Now that you are an expert code breaker, we can start to talk about translation. Let's go over the key players in the process.

• mRNA. The mRNA is the code that is translated into a functional protein. It is created through transcription and a series of subsequent editing steps, which we have described in detail already. The mature mRNA comprises codons that will code for the production of a protein.

• tRNAs. We've told you about codons, but what we haven't told you is how the codon is actually recognized and used to insert an amino acid. The key player in this process is the tRNA. The tRNA cannot only recognize a specific codon, it can also carry the correct amino acid. Together this process insures that the correct amino acid is brought to the site of the codon.

How does the tRNA read the RNA sequence? Excellent question. Our friends the base pairing rules return again. The tRNA is an RNA, and therefore, the tRNA comprises nucleotides. Can you figure out how this matching process might work?

If you said by having the reverse complement to the RNA codon, then you are absolutely correct. The tRNA has a region that carries the complete reverse complement to the codon on the RNA. This three-nucleotide sequence is called the anticodon. Most of the tRNA is actually elaborately folded back upon itself to create a clover-like shape. The anticodon is one of the few regions that is actually not paired to itself. Another region that is not paired to itself is the 3' end. This region is used to bind the amino acid.

You may have noticed in our code breaking exercise above that the genetic code is redundant. Therefore, one amino acid is coded for by more than one codon.

How does this work in response to the tRNAs? You can probably imagine two solutions.

1. There could be multiple tRNAs that code for a particular amino acid.
     
2. Alternatively, a single tRNA could actually be able to bind more than one codon.

Red Alert. It turns out that actually both are true. But wait, you are saying. Doesn't the second scenario go against the base pairing laws? Yep, it does. Occasionally some tRNAs can base pair to a codon that is not a perfect match, as long as the first two bases can pair. This mismatching on the third nucleotide is called a wobble. This helps explain why the same amino acid is often coded for by several codons that differ only in their third base pair.

The nucleotides of the tRNA undergo many different modifications. These modifications help to ensure that the codon binds correctly to the anticodon, and that the tRNA binds the correct amino acid. Enzymes called aminoacyl-tRNA synthases make sure that the tRNA is attached to the appropriate tRNA molecule. They catalyze a high-energy bond to attach the tRNA to the correct amino acid. Think of them as translation's proofreader.

rRNA and the Ribosome

Another type of RNA plays a critical role in translation. It is probably best to think of the ribosome as a RNA reading machine, made of both proteins and rRNA molecules. The RNAs of the ribosome (rRNAs) are pretty much the motor of the ribosome. They do all the work: the catalysis and creation of peptide bonds. In fact, the rRNAs are produced in massive quantities to meet the cell's translation needs. To facilitate this process there are multiple copies of rRNA genes in both eukaryotic and prokaryotic genomes.

Together the proteins and RNA compile to make the two separate subunits (or pieces) of the ribosome. These two subunits are only together when they are actively participating in translation. The ribosome subunits bind to the mRNA and then pull the mRNA through the subunits. Let's look at some pictures again:

The tRNAs loaded with an amino acid arrive at the ribosome's active site, and the ribosome then catalyzes the conversion of the amino acid into the growing polypeptide chain. When the ribosome reaches the stop codon, the mRNA is released.

Accessory Factors

Translation is best thought of in three steps: initiation, elongation, and termination. It is perhaps not surprising that there's a ton of accessory factors that help with each of these steps. Let's go over each of the steps of translation. We will talk about the accessory factors in the context of each of the steps.

Initiation

Have you ever wondered how the ribosome knows where to start? The ribosome needs to attach at the right spot and begin translating at the correct AUG. This isn't a straightforward task, because often an RNA contains more than one AUG. Prokaryotes use a recognition sequence that is near the AUG initiation codon. The ribosome binds to this recognition sequence on the mRNA by base pairing to it. In bacteria, this recognition initiation sequence is called the Shine-Dalgarno sequence after the scientists who discovered it. In eukaryotes, the ribosome seems to scan from the 5' cap, looking for the first AUG.

Bacteria only have a few initiation factors, but eukaryotes have many more. These factors can prevent the premature binding of the second half of the ribosome, and also help with the recognition of the initiator tRNA.

Once a few amino acids have been linked together, translation is said to be in elongation phase. Elongation can be thought of in three steps. First the correct tRNA needs to bind to the correct site on the ribosome. Then the bond between the amino acid and the tRNA must be broken and transferred to the amino acid chain. This step is catalyzed by an enzyme called a peptidyl transferase. Finally, the ribosome must move over exactly three nucleotides to get ready for the next tRNA. Elongation factors make sure that the message is read accurately and efficiently.

Finally translation must come to an end, a step called termination. We mentioned earlier that stop codons signal the end of the peptide chain. There is no tRNA that recognizes a stop codon, and no amino acid will be added at this site. Instead, special accessory factors called release factors bind to the ribosome force the release of the polypeptide chain. The two-ribosome subunits dissociate. The release factors mimic the size and shape of a tRNA, which makes them effective at interacting with the ribosomes.

Mission Accomplished…Almost.

We've now told you about all the key factors of translation and how they contribute to the three major steps of the process: initiation, elongation, and termination. While at this point translation is indeed complete, the protein will still likely undergo many more additional changes.

• Folding. The peptide chain must be converted from a long chain of amino acids into a three dimensional structure. The protein does this action by making numerous connections between different amino acids. A special group of proteins, called chaperones, assist with this process. This family of proteins can bind to proteins that are not folded correctly. They then provide a thermodynamically favorable environment for the protein to reach its correctly folded state.
    
  What happens when the proteins don't fold correctly? The misfolded proteins can aggregate in the cell. These "protein globs" are kind of like glue. They attract other proteins, preventing them from doing their jobs effectively.
   
  This aggregation can be deadly for the cell, and the organism. In fact, several disease states, such as Alzheimer's, and mad cow disease, have been linked to protein aggregation. The cell attempts to eliminate any misfolded proteins by promoting their destruction. It turns out that many newly synthesized proteins end up degrading. While some of these proteins are proteins that did not fold correctly, others are actually a result of errors in translation.

• Post-translational modifications. Enzyme catalyzed changes to a protein (examples are phosporylation, ubitquination, and methylation). These modifications can alter the three dimensional structure of a protein, regulate its ability to bind to different proteins, and alter its activity.

Brain Snack

Having a hard time keeping transcription and translation straight? Maybe a song will help.