Transcription (as described in previous section) as a means of information transfer is simple to understand. DNA and RNA are chemically and structurally similar, and DNA can act as a direct template for the synthesis of RNA through complementary base-pairing. As the term transcription signifies, it is as if a message written out by hand were being converted, say into a typewritten text. The language itself and the form of the message do not change, and the symbols used are closely related. [p. 244]
In contrast, the conversion of the information contained in RNA into an amino acid requires translation from one language to another, using different symbols. Like taking the letters ‘H’, ‘A’ and ‘T’ and converting them into an actual hat.
Using 3-letter words (called a codon), the four letters of the genetic code can be arranged in 64 unique combinations. Below is a table [figure 7-27] that shows the specific mapping of each codon into a specific amino acid.
The mRNA molecule consists of a string of nucleotides, U, A, G and C. How this string gets interpreted depends on where the translation begins. For any particular string of nucleotides, three different reading frames are possible, each one of them representing a different sequence of amino acids. See the example below [figure 7-28]:
The site at which protein synthesis begins on an mRNA is crucial, because it sets the reading frame for the entire message. An error of one nucleotide either way at this stage will cause every subsequent codon in the mRNA to be misread, resulting in a nonfunctional protein with a garbled sequence of amino acids. [p. 253]
There are a couple of interesting implications to this. For one thing, the decision has to be made which reading frame will be used. A special signaling protein will be applied, providing a local, tactical explanation, but one that does not provide how the location is determined. Also, it should be noted that a point-mutation in the DNA for this gene will necessarily cause the wrong nucleotide to be included in the mRNA. This will result in the wrong amino acids being translated, and therefore the wrong protein assembled. The wrong protein will likely be ineffectual, leading to a detrimental effect on the cell, and perhaps the entire organism. Several genetic diseases are related to this kind of mutation. Alternatively, the likelihood that a positive effect will take place within the cell, one where an altered protein will function better than the one originally coded seems highly unlikely.
Another variable to consider is the fact that a particular gene that is transcribed into mRNA can be spliced in multiple ways in order to produce different proteins:
This represents another example of decisions made, designs selected, and coordination necessary to determine which proteins are produced.
Now for one of the most interesting and amazing aspects of the entire process of protein synthesis. The codons (three letter group of nucleotides) do not chemically or physically relate to amino acids. Several complex steps are required to translate the one to the other. An adapter is required to link the two.
The adapter is called a transfer RNA (tRNA), a molecule that consists of about 80 nucleotides. The tRNA will connect an amino acid on one end and a binding site for the codon, called an anti-codon, to the other. The anti-codon will be a mirror image of the codon being translated.
In order to create the tRNA, it must be ‘charged’. This is done by an aminoacyl-tRNA synthetase, one that covalently bonds the proper amino acid to the tRNA with the appropriate anticodon. [figure 7-33 below] There are exactly 20 of these synthetases, one for each amino acid.
If we could actually see the charging action, it might look something like this: [figure 7-32]
Given some of the flexibility in the 3rd codon to ‘wobble’, all 61 codons can be matched by as few as 31 tRNAs. Humans create about 500 different tRNAs with 48 different anticodons. [p. 248]
At this point it is worth noting that the machine-like synthetase is created with this same process we are reviewing. In other words, they are coded in DNA, transcripted into mRNA, multiple tRNAs charged with a synthetase, and translated into the proteins that make up the 20 different synthetases. This reflects the conundrum we touched upon in chapter 4:
The most difficult problem in accounting for the origin of life is that in known living systems, only nucleic acids replicate, but their replication requires the action of proteins that are encoded by the nucleic acids.
Douglas Futuyma, Evolution
In other words, the same machine (RNA polymerase, for example) is required to make the same machine (another RNA polymerase).
In addition, these are examples of molecules just floating around the cytosol ready to meet. After the tRNAs are transcripted in the nucleus and spit out into the cytosol, they bounce around the interior space of the cell until they come into perfect 3 dimensional contact with the correct synthetase. And it can’t be just any synthetase: it must be the exact one (among 20) that matches that particular tRNA.
Moving on, the synthetases are thus equal in importance to the tRNAs in the decoding process, because it is the combined action of the synthetases and tRNAs that allow each codon in the mRNA molecule to be correctly matched to its amino acid. [p. 249]
The tRNAs themselves are quite complex. How they are coded, folded, and charged with an appropriate amino acid can be seen below. [figure 7-31]
At this point, we have numerous charged tRNAs roaming around the cytosol. The mRNA has emerged from the nucleus in search of a ribosome, the molecular factory that will perform the translation and build the protein.
Once all these elements come together...
...the mRNA is then pulled through the ribosome like a long piece of tape. As the mRNA inches forward in a 5’—to – 3’ direction, the ribosome translates the nucleotide sequence into an amino acid sequence, one codon at a time, using the tRNAs as adaptors. Each amino acid is thereby added in the correct sequence to the end of the growing polypeptide chain [protein]. [p. 251]
An example of the various steps is shown below. [figure 7-38]
The ribosome itself is constructed of proteins, and must also be created using the process under review.
How do all these different elements – mRNA, multiple tRNAs, and ribosome – come together and perform this translation? Even if any two of them come into contact, the contact must align perfectly in order for them to function properly. In particular, how does the ribosome ‘recruit’ the proper tRNA in order to ‘place’ it in line to add to the growing polypeptide? It must read the mRNA and then somehow maneuver the proper tRNA into the ‘A’ slot. How is this done? The only movement we have been allowed for small molecules is ‘random walking’ in the cytosol. Does the process simply wait until the exact proper molecule (among the thousands floating around) happens to perform a 3-point landing and bind properly to the assembly line? If not that, then how is this arranged?
At this point, it may help to revisit the question of scale. A eukaryotic cell is much larger than its nucleus, on average 10 – 100 micro meters. For the sake of argument, let’s assume one that is 50 micro meters (50 * 10-6). Most of the small molecules are much smaller than the mRNA we considered previously, which measured 1-2 nano meters in size. Let’s make all of them (tRNAs, ribosome, synthetases, amino acids, etc.) at 1 nano meter (1 * 10-9).
Changing the scale to something we can grasp, if the small molecules are 1 inch long, the cell would be 50,000 inches in diameter, or about 4000 feet. Assuming for the sake of argument that the cells is spherical, the volume within the cell would be about 265 billion cubic feet (Volume=4/3 * π * r3).
That means that all of these elements – mRNA, tRNAs, and ribosome, each of them measuring in mere inches, need to come together somehow within this vast three dimensional space in order to assemble the required proteins.
Once again, it’s not adequate that they simply randomly bump into each other. They must be manipulated in a specific manner so that the appropriate surfaces are able to bond together. In all of these textbook descriptions, it is taken for granted that these molecules can readily find each other and combine in complex configurations and reactions. They obviously do. But how? Can we be satisfied that the known physical and chemical processes of the universe suffice? This is the principle question being posed in this site.
As we reviewed above, the ribosome extrudes the new polypeptide (protein) one amino acid at a time. These proteins range in size from 30 amino acids to more than 10,000, most of them ranging between 50 and 2000 amino acids long. [p. 124]