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Stages of translation
An in-depth look how polypeptides (proteins) are made. Initiation, elongation, and termination.
Introduction
Ever wonder how antibiotics kill bacteria—for instance, when you have a sinus infection? Different antibiotics work in different ways, but some attack a very basic process in bacterial cells: they knock out the ability to make new proteins.
To use a little molecular biology vocab, these antibiotics block translation. In the process of translation, a cell reads information from a molecule called a messenger RNA (mRNA) and uses this information to build a protein. Translation is happening constantly in a normal bacterial cell, just like it is in most of the cells of your body, and it's key to keeping you (and your bacterial "visitors") alive.
When you take certain antibiotics (e.g., erythromycin), the antibiotic molecule will latch onto key translation molecules inside of bacterial cells and basically "stall" them. With no way to make proteins, the bacteria will stop functioning and, eventually, die. That's why infections clear up when they're treated with the antibiotic.start superscript, 1, comma, 2, end superscript
Cells need translation to stay alive, and understanding how it works (so we can shut it down with antibiotics) can save us from bacterial infections. Let's take a closer look at how translation happens, from the first step to the final product.
Translation: The big picture
Translation involves “decoding” a messenger RNA (mRNA) and using its information to build a polypeptide, or chain of amino acids. For most purposes, a polypeptide is basically just a protein (with the technical difference being that some large proteins are made up of several polypeptide chains).
The genetic code
In an mRNA, the instructions for building a polypeptide come in groups of three nucleotides called codons. Here are some key features of codons to keep in mind as we move forward:
- There are 61 different codons for amino acids
- Three “stop” codons mark the polypeptide as finished
- One codon, AUG, is a “start” signal to kick off translation (it also specifies the amino acid methionine)
These relationships between mRNA codons and amino acids are known as the genetic code (which you can explore further in the genetic code article).
Codons to amino acids
In translation, the codons of an mRNA are read in order (from the 5' end to the 3' end) by molecules called transfer RNAs, or tRNAs.
Each tRNA has an anticodon, a set of three nucleotides that binds to a matching mRNA codon through base pairing. The other end of the tRNA carries the amino acid that's specified by the codon.
tRNAs bind to mRNAs inside of a protein-and-RNA structure called the ribosome. As tRNAs enter slots in the ribosome and bind to codons, their amino acids are linked to the growing polypeptide chain in a chemical reaction. The end result is a polypeptide whose amino acid sequence mirrors the sequence of codons in the mRNA.
That's the big picture of translation. But what about the nitty gritty of how translation begins, proceeds, and finishes? Let's take a look.
Translation: Beginning, middle, and end
A book or movie has three basic parts: a beginning, middle, and end. Translation has pretty much the same three parts, but they have fancier names: initiation, elongation, and termination.
- Initiation ("beginning"): in this stage, the ribosome gets together with the mRNA and the first tRNA so translation can begin.
- Elongation ("middle"): in this stage, amino acids are brought to the ribosome by tRNAs and linked together to form a chain.
- Termination ("end"): in the last stage, the finished polypeptide is released to go and do its job in the cell.
Let’s take a closer look at how each stage works.
Initiation
In order for translation to start, we need a few key ingredients. These include:
- A ribosome (which comes in two pieces, large and small)
- An mRNA with instructions for the protein we'll build
- An "initiator" tRNA carrying the first amino acid in the protein, which is almost always methionine (Met)
During initiation, these pieces must come together in just the right way. Together, they form the initiation complex, the molecular setup needed to start making a new protein.
Inside your cells (and the cells of other eukaryotes), translation initiation goes like this: first, the tRNA carrying methionine attaches to the small ribosomal subunit. Together, they bind to the 5' end of the mRNA by recognizing the 5' GTP cap (added during processing in the nucleus). Then, they "walk" along the mRNA in the 3' direction, stopping when they reach the start codon (often, but not always, the first AUG).start superscript, 6, end superscript
In bacteria, the situation is a little different. Here, the small ribosomal subunit doesn't start at the 5' end of the mRNA and travel toward the 3' end. Instead, it attaches directly to certain sequences in the mRNA. These Shine-Dalgarno sequences come just before start codons and "point them out" to the ribosome.
Why use Shine-Dalgarno sequences? Bacterial genes are often transcribed in groups (called operons), so one bacterial mRNA can contain the coding sequences for several genes. A Shine-Dalgarno sequence marks the start of each coding sequence, letting the ribosome find the right start codon for each gene.
Elongation
I like to remember what happens in this "middle" stage of translation by its handy name: elongation is when the polypeptide chain gets longer.
But how does the chain actually grow? To find out, let's take a look at the first round of elongation—after the initiation complex has formed, but before any amino acids have been linked to make a chain.
Our first, methionine-carrying tRNA starts out in the middle slot of the ribosome, called the P site. Next to it, a fresh codon is exposed in another slot, called the A site. The A site will be the "landing site" for the next tRNA, one whose anticodon is a perfect (complementary) match for the exposed codon.
Once the matching tRNA has landed in the A site, it's time for the action: that is, the formation of the peptide bond that connects one amino acid to another. This step transfers the methionine from the first tRNA onto the amino acid of the second tRNA in the A site.
Not bad—we now have two amino acids, a (very tiny) polypeptide! The methionine forms the N-terminus of the polypeptide, and the other amino acid is the C-terminus.
But...odds are we may want a longer polypeptide than two amino acids. How does the chain continue to grow? Once the peptide bond is formed, the mRNA is pulled onward through the ribosome by exactly one codon. This shift allows the first, empty tRNA to drift out via the E ("exit") site. It also exposes a new codon in the A site, so the whole cycle can repeat.
And repeat it does...from a few times up to a mind-boggling 33, comma000 times! The protein titin, which is found in your muscles and is the longest known polypeptide, can have up to 33, comma000 amino acidsstart superscript, 8, comma, 9, end superscript.
Termination
Polypeptides, like all good things, must eventually come to an end. Translation ends in a process called termination. Termination happens when a stop codon in the mRNA (UAA, UAG, or UGA) enters the A site.
Stop codons are recognized by proteins called release factors, which fit neatly into the P site (though they aren't tRNAs). Release factors mess with the enzyme that normally forms peptide bonds: they make it add a water molecule to the last amino acid of the chain. This reaction separates the chain from the tRNA, and the newly made protein is released.
What next? Luckily, translation "equipment" is very reusable. After the small and large ribosomal subunits separate from the mRNA and from each other, each element can (and usually quickly does) take part in another round of translation.
Epilogue: Processing
Our polypeptide now has all its amino acids—does that mean it's ready to do its job in the cell?
Not necessarily. Polypeptides often need some "edits." During and after translation, amino acids may be chemically altered or removed. The new polypeptide will also fold into a distinct 3D structure, and may join with other polypeptides to make a multi-part protein.
Many proteins are good at folding on their own, but some need helpers ("chaperones") to keep them from sticking together incorrectly during the complex process of folding.
Some proteins also contain special amino acid sequences that direct them to certain parts of the cell. These sequences, often found close to the N- or C-terminus, can be thought of as the protein’s “train ticket” to its final destination. For more about how this works, see the article on protein targeting.
Want to join the conversation?
The part about mRNA shifting one codon, isn't it the ribosome that shifts one codon?(11 votes)
No. The ribosome is the workbench and the mRNA is being moved through the ribosome shifting downwards every codon.(10 votes)
What about Initiation factors? IF1, IF2 & IF3. Please could you explain their roles? Thanks(6 votes)- IF1, Binds to the 30S subunit to the A site, prevents tRNA binding
IF2, Binds initiator tRNA (f-Met) and controls its entry to the ribosome at the P site
IF3, Required for the 30S to bind mRNA(5 votes)
what about untranslated regions? such as the 5' and 3' UTR(4 votes)
They don't get translated!
The 5' UTR is everything 5' of the start codon.
The interesting question is how does the ribosome know which start codon to start with?
The short answer to that is that the sequence of the mRNA around a potential start codon influences whether or not it will be used§. These sequences are bound by proteins that help guide the ribosome to assemble at the correct place to start translation.
(In fact, codons other than AUG are sometimes used as start codons!)
This is covered in a bit more detail in another article:
https://www.khanacademy.org/science/biology/gene-expression-central-dogma/translation-polypeptides/a/the-stages-of-translation
I also encourage you to look at some of the references for that section, which will help give you more detail on this high complex process that is still being actively studied.
The 3' UTR is simpler to identify — it is typically† everything after the first in frame stop codon and before the polyadenylation signal (where the polyA tail gets added.
Does that help?
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§Note: The mechanisms are very different in prokaryotic and eukaryotic organisms — they can also vary between different species and even for different genes!
†Note: As is often true in biology there are numerous caveats and exceptions. A common example is found in eukaryotic genes — these genes often have introns, some of which are only spliced in some circumstances, so the in frame stop may be in different places for different transcripts from the same gene. This is knowns as alternative splicing.(8 votes)
- what is the total atp or gtp utilised?(4 votes)
- It costs 4n high-energy bonds to make a peptide chain. n= the number of amino acids in the chain.
For example:
How many high-energy phosphate bonds are required to make a 50 amino acid polypeptide chain?
Solution: 200.
-2 phosphate bonds hydrolyzed per amino acid to make the amino-acyl tRNAs (or 100 for the 50 AAs)
-2 phosphate bonds required for each elongation step (49 steps in a chain of 50, so 98 for the chain)
-1 GTP for initiation to position the first tRNA and mRNA on the ribosome
-1 GTP for termination
For a total of 200.(3 votes)
During translation, is the tRNA used up or can it be recycled?(3 votes)
Great question!
The tRNA is released into the cell and can again be joined with an amino acid. (Details on the joining are in the previous section.)(5 votes)
What happens to mRNA after the polypeptide chain is formed?(4 votes)
It's released and might be used again. I believe after being used enough, they can break down.(1 vote)
After peptide bond formation, what pulls mRNA to a new position?(2 votes)
Does the water molecule that the release factors added on the polypeptide chain get deattached once termination is done? Or does it stay on the protein?(2 votes)
In eukaryotic mRNA, is the start codon always at the start of the first exon?(1 vote)
Yes, it is.
It cannot be considered start codon if it is not AUG at the beginning of first exon.
What might confuse is that it does not have to be on the very strict beginning, there might be nucleotides before, but that is 5' untranslated region.
The first AUG is usually considered as a start codon, but probably GGC could take place in front of that AUG and be not translated by the ribosome.(3 votes)
- Don't release factors bind in the A site (not the P site)?(2 votes)
A release factor (RF) refers to a type of translation factor that triggers translation termination. Release factors fall into two classes; Class I release factors that bind the ribosome in response to the presence of a stop codon within the ribosomal A-site. Thus it binds with A site (not P site).(1 vote)
