BIOCHEMISTRY DISCUSSION 10
Biochemistry: A Short Course Fourth Edition CHAPTER 39 The Genetic Code
Tymoczko • Berg • Gatto • Stryer
© 2019 W. H. Freeman and Company.
Created by Brett Barbaro
Now, we're coming to the last section of this course, and that will highlight protein synthesis. We started in the beginning with amino acids and atoms, and proteins are some of the largest structures in cells - so now we will see how all of this stuff comes together to make these proteins. The first step in studying this is going to be the genetic code.
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Chapter 39: Outline
39.1 The Genetic Code Links Nucleic Acid and Protein Information
39.2 Amino Acids Are Activated by Attachment to Transfer RNA
39.3 A Ribosome Is a Ribonucleoprotein Particle Made of Two Subunits
Created by Brett Barbaro
The genetic code is the DNA and RNA code which tells the ribosomes which amino acids to add to a growing peptide chain. It’s essentially a blueprint for creating a new protein. A very important part of this process, though, is the activation of amino acids and their attachment to transfer RNA. The transfer RNA acts as an intermediary between the genetic code and the protein. And we'll start our discussion of the ribosome, which is a very large complex of RNA and proteins, that has two major subunits.
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Section 39.1 The Genetic Code Links Nucleic Acid and Protein Information
Learning objective 1: Describe the genetic code.
Protein synthesis is a process of translation. Nucleic acid sequence information is translated into amino acid sequence information. The genetic code links these two types of information.
Characteristics of the genetic code:
Three nucleotides, called a codon, encode an amino acid.
The code is nonoverlapping.
The code has no punctuation.
The code is read in the 5’-to-3’ direction.
The code is degenerate in that some amino acids are encoded by more than one codon.
Recent research revealed that different organisms may prefer different sets of synonymous codons, although the biochemical benefit of codon bias is not yet clearly established.
Created by Brett Barbaro
Protein synthesis is the process of translating the nucleotide sequence of an mRNA into…the primary amino acid sequence of a protein. The mRNA is read in blocks of three nucleotides. And each one of these blocks of three nucleotides is called a codon. And each codon has a different amino acid that it encodes. This code is non-overlapping, and also has no “punctuation”, so it's just three nucleotides, followed by three nucleotides, followed by three nucleotides - which can cause problems, because if somehow one or two of those nucleotides gets removed, then it can screw up the entire protein from that point forward.
The code is read in the 5' to 3' direction, which is nice for us because things are synthesized in the 5' to 3' direction, so it's basically the only direction you need to think about. Things are very directional in the world of RNA and DNA and proteins. And you have also the advantage that because it's synthesized in the 5' to 3' direction, in bacteria at least, translation can actually start before the mRNA is completely synthesized.
One last thing to note about the genetic code is that there are three nucleotides per codon, and each one of those nucleotides could be one of four different nucleotides, so the possible combinations of three nucleotides would be 4x4x4 - which is 64. And we only have 20 amino acids. So, as a necessity, these amino acids need to be coded by more than one trinucleotide, more than one combination of three nucleotides. And that's what we call degeneracy in the code; there's more than one way to encode most of the amino acids.
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Table 39.1 The Genetic Code
Created by Brett Barbaro
Well, here are all possible combinations of bases that you can find in a codon laid out in a 16x4 grid. The first base is laid out along the left hand side, the second is along the top, and the third is along the right. So if you were to find what the amino acid that's coded for by UGA, for example, you would look on the left hand side and you see the U, so you know it's in that row, and then up along the top you see the G and you see it's in that column, so it's either cysteine, cysteine, stop or tryptophan. Then in the third position is an A, so it would be a stop codon.
There's some interesting things to be learned just by looking at this chart. For example, we can see that leucine, arginine, and serine are the three most-represented amino acids in this chart. Now, correspondingly, serine and leucine are actually two of the most abundant amino acids in human proteins - in fact, in vertebrate proteins in general. Similarly, methionine and tryptophan are only represented by single codons, and those, correspondingly, are two of the least abundant amino acids in vertebrate proteins. So there is some correlation between the number of times that an amino acid shows up in this chart and the abundance of the amino acid in nature - or rather, in vertebrate proteins. I can't say "in nature" because I'm really not sure what's the most abundant amino acid in nature. Amino acids do a whole bunch of things, and there are more than just these twenty amino acids. These are the 20 amino acids that make up proteins, but there's a ton of other ones that do completely different biochemical things.
Another thing which you can learn by looking at this is that, a lot of the time, the third position doesn't matter. You see these blocks of leucine and valine and alanine, and those are determined entirely by the first position and second position in the codon. The third position could be anything and it will still be the same amino acid. That's what we call degeneracy in the code. And we're going to talk about that a little bit more later.
There are 3 “stop” codons that you can see in the upper right, and those are codons that tell the ribosome to stop translating.
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The Genetic Code Is Nearly Universal
Most organisms use the same genetic code. However, some organisms have slight modifications.
For instance, in ciliated protozoa, codons that are stop signals in most organisms encode amino acids.
Mitochondria also use variations of the genetic code.
Created by Brett Barbaro
The genetic code that was laid out in the previous slide is pretty much universal for most organisms - but there are some variations. For example, in some organisms, like ciliated protozoa, there are codons that are stop signals in most organisms, but encode amino acids. And, interestingly, our own mitochondria also use variations of the genetic code. And that's one of the reasons that people think mitochondria started out as a separate organism.
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Table 39.2 Distinctive Codons of Human Mitochondria
Created by Brett Barbaro
Whereas in the standard code, the UGA encodes a stop, in the mitochondria it encodes a tryptophan. Whereas an AGA, which would normally encode arginine, in mitochondria encodes a stop codon. I believe that the mitochondrial code that is used is similar to the organism from which mitochondria are believed to be developed. But that's pretty wild - I mean, think about that. Our own mitochondria have a separate genetic code! I mean, wow.
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Transfer RNA Molecules Have a Common Design (1/2)
Transfer RNA (tRNA) molecules function as an adaptor molecule between a codon and an amino acid.
There is at least one tRNA molecule for each amino acid.
General characteristics of tRNA molecules include the following:
Each is a single strand of RNA between 73 and 93 ribonucleotides in length.
The three-dimensional structure of the molecule is L-shaped.
Transfer RNA molecules contain unusual bases such as inosine or bases that have been modified.
Created by Brett Barbaro
Now let's talk about tRNA, the transfer RNA molecules which are the intermediaries between the genetic code and protein synthesis. Each amino acid has its own tRNA, and some of them have more than one. The tRNAs are between 73 and 93 nucleotides in length. And they have a 3-dimensional structure that is L-shaped. One other thing about tRNAs is that they can contain unusual bases, as pictured in the upper right hand of the slide. Inosine, methylcytidine, and dihydrouridine are three examples. These strange bases that get incorporated help to stabilize the tRNAs, but also help for the proteins to identify which is which. Once again, incorporating new bases increases the palette of possible shapes and charge distributions that a molecule can have.
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Transfer RNA Molecules Have a Common Design (slide 2/2)
In a two-dimensional representation, all tRNA molecules appear as a cloverleaf pattern. The amino acid–accepting region is the acceptor stem, which contains the 3’ CCA terminal region. Many of the nucleotides are involved in hydrogen bonds that form stems and loops.
The 5’ end is phosphorylated, and the 5’ terminal residue is usually pG.
The amino acid is attached to a hydroxyl group of adenosine in the CCA region of the acceptor stem.
The anticodon is in a loop near the center of the sequence.
Created by Brett Barbaro
Figure 39.2 The general structure of transfer RNA molecules. The structure of the tRNA molecule is shown in the cloverleaf pattern. Comparison of the base sequences of many tRNAs reveals a number of conserved features.
Now, if you lay them out flat, and look at the interactions, tRNA molecules kind of have a cloverleaf pattern.
The amino acids are attached to the 3' end of the tRNAs, which all have the characteristic CCA sequence. This region is called the acceptor stem.
The 5' end of the tRNAs are phosphorylated, and the terminal residue is usually G (for guanine). And they use the notation “pG” to indicate that there is a phosphoryl group attached there.
The amino acid gets attached to either the 2' or the 3' hydroxyl group of the 3' terminal adenosine.
And then near the middle of the sequence is the anticodon, which forms its own loop.
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Diagram of Transfer RNA Structure
Created by Brett Barbaro
Figure 39.1 Transfer RNA structure. Notice the L-shaped structure revealed by this skeletal model of yeast phenylalanyl-tRNA. The CCA region is at the end of one arm, and the anticodon loop is at the end of the other. [Drawn from 1EHZ.pdb.]
Here's a nice “stick” representation of a tRNA, highlighting the anticodon loop at the bottom and the stem acceptor/CCA terminus up at the top. And you can actually even see the little adenine residue poking out there at the very end. Note the overall L-shape of the molecule.
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http://www.rcsb.org/pdb/education_discussion/molecule_of_the_month/images/two-trna-figure.gif
David Goodsell illustrations of different tRNAs
Created by Brett Barbaro
Here you can see two David Goodsell illustrations of different tRNAs, one for phenylalanine and one for aspartate, and I think you can appreciate that they are very similar, but do have some significant differences. I might point out the very center of the diagram on each side looks slightly different, and those are possibly recognition sites that proteins would be able to use to find them.
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Some Transfer RNA Molecules Recognize More Than One Codon Because of Wobble in Base-Pairing
The anticodon forms base pairs with the codon.
By convention, sequences are written in the 5’-to-3’ direction. Thus, the anticodon that pairs with AUG is written as CAU.
Some tRNA molecules can recognize more than one codon. The recognition of the third base in the codon by the anticodon is sometimes less discriminating, a phenomenon called wobble.
Generalizations of the codon–anticodon interactions are:
Codons that differ in either of the first two nucleotides must be recognized by different tRNA.
The first base of the anticodon determines the degree of wobble. If the first base is inosine, the anticodon can recognize three codons.
Created by Brett Barbaro
Now, the anticodon in the tRNA forms base pairs with the codon in the RNA. These are just the standard base pairs that we've always seen - U with A, and C with G, although occasionally there are some interesting variations. Now, these sequences are written in the 5' to 3' direction. So when we're talking about the codon, we will say AUG, for example, and the anticodon would be CAU - which might seem backwards, but just remember they’re always written 5' to 3'. So these are two complementary sequences.
The first two nucleotides in the codon are the most important ones. The third one actually is a little bit less discriminating and sometimes doesn't get as clearly recognized by the anticodon. This is called “wobble”. Now, remember, we have the anticodon, and the first base of the anticodon (which binds to the third base of the codon) will determine how much wobble there is. And the first base of the tRNA anticodon might be inosine, which means that it can actually recognize three different partners.
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Table 39.3 Allowed Pairings at the Third Base of the Codon According to the Wobble Hypothesis
Created by Brett Barbaro
So you can see here that if the first base of the anticodon is C or A, then it will only pair with its normal, natural partner. But a U in the anticodon could pair with G and the G in the anticodon could also pair with a U. And finally the inosine, which is labelled as an I, could pair with the U, C, or A. So you can kind of get a sense of what's going on here. It's a slightly loose fit.
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The Synthesis of Long Proteins Requires a Low Error Frequency
Error frequencies of 10−4 allow for the accurate synthesis of even large proteins at a very rapid rate.
Created by Brett Barbaro
Nevertheless, long proteins need to have a very low error frequency. So it's really important that they get the right amino acids in the right places. There's a balance that occurs between accuracy and speed. And the ideal point of balance there is ribosomes will allow about 1 in 10,000 amino acids to be inserted incorrectly.
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Table 39.4 Accuracy of Protein Synthesis
Created by Brett Barbaro
As you can see from this chart, 10^-4 (or 1 in 10,000) incorrect amino acids means that if you have a 100 amino acid protein, then it will be accurately translated about 99 percent of the time. If you make a 300 amino acid protein, then that would be accurate 97 percent of the time, and a 1000 amino acid protein would be perfectly accurate about 90 percent of the time.
Now, that might not seem like enough - you're investing a lot of energy into the making of these proteins. But remember, first of all, that a lot of these mutations that might occur in protein synthesis probably have no effect, or very little effect, or negligible effect. Changing a glycine into an alanine, a lot of the time, is not going to alter the function of the protein. But even if it did, the most likely result of that would be that your protein would be nonfunctional. Generally several copies of the protein are made from a single mRNA, so if you have one or two nonfunctional proteins, then you will usually have several other functional ones that are able to do the job that needs to be done.
Now, nature possibly could have come up with a system where there was only an error in every 100,000 amino acids, which would mean that you would have a lot more fidelity - but it would probably be slower. And this is where the tradeoff between speed and accuracy has finally landed. One error in 10,000 amino acids is accurate enough to rapidly produce functional protein at the scale that the body and cells need it.
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Section 39.2 Amino Acids Are Activated by Attachment to Transfer RNA
Learning objective 2: Identify the step in protein synthesis in which translation takes place.
In order to be incorporated into proteins, amino acids must be activated.
Amino acids are activated by formation of an ester linkage between the carboxyl group of the amino acid and either the 2’ or 3’ hydroxyl group of the terminal adenosine of the tRNA, forming an aminoacyl-tRNA or charged tRNA.
Created by Brett Barbaro
So let's talk a little bit about how the amino acids get attached to the tRNAs. That has to take place before any of this protein synthesis can occur. And the amino acids are attached to the 3' end of the tRNA molecule, to the 2' or 3' hydroxyl group on the ribose portion of the terminal adenosine. Those hydroxyl groups attack the carboxyl group of the amino acid, forming an ester linkage. This is a pretty weak linkage, and good for passing things around.
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Amino Acids Are First Activated by Adenylation
Aminoacyl-tRNA synthetases catalyze the activation of amino acids. The first step is the formation of aminoacyl adenylate, aka aminoacyl-AMP.
The aminoacyl group is then transferred to a specific tRNA recognized by the synthetase.
The aminoacyl-AMP never leaves the active site of the synthetase. The sum of the reactions, including hydrolysis of the pyrophosphate, is
Created by Brett Barbaro
So the addition of these amino acids to the tRNAs is catalyzed by specific synthetases. And, once again, there is a different synthetase protein for each one of these tRNAs. So you've got to have at least 20 of these large synthetases to actually just attach the amino acids to the tRNAs. All of these synthetases are different, but they have certain things in common. For example, the active sites of all of the synthetases contain a binding place for ATP, and when the proper amino acid gets into that active site it's first combined with ATP to create aminoacyl adenylate (or aminoacyl-AMP), as you can see it in the picture there on the right. Of course, this reaction is readily reversible - but remember the PPi, the two released phosphates, get rapidly degraded in the cell so that they cannot go back and recreate the original ATP molecule. So that helps to drive this reaction.
And then from this point it's relatively easy for the hydroxyl group to attack the carboxyl group on the amino acid and create an ester linkage, at which point the AMP can dissociate, and the activated amino acid and its tRNA are able to go on to the next stage of protein synthesis.
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Diagram of Aminoacyl-tRNA
Created by Brett Barbaro
Figure 39.3 Aminoacyl-tRNA. Amino acids are coupled to tRNAs through ester linkages to either the 2′- or 3′-hydroxyl group of the 3′-adenosine residue. A linkage to the 3′-hydroxyl group is shown.
Here's a figure showing an aminoacyl-tRNA with the amino acid attached to the 3' hydroxyl group of the CCA arm of the tRNA. It can also be attached to the 2' hydroxyl group, and that depends on which aminoacyl synthetase is involved.
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Five complexes of an aminoacyl-tRNA synthetase with tRNA
See https://pdb101.rcsb.org/motm/16 for more!
Created by Brett Barbaro
Figure: In this picture, five complexes of an aminoacyl-tRNA synthetase with tRNA are shown, aligned so that the tRNA molecules (shown in red) are in the same orientation. Notice that the enzymes approach the tRNA from different angles. The isoleucine (entry 1ffy), valine (entry 1gax) and glutamine (entry 1euq) enzymes cradle the tRNA, gripping the anticodon loop (at the bottom in each tRNA), and placing the amino-acid acceptor end of the tRNA in the active site (at the top right in each tRNA). These share a similar protein framework, known as "Type I," approaching the tRNA similarly and adding the amino acid to the last 2' hydroxyl group in the tRNA. The phenylalanine (entry 1eiy) and threonine (entry 1qf6) enzymes are part of a second class of enzymes, known as "Type II." They approach the tRNA from the other side, and add the amino acid to the other (3’) hydroxyl on the last tRNA base.
Here are five aminoacyl synthetases that are in complex with tRNA -and you can see the tRNA is in more or less the same position in all of these. The top three - isoleucine, valine, and glutamine - have a very similar framework, and attach the amino acid to the 2' hydroxyl group. Whereas the phenylalanine and threonine synthetases pictured here attach to the 3' hydroxyl group.
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Aminoacyl-tRNA Synthetases Have Highly Discriminating Amino Acid Activation Sites
Each aminoacyl-tRNA synthetase is specific for a particular amino acid.
Specificity is attained by various means in different enzymes.
Threonyl-tRNA synthetase contains a zinc ion at the active site that interacts with the hydroxyl group of threonine. Valine is similar in overall structure to threonine but lacks the hydroxyl group and thus is not joined to the tRNAThr.
Serine, although smaller than threonine, is occasionally linked to tRNAThr because of the presence of the hydroxyl group.
MAKE SURE YOU UNDERSTAND THIS! IT WILL BE ON THE TEST
Created by Brett Barbaro
So, as I mentioned, each aminoacyl-tRNA synthetase has a specific amino acid and specific tRNA that it matches with. So it's very important that these are matched properly. This is a critical step in the protein synthesis process.
So here's a pretty interesting example, I think, of how this specificity is achieved. You can see on the right the structures of threonine, valine, and serine - and if you’ll look at them you’ll notice that they are pretty similar in structure. Threonine has a carbon with an oxygen and a carbon attached to it in its side chain, whereas valine has a carbon and a carbon attached to it, and a serine only has an oxygen attached to it. So these similar structures need to be differentiated when attaching amino acids to their corresponding tRNAs. So how does the synthetase distinguish between threonine and valine? Well, there is a hydroxyl group on the threonine that is not present on the valine, and that hydroxyl group interacts with a zinc ion in the active site, so that only the threonine will fit that proper hole in the active site, and therefore only threonine will be attached to the chain. But remember, serine has that oxygen, too, and that oxygen can interact with the zinc ion. It's just missing a methyl group which doesn't have any interactions usually, so actually serine DOES get attached to the end of the tRNA for threonine occasionally.
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Diagram of the Active Site of Threonyl-tRNA Synthetase
MAKE SURE YOU UNDERSTAND THIS! IT WILL BE ON THE TEST
Created by Brett Barbaro
Figure 39.4 The active site of threonyl-tRNA synthetase. Notice that the site for binding the amino acid includes a zinc ion (green ball) that coordinates threonine through its amino and hydroxyl groups.
So you can see here in this diagram, the threonine is in the center, and the hydroxyl group on the threonine is in the very center of this diagram. And you can see there that it is interacting with an aspartate residue on the left and with a zinc ion on the right. These interactions, one might imagine, help to draw the active site into the proper position so that catalysis can occur. A valine would not interact with the zinc ion or the aspartate residue, and therefore would not result in having the proper formation there at the active site and catalysis would not occur. A serine, however, would have those interactions and so could get added to the tRNA. It might be interesting to just notice that the zinc ion is attached to the protein via some histidine residues and a cysteine residue. Those are common ways to attach metal ions into proteins.
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Proofreading by Aminoacyl-tRNA Synthetases Increases the Fidelity of Protein Synthesis
Threonyl-tRNA synthetase has an editing site in addition to an active site to remove a serine inappropriately joined to tRNAThr.
The CCA arm of tRNAThr can swing into the editing site where the serine is removed.
Because threonine is larger than serine, it cannot fit into the editing site.
The double sieve of an acylation site and an editing site increases the fidelity of many synthetases.
MAKE SURE YOU UNDERSTAND THIS! IT WILL BE ON THE TEST
Created by Brett Barbaro
Figure 39.5 The editing of aminoacyl-tRNA. The flexible CCA arm of an aminoacyl-tRNA can move the amino acid between the activation site and the editing site. If the amino acid fits well into the editing site, the amino acid is removed by hydrolysis.
So what are you going to do if you've attached an inappropriate serine to the tRNA for threonine? Well, as it turns out, the threonyl-tRNA synthetase has an editing site. After attaching an amino acid to the end of the chain, it is able to swing around - and if it can fit into this editing site then it will be removed. Well, serine fits into the editing site, but threonine has got an extra methyl group on it so it doesn't. So if you have an inappropriate serine on there then it will get cleaved off, but a threonine will stay on and continue with protein synthesis. This is an interesting and common mechanism for making sure that there is specificity. You might recall in DNA synthesis, if there is an incorrect nucleotide inserted into the DNA sequence, then that can swing out and be removed by an editing site on the polymerase. So it's very much the same method.
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Synthetases Recognize the Anticodon Loops and Acceptor Stems of Transfer RNA Molecules
Synthetases are the true translators of the genetic code in that they assign a particular amino acid to a specific tRNA.
Many aspects of the tRNA molecule, in addition to the anticodon, are used as recognition sites by the synthetases to achieve this specificity.
The precise recognition of tRNAs by aminoacyl-tRNA synthetases is as important for high-fidelity protein synthesis as is the accurate selection of amino acids, and this recognition is sometimes referred to as the “second genetic code.”
Created by Brett Barbaro
So how do synthetases recognize which is the correct tRNA to bind to them? Well, you might say it's the anticodon - which is a good point, and most of the synthetases do interact with the anticodon, but they actually also interact with several other points on the tRNA.
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Diagram of the Recognition Sites on tRNA
Many scientists gave their careers to bring you this figure...
Created by Brett Barbaro
Figure 39.6 Recognition sites on tRNA. Circles represent nucleotides, and the sizes of the circles are proportional to the frequency with which they are used as recognition sites by aminoacyl-tRNA synthetases. The numbers indicate the positions of the nucleotides in the base sequence, beginning from the 5 end of the tRNA molecule. [After M. Ibba and D. Söll, Annu. Rev. Biochem. 69:617–650, 1981, p. 636.]
This diagram shows where the important points of interaction are. Each nucleotide in the tRNA is represented by a circle. And the size of the circle represents how frequently the nucleotide at that position is used for recognition. The largest circles are down at the bottom near the anticodon loop. Interestingly, you can see that it's the second two positions of the anticodon loop, at positions 35 and 36, that are the most important - and this is reflecting the wobble of the protein synthesis. That first position in the anticodon is less important. But almost equally important are several residues up at the top near the CCA terminus. You see several large circles there, and those are important recognition sites for synthetases to recognize which of the tRNAs it's dealing with. In addition, sprinkled around the tRNA, there are some other large circles, at position 51, 13, 22, and 41 that are also commonly used to help recognize the tRNA. These are all usually on the outside of the tRNA where they can interact with other proteins.
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Section 39.3 A Ribosome Is a Ribonucleoprotein Particle Made of Two Subunits
The ribosome is the site of protein synthesis. In E. coli, the ribosome sediments at 70S and is composed of two subunits, a large 50S subunit and a smaller 30S subunit.
The 50S subunit is composed of 34 proteins and a 23S RNA as well as a 5S RNA.
The 30S subunit contains 21 proteins and a molecule of 16S RNA.
Created by Brett Barbaro
Now - the ribosome. This is the big one.
The ribosome is one of the biggest complexes in all cells. And all cells have ribosomes. They need to have ribosomes in order to make proteins. There are slight variations between the ribosomes in different organisms. But these are critical, and very complicated and interesting molecules - well, complexes. They are made out of several molecules.
We're going to talk about the E. coli ribosome here, possibly because it's a little bit simpler than the human ribosome. In an attempt to confuse you, they have once again used the sedimentary positions of these ribosomes in order to label them. The whole ribosome sediments at 70S. And it's got two parts, which sediment at 50S and 30S, which don't add up to 70S. But remember these are not molecular weights, these are just the positions that they find themselves in sedimentation in a centrifuge. The larger, 50S subunit has got 34 proteins and 2 rRNAs, there’s a 23S rRNA and a 5S rRNA. The smaller, 30S subunit has 21 proteins and 1 long 16S rRNA. I guess it’s not as long as the 23S rRNA, but you know, it’s not short.
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Diagram of the Ribosome at High Resolution
Created by Brett Barbaro
Figure 39.7 The ribosome at high resolution. Detailed models of the ribosome based on the results of X-ray crystallographic studies of the 70S ribosome and the 30S and 50S subunits. (Left) View of the part of the 50S subunit that interacts with the 30S subunit; (center) side view of the 70S ribosome; (right) view of the part of the 30S subunit that interacts with the 50S subunit. 23S RNA is shown in yellow, 5S RNA in orange, 16S RNA in green, proteins of the 50S subunit in red, and proteins of the 30S subunit in blue. Notice that the interface between the 50S and 30S subunits consists entirely of RNA. [Drawn from 1GIX.pdb and 1GIY.pdb.]
So you can see from these diagrams that the majority of the ribosome is actually RNA. That's where it gets its name from. Ribose is the component of RNA that is very prevalent in ribosome. It was probably the first component of the ribosome that was discovered, so they named it that. And, not surprisingly, I guess, most of the catalytic ability of ribosomes is due to the RNA. The proteins play important roles, but it’s the RNA that is the core of the ribosome.
You can see here in these images, these are based on crystal structures of - not the human ribosome, or the E. coli ribosome, but thermus thermophilus, which is the only ribosome that they've been able to successfully crystalize - once again, our knowledge being restricted by our experimental capabilities. It’s very hard to crystalize something this large - but if you're going to crystalize it, thermophilus would probably be a good one because it's probably very able to withstand high temperatures because it loves heat - "thermo” + "philus”.
Anyway we have David Goodsell representations on the top, and then we have sort of spaghetti representations there on the bottom. And in the spaghetti representations, the RNA is represented by the yellow and the proteins are represented by the red. On the right hand side, the RNA is represented by green and the proteins are represented by blue. Also the 5S rRNA on the left hand side is pink, near the top. On the top left diagram you can see a green site in the middle of the ribosome. That is the active site of the ribosome, where the attachment of the proteins takes place. And these two pieces fit together to form a single unit, and the interface between them is entirely RNA. So, once again, this is demonstrating how important RNA is for fundamental aspects of nature.
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http://pdb101.rcsb.org/motm/10
David Goodsell - small and large ribosomal subunits
Created by Brett Barbaro
Figure: Ribosomes are composed of two subunits: a large subunit, shown on the right, and a small subunit, shown on the left. Of course, the term "small" is used in a relative sense here: both the large and the small subunits are huge compared to a typical protein. Both subunits are composed of long strands of RNA, shown here in orange and yellow, dotted with protein chains, shown in blue. When synthesizing a new protein, the two subunits lock together with a messenger RNA trapped in the space between. The ribosome then walks down the messenger RNA three nucleotides at a time, building a new protein piece-by-piece.
Here's another David Goodsell illustration showing how these two parts fit together. And I would really encourage you to take a look at the Molecule of the Month webpage - I have included a link here at the bottom of the slide - because it's got some fascinating information about these molecules.
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Moving GIF https://en.wikipedia.org/wiki/Ribosome#/media/File:10_large_subunit.gif
Goodsell - Large ribosomal subunit
Created by Brett Barbaro
Figure: The large subunit is composed of two RNA strands: a long one colored orange and a shorter one colored yellow. Dozens of proteins bind on the surface of the ribosome. Many have long, snaky tails that extend into the body of the ribosome, gluing the RNA strands into their proper shape. Several of the proteins were not seen in this crystallographic structure, perhaps because they are too flexible. Approximate shapes for these proteins, which form two prominent stalks commonly used as landmarks in electron micrographs, are indicated here in light blue.
Here's another look at the large subunit - but the important thing here is the link at the bottom. That will take you to a neat animation of the subunit rotating in three dimensions and you'll be able to get a better sense of what its structure is.
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Moving GIF https://commons.wikimedia.org/wiki/File:10_small_subunit.gif
Goodsell - Small ribosomal subunit
Created by Brett Barbaro
Figure. The small subunit is in charge of information flow during protein synthesis. It initially finds a messenger RNA strand and after combining with a large subunit, ensures that each codon in the message is paired with the anticodon in the proper transfer RNA. The messenger RNA is thought to enter through a small hole (seen here on the left side of the molecule) and then extend up into the "decoding center" in the cleft between the "head" at top and the "body" at the bottom. The messenger RNA does not have to thread through this hole like a needle, however, because the hole is actually formed by a loop of the ribosomal RNA, which can open like a latch to admit the messenger.
Similarly, please follow the link at the bottom of this page to look at the three dimensional structure of the small ribosomal subunit. But I will point out, actually - in this structure, you can see a small hole on the left side of the diagram here. It's about halfway up. And that's where the mRNA goes. It comes through that hole and then travels through the cleft and up through the - you can see the sort of cleft on the upper right hand side. That is where the mRNA is decoded.
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Ribosomal RNAs Play a Central Role in Protein Synthesis
Two-thirds of the mass of ribosomes is RNA, which is critical for the structure and function of the ribosome.
The ribosomal RNAs fold into complex structures with many short duplex regions.
Ribosomal RNA is the actual catalyst for protein synthesis, with the ribosomal proteins making only a minor contribution.
Created by Brett Barbaro
So two-thirds of the mass of ribosomes is RNA. And it's decorated with proteins that do play important roles, but probably, a long time ago, the RNA was the only thing that was involved in this type of synthesis. It's kind of a who came first, the chicken or the egg problem. You know, how are you going to get proteins to make ribosomes if you don't have ribosomes to make proteins? Well, it comes down to the RNA. The RNA is the critical element here.
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Diagram of the Ribosomal RNA Folding Pattern
Created by Brett Barbaro
Figure 39.8 Ribosomal RNA folding pattern. (A) The secondary structure of 16S ribosomal RNA deduced from sequence comparison and the results of chemical studies. (B) The tertiary structure of 16S RNA determined by X-ray crystallography. [(A) Courtesy of Dr. Bryn Weiser and Dr. Harry Noller; (B) drawn from 1FJG.pdb.]
Here's a two dimensional diagram of the 16S ribosomal RNA - this is the intermediate-sized one. But you can see it's quite large and has a great deal of complicated interactions. And this is not even touching on the three dimensional tertiary structure. This just shows where the stems and loops are. You can look at the tertiary structure in the lower right hand corner. And the colors there correspond to the colors in the two dimensional diagram.
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Messenger RNA Is Translated in the 5’-to-3’ Direction
Because transcription and translation both occur in the 5’-to-3’ direction, bacterial protein synthesis begins before transcription is complete.
Several ribosomes can translate an mRNA molecule at the same time, forming polyribosomes or polysomes.
Created by Brett Barbaro
As I mentioned before, transcription and translation all occur in the 5' to 3' direction. Which means that in bacteria, where there's no nucleus, the ribosomes are free to start translating the mRNA as soon as it's started to be transcribed. And even in eukaryotic organisms you can get several ribosomes that are translating an mRNA at the same time.
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Image of Polysomes
Created by Brett Barbaro
Figure 39.9 Polysomes. Transcription of a segment of DNA from E. coli generates mRNA molecules that are immediately translated by multiple ribosomes. [From O. L. Miller, Jr., B. A. Hamkalo, and C. A. Thomas, Jr. Science 169:392–395, 1970.]
So here's an example of ribosomes on mRNA. This would be in bacteria, because you can see the DNA is being transcribed and translated directly. You can see the upper left hand side is where the gene would start, and as it continues the mRNA gets longer and longer, and ribosomes attach to it, and start translating it to protein immediately. If we were able to see it on this electron micrograph, we would also see RNA polymerase at each one of these points where the RNA is being created.
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