mRNA to Protein
Aminoacyl tRNA synthetases
Mechanism of translation
Number of human diseases related to defects in translation process.
• The genetic code “spells” out the amino acid sequence in 3 “letter” “words” called codons
• Why is each codon 3 bases?
• We know there are 20 a.a. If codons were only one base, then we could only code 4^1 a.a. if 2
bases, then we could only code for 4^2=16 a.a so that’s not enough. BUT when code is 3 bases, we
can code for 4^3= 64 a.a which is enough to include the 20 a.a.
• So 3 bases is the minimum needed to code for all 20 a.a, which is why codons are 3 bases.
• QUESTION: How many amino acids must be coded for in the genetic code- how many amino acids
are used for protein synthesis in the cell?
• QUESTION: given that any nucleotide can be A, U, G, C how many different 3 base codons are
• 3 letter code: 64 (4x4x4)
• Often, we use analogies to language with the genetic code.
Key features of the genetic code
The code is non overlapping, so the codons are consecutive. An overlapping code would look like this,
which does not happen
Why is non overlapping better?
If the code were overlapping, the codon for the preceding a.a would in part determine the following
codon. That would impose restrictions then on the sequence of a.a in proteins, because what was in front
would determine what was behind, and thus the diversity and function of proteins would be limited. The
restrictions would be greater if it was a 2 base overlap.
By having it non-overlapping we can put each of the a.a at each of the positions of the proteins and that
gives more diversity possible for proteins. The code has evolved once, life evolved from one common ancestor- every organism is using the same
Second feature: it is non overlapping. Overlap would allow more coding in the genome, BUT it would
place significant restrictions on what amino acid could follow each other. You couldn’t get all 20 residues
at one position, you couldn’t put and codon at any place.
There are no gaps in the code shown here. what’s evolved is this non gap codes.
So why did it evolve like this with no gaps?
If there was a gap between every codon, that would take up extra space and would sever no function. By
having no gaps we minimize the size of the genome.
There is not a gap where you would miss a 3 base codon in the middle
Redundancy - some codons specify the same amino acid
4 x 4 x 4 = 64 words for 20 amino acids
Redundancy often occurs at the third position of the codon: wobble position
20 amino acids, 64 codons, some can code for the same amino acids.
Looking at proline, there are 4 codons that code for proline. They are the same at the front 2 positions,
the 3 position of codon is the one that shows variability. There are a few cases where 2 positions vary, like Arganine.
Wobble is usually at third position but there’s variability sometimes at other positions.
There are 3 stop codons. Generally AUG is the start but sometimes isoluecine can be the start too.
The start codon AUG codes for a special met.
In general amino acids less frequently found in proteins have fewer codons.
Generally a.a that are found more commonly in proteins have more codons and those found less in
proteins have less codons.
Met-AUG and Trp-UGG are not found much in proteins so they have only one codon coding for
Where as something like Ser and Arg- it has as much as 6 codons.
You can tell how often a residue is used by how many codons there are. You can guess which ones
are found more commonly in proteins.
Functionally related amino acids have similar codons.
So why is this advantageous/ why is it been selected for?
It has to do with mutations.
Evolution has likely selected for similarities in the code between a.a so that if a missense mutation
occurs in a gene, the a.a chain that’s synthesized will likely be conserved because of these
If similar a.a have similar codons, then if the codon changes by one base, we can still put a similar
a.a and the proteins will still have similar function. So these help maintain function of proteins
should a mutation happen.
Aspartic acid and glutamic are both charged, they both start with codons GA- same at the first 2
positions. Gln is similar because even though it begins with C, it its otherwise the same.
- All 3 are functionally related and they have very similar codons.
Q: Functionally related amino acids have similar codons. Why is this adventageous?
d) Increases the chance of a functional protein in the case of a single base mutation.
- There is a chance that the protein will still stay functional in single base mutation
Every organisms has the genetic code, and the code has evolved once, emphasizing the unity of life issue.
Types of Mutations There are 3 types of mutations.
First is called missense mutation = mutation that result in a single a.a base change in the protein.
This may have consequences or may not on the protein because it’s a small change.
There was a spontaneous mutation that happened where the C was converted to a G. This would
convert that alanine to a glycine. Alanine is very similar to glycine so it isnt a drastic change.
In this case it’s the insertion of a base.
In this example an A was inserted into the sequence; the first 2 codons before the insertion are
fine but after that because of the insertion the a.a sequence changed dramatically.
The insertion puts the sequence out of frame resulting in a huge change in the a.a sequence. This
type of mutation is very deleterious. Mutations that cause insertion/deletion of 1 or 2 bases will
cause a sever change in coding sequence and in protein unless this change happens right at the
end of the sequence coding for the protein.
However, if we add/delete 3 bases it may or may not have a huge consequences because the frame
will not change but only an a.a is added or deleted.
(insertion or deletion of bases)
Q: what does a frameshift mutation do to a protein
b) Changes the encoded protein completely from the point of the mutation.
Frameshift results in a dramatic change in a protein- unless you add or delete 3 (may still be deleterious,
but maybe not) Third type is called nonsense.
In this case a mutation base change happened where a codon was changed so now instead of coding for
a.a it’s a stop codon.
If this happens anywhere but near the end of the protein, it will have a dramatic effect on function of
Where you insert a stop codon. It stops the protein from that point. If it happens anywhere other then
close to the end it will have severe consequences.
• Serve as the vehicle that brings the amino acid to the growing polypeptide chain
• Similar structure for all tRNAs
• The molecule that moves a.a that are going to be inserted into the protein to make polypeptide
In 2-D they have a clover leaf type structure.
Roughly they are 80 bases in long, they have nonconventional bases that are post-
Stem-loop structure is created by internal base pairing of the RNA. (RNA-RNA base pairing). All tRNAs have a very similar structure- not identical sequence.
Feature 2 is that they have non conventional bases , these bases are not put in transcriptionaly, they are
modified post transcription.
tRNA’s have this very unique structure in 2D caused by the internal base pairing of tRNAs. There are 4
stems cause by this base pairing. These are due to the folding up of the RNA.
For all of them there are 2 key single stranded regions.
• The anti-codon; shown is the anti-codon loop with the anti-codon sequence which base pairs with
the codon in mRNA and determines base pair specifity. (Normal base pair rules apply, keep in
mind the 3’ and 5’ end and that base pairing is still anti-parallel.) Key in codon recognition. Base
pairs with the codon. Normal base pairing rules apply.
• The 3’ acceptor region (blue circle); all tRNAs have this same CCA sequence at this 3’ end region.
This CAA sequence is also added post-transcriptionally. It’s this sequence that attaches to the a.a
through a high energy ester linkage. All the tRNAs ending with CCA are added afterwords.
Coupled in a high energy ester linkage to a specific amino acid The real 3-D structure looks more like an L (picture on right) than a clover leaf, because of folding.
RNAs are similar to proteins in that they have complex 3-D structures. DNA on the other hand tend to be
a stiff molecule.
Molecular Basis for Wobble
1. Some amino acids have more than one tRNA- this will obviously lead to differences in the codons.
2. Accurate base pairing for some of the tRNAs only requires matching at the first two positions of
Most organisms only have 45 different tRNAs, but we know there are 61 aa coding codons- so how does
this add up? Some tRNA species must pair with more than 1 codon.
Base pairing between the anticodon of some tRNAs and the codon, only requires matching at 2 positions.
Basepairing interactions for the two Phe codons, UUC and UUU, with the Phe-tRNA
Aminoacyl tRNA synthetases Enzymes that couple the 3’ end of specific tRNAs to specific amino acids.
One for each amino acid (twenty in all).
Another crucial molecule in translation is aminoacyl tRNA-synthetase. These enzyme couple the 3’ end of
specific tRNAs to a specific amino acid.
There are 20 of these enzymes, one for each of the a.a.
Specifity here is crucial:
These are one of the few enzymes that actually have proofreading activity, because everything has to be
correct or the protein made won’t be correct.
The aminoacyl tRNA synthetases have recognition sites for their specific tRNAs, and they are also specific
for a.a. They can recognize both tRNAs and a.a, so they have 2 binding sites.
They use the energy of ATP to couple the a.a to the 3’ end of tRNA in a high energy ester linkage. This
energy will be used later on in translation. (charged amino acid)
These can provide information on the level of a.a in the cell.
Provide specifity by coupling an amino acid with its correct tRNA- proofreading function.
The ribosome reads the tRNAs, it doesn’t read the amino acid. Because it is so crucial, the enzymes have a
It has to recoginize the amino acid and it has to recognize the tRNA.
The molecular assembly that catalyzes protein synthesis.
Another key molecule. An extremely complex molecule. This is the 3-D structure.
The enzyme that does peptide bond synthesis. Its structure is known entirely It can be broken into a large subunit and a small subunit. RNA plays a crucial role in ribosome, it has both
a structural and catalytic roles.
Together the 2 subunits form a molecule with a mass of 4.2 mill