAG-5'. It can pair with an mRNA codon of either 5'-UUC-3' or 5'-UUU-3' (both of which are codons that specify phenylalanine). The tRNA can bind to both codons because it can form both a normal base pair with the third codon position (5'-UUC-3' codon with 3'-AAG-5' anticodon) and an atypical base pair with the third codon position (5'-UUU-3' codon with 3'-AAG-5' anticodon).
The rules of wobble pairing ensure that a tRNA does not bind to the wrong codon. The tRNA for phenylalanine has an anticodon of 3'-AAG-5', which can pair with two codons for phenylalanine (described above), but not with 5'-UUA-3' or 5'-UUG-3' codons. These codons specify leucine, not phenylalanine, so this is an example of how the rules of wobble pairing allow a single tRNA to cover multiple codons for the same amino acid, but don't introduce any uncertainty about which amino acid will be delivered to a particular codon.
You may be wondering: why on Earth would a cell "want" a complicating factor like wobble? The answer may be that wobble pairing allows fewer tRNAs to cover all the codons of the genetic code, while still making sure that the code is read accurately.
The 3D structure of a tRNA
I like to draw tRNAs as little rectangles, to make it clear what's going on (and to have plenty of room to fit the letters of the anticodon on there). But a real tRNA actually has a much more interesting shape, one that helps it do its job.
A tRNA, like the one modeled below, is made from a single strand of RNA (just like an mRNA is). However, the strand takes on a complex 3D structure because base pairs form between nucleotides in different parts of the molecule. This makes double-stranded regions and loops, folding the tRNA into an L shape.
A tRNA molecule has an "L" structure held together by hydrogen bonds between bases in different parts of the tRNA sequence. One end of the tRNA binds to a specific amino acid (amino acid attachment site) and the other end has an anticodon that will bind to an mRNA codon.
One end of the L shape has the anticodon, while the other has the attachment site for the amino acid. Different tRNAs have slightly different structures, and this is important for making sure they get loaded up with the right amino acid.
Loading a tRNA with an amino acid
How does the right amino acid get linked to the right tRNA (making sure that codons are read correctly)? Enzymes called aminoacyl-tRNA synthetases have this very important job.
There's a different synthetase enzyme for each amino acid, one that recognizes only that amino acid and its tRNAs (and no others). Once both the amino acid and its tRNA have attached to the enzyme, the enzyme links them together, in a reaction fueled by the "energy currency" molecule adenosine triphosphate (ATP).
The active site of each aminoacyl-tRNA synthetase fits an associated tRNA and a particular amino acid like a "lock and key." ATP is then used to attach the amino acid to the tRNA.
Occasionally, an aminoacyl-tRNA synthetase makes a mistake: it binds to the wrong amino acid (one that "looks similar" to its correct target). For example, the threonine synthetase sometimes grabs serine by accident and attaches it to the threonine tRNA. Luckily, the threonine synthetase has a proofreading site, which pops the amino acid back off the tRNA if it's incorrect.
Putting it all together
Once they're loaded up with the right amino acid, how do tRNAs interact with mRNAs and the ribosome to build a brand-new protein? Learn more about how this process works in the next article, on the stages of translation.
Want to join the conversation?
- where does tRNA form ( where does it come from) ?(9 votes)
- It is coded by DNA, then it's transcribed by special polymerase, spliced and there we have it.(18 votes)
- What is the difference between DNA replication and the process of DNA translation/transcription(3 votes)
- Replication is making more DNA, transcription is DNA to mRNA, and translation is mRNA to proteins!(31 votes)
- Hi, where does the Amino Acid comes from? The one the tRNA transports. Does it come from the Lysosome?(6 votes)
- Amino Acids either come from exogenous origins (from the catabolism of ingested food), or anabolic from other precursors.
These free amino acids are found in the cytoplasm and are brought to the ribosome.(9 votes)
- What happens to tRNA molecules when they leave a ribosome?(5 votes)
- They attach to amino acids (that have been obtained from our diet) in the cytosol and return to the ribosome if the same codons appear in the mRNA sequence, for them to be translated.(6 votes)
- ATP is used to bind the amino acid to a tRNA.
How is the actual peptide bond formed during translation? Wouldn't that also need energy?(4 votes)
- Another good question.
The bond in the aminoacyl-tRNA is higher energy than the peptide bond, so there is no new energy input required to form the peptide bond — the energy came from hydrolyzing ATP to AMP plus PPᵢ (pyrophosphate). However, a GTP is hydrolyzed to ensure that the correct aminoacyl-tRNA binds to mRNA-ribosome complex and another is used to move the ribosome along the mRNA by one codon.
This discussion does a reasonable job of explaining the energetics of this process:
- Does the Wobble Position apply to START and STOP codons as well?(5 votes)
- From my understanding, it won't apply to the start codon, AUG, because there is only one possible codon available. If you look at the codons for an amino acid such as Leucine; CUU,CUC,CUA,CUG, there are multiple options available and the third letter varies, but all four codons code for Leucine.
I think the wobble position will apply to the stop codons; UAA, UAG and UGA, because there is variation in the third letter.
Note - I got the codons from the genetic code table, on the article 'The genetic code'.
I'm not 100% sure that I am correct though(2 votes)
- So, a tRNA is is L shaped in 3D and clover leaf shaped in 2D?
That's a bit confusing..(3 votes)
- You might find this exercise helpful to get a feel for how that works:
Basically two of the loops (D and T) are wrapped around each other, which converts the 2D clover leaf into an L-shape.(4 votes)
- What is meant by the third position in reference to the 'wobble binding' of tRNA?(1 vote)
- The third position refers to the third letter of the codon, reading from left to right (5' - 3' direction). If the codon was UUC, the third position would be C. There are some tRNA molecules that can bind with more than one codon, as in the example above. This is called wobble pairing, because the first position of the tRNA anticodon does not bind as tightly to the third postion of the codon, meaning the pairing between codon and anticodon is more flexible.(5 votes)
- You have mentioned that the two subunits (both) come together for initiation. Isn't that only true for prokaryotic cells?(2 votes)
- You are correct, this article deals with prokaryotic translation. In eukaryotic translation, there are also ribosomal subunits which must come together around an mRNA, but the process is a whole lot more complex with lots of protein-RNA interactions and protein-protein interactions. The wiki article on eukaryotic translation has a nice overview diagram. I think people are still figuring out exactly how the process works in eukaryotes.
- What does it mean when tRNA is charged?(2 votes)
- when tRNA has bound amino acid on its end and carrying it to the A site of the ribosome.(2 votes)