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10.6.2. Mechanism of translation of RNA to proteins

The mechanism of translation of mRNA to proteins

The translation process consists of transforming the information provided by the nucleotide sequence of the mRNA into an amino acid sequence.

The translation is similar in prokaryotes and eukaryotes, but there is some difference. For example, the mRNA  of prokaryotes  does not need maturation, so as it is synthesized, it is read by ribosomes to translate its information into amino acids of a protein.

In contrast, in eukaryotic cells, the primary transcribed mRNA is synthesized in the nucleus and has to undergo a maturation process before becoming functional RNA that traverses the pores of the nuclear membrane into the cytoplasm. Then, in the rough endoplasmic reticulum or in the cytosol, ribosomes will translate their information into proteins.

Before starting to discuss the translation mechanism, it would be convenient for you to review the structure of the ribosome and the transfer RNA.

The following stages are distinguished in the biosynthesis of proteins:

  1. Activation of amino acids or formation of the amino acid-transfer RNA complex.
  2. Translation initiation.
  3. Elongation or elongation of the polypeptide chain.
  4. Termination.
  5. Association of several polypeptide chains and, sometimes, prosthetic groups, to constitute proteins.

Previous phase: activation of amino acids or formation of the amino acid-transfer RNA complex

Before starting protein synthesis, it is necessary for the amino acid to be activated, binding to the CCA triplet of tRNA. The aminoacyl-tRNA synthetases enzymes are specific for each amino acid, and are responsible for making this union, but the energy provided by the hydrolysis of ATP is necessary. There are 20 aminoacyl-tRNA-synthetase, one for each amino acid. These enzymes are very specific, as they have to bind each amino acid to the corresponding tRNA.

This preliminary phase takes place in the  cytoplasm and not in the ribosomes.

The amino acid joins at its carboxyl end (-COOH) to the 3' end of the tRNA (specifically, to the hydroxyl group (-OH) of the 3' carbon of the last nucleotide , which always carries adenine), and is renamed aminoacyl-tRNA.

Amino acid + ATP + tRNA ↔ aminoacyl-tRNA + AMP + PPi

As you may recall, tRNA molecules have four arms: D, T, amino acid acceptor, and anticodon.

The 3' and 5' ends of the chain are located on the amino acid acceptor arn:

  • At the 3' end, the CCA triplet always appears, to which the amino acid binds.
  • The 5' end always ends with a guanine nucleotide.

The anticodon arm  contains a specific nitrogenous base triplet for each type of tRNA. It has the function of binding to the corresponding complementary codon of the mRNA.

The tRNA molecules are the intermediaries between the nucleotide sequence of the mRNA and the amino acid sequence, since, in addition to providing the amino acid attached to their 3 'end, they are responsible for recognizing the RNA codon complementary to its anticodon.

When the aminoacyl-tRNAs have already been formed , protein synthesis occurs. The process is carried out in three stages:

First stage of translation: initiation

In prokaryotes

In prokaryotes, mRNA does not require maturation to be functional. You can even start translating before you finish synthesizing.

The mRNA binds, at its 5' end, to the minor subunit of ribosomes thanks to an initial sequence called the leader region, which is not translated, in which there are about 10 nucleotides complementary to the ribosomal RNA. The mRNA moves until it reaches the AUG codon, which codes for the amino acid methionine and is the triplet that acts as the initiation signal. The complex formed by aminoacyl-tRNA is attached to them. The union is made between the codon of the mRNA and the anticodon of the tRNA that carries the amino acid. Finally, the major subunit joins the minor subunit, completing theribosome .

As we can see, the first triplet that is translated is the AUG initiation codon and, therefore, the anticodon of the first tRNA has to be UAC, its complement. And methionine (in prokaryotes, formyl-methionine ) will always be the first amino acid in the peptide chain, although it is usually eliminated at the end of the translation.

The minor subunit of the ribosome, together with the mRNA and the first aminoacyl-tRNA form the initiation complex, to which the major subunit of the ribosome will later bind.

At the end of this stage, the major ribosome subunit attaches to the initiation complex, forming the complete ribosome. This ribosomal complex or active complex has two binding sites:

  • The peptidyl site or P site, which occupies the first aminoacyl-tRNA , the tRNA-methionine.
  • The aminoacyl site or A site, which is free and ready to receive the second tRNA with another amino acid.

All of these processes require GTP spending.

600px-Prokaryotic_Translation_Initiation.png (Imagen PNG, 600 × 600 píxeles) - Escalado (0 %). (s. f.). Recuperado a partir de https://upload.wikimedia.org/wikipedia/commons/thumb/9/91/Prokaryotic_Translation_Initiation.png/600px-Prokaryotic_Translation_Initiation.png 

In eukaryotic cells

In eukaryotic cells, mRNA is synthesized in the nucleus and has to undergo a maturation process before passing into the cytoplasm. At its 5' end it bears a cap made of a methyl guanosine triphosphate, which allows it to be recognized by ribosomes, and then the so-called leader region, which is not translated. After the initiation signal, the AUG triplet is translated by the amino acid methionine, which is frequently removed at the end of the process.

Second stage of translation: elongation

The elongation is the addition of amino acids to the end carboxyl chain. It begins when another aminoacyl-tRNA, with anticodon complementary to the codon of the mRNA that follows the initiation codon, AUG, occupies the A (aminoacyl) site of the ribosome that was free.

The carboxyl group of the first amino acid is linked by a peptide bond with the amino group of the second amino acid, catalyzed by the enzyme peptidyl-transferase .

The P site (peptidyl) will then be occupied by a tRNA without amino acid, since it will have joined to the one that carried the tRNA that now occupies the A site. Then the ribosomal translocation takes place, the ribosome moving three nucleotides in the 5' direction → 3', releasing the tRNA that previously had methionine and that occupied the P site. The tRNA with the newly formed dipeptide that occupied the A site will now occupy the P site, leaving the A site empty. This A site will be occupied again by another aminoacyl-tRNA with anticodoncomplementary to the codon to be translated, and so on. For all these processes, energy is needed, which is obtained from the GTP .

Thus the peptide chain is formed, joining the successive amino acids that are reaching the ribosome transported by the corresponding tRNAs .

Reviewing this phase, we can divide it into three stages:

  • Union of aminoacyl-tRNA to the A site. The anticodon of the tRNA is the one complementary to the codon of the mRNA that is in the aminoacyl site. The energy provided by the GTP is necessary to make this union.
  • Formation of the peptide bond. The enzyme peptidyltransferase, in the largest subunit of the ribosome, is responsible for joining the two amino acids that contain the two aminoacyl-tRNA (the one at the P site and the one at the A site).

When the first amino acid (formylmethionine) binds to the second, it is shed from its tRNA, which is released from the ribosome. Only the second tRNA will remain at site A, bound to a dipeptide.

  • Translocation of the dipeptide to the P site. The ribosome travels on the mRNA in a 5' → 3' direction. The codon that occupied site A, with the tRNA attached to it and bound to the dipeptide, will now occupy site P. When site A is free, it will be occupied by the third codon of mRNA to which another aminoacyl-tRNA will bind .

The new amino acid will then be attached to the dipeptide with a peptide bond , and the ribosome translocation will take place again.

This stage can be outlined as follows:

By OpenStax [CC BY 4.0], via Wikimedia Commons

Third stage of translation: completion

The elongation continues until the ribosome reaches the stop codons (UAA, UAG and UGA), which is the signal that indicates that translation has finished. There is no tRNA that has an anticodon complementary to these stop codons, so the A site will not be occupied by any aminoacyl-tRNA and will terminate the peptide chain.

Instead, protein releasing factor (FR) binds to the stop codon , prevents another aminoacyl-tRNA from binding, and causes peptidyltransferase to bind the latter –COOH to water, releasing:

  • The peptide chain.
  • The two ribosome subunits separate.
  • The mRNA, which can be reused or removed after reading.

The power provided by the GTP is also required.

The speed of protein synthesis is very high, since they can bind up to 1,400 amino acids per minute.

Normally, the mRNA chains are translated by more than one ribosome  at a time, and form polyribosomes or polysomes, which allows the translation to be much more efficient and fast.

In prokaryotes, as there is no nuclear membrane, transcription and translation occur simultaneously. The mRNA begins to translate before it is fully transcribed.

Association of several polypeptide chains to make proteins

The newly synthesized peptide chain is adopting the secondary structure and tertiary as will synthesising through links hydrogen bonding and disulfide bonds.

There are enzymatic proteins that are active after translation is complete, although others need to remove some amino acids, such as the amino acid that started translation methionine. Others will bind to ions or coenzymes to be functional.

As we saw in the subject of proteins, these can be made up of a single polypeptide chain or of several, the same or different, depending on whether they come from the same translated gene or from another.

 

Fundamental ideas about the translation mechanism

The following stages are distinguished in the biosynthesis of proteins:

  • Activation of amino acids or formation of  the amino acid-transfer RNA complex.
    • The enzymes aminoacyl-tRNA synthetases  are specific for each amino acid, and are responsible for the amino acid to be activated, binding to the CCA triplet of tRNA. This requires the energy provided by the hydrolysis of  ATP.
    • This preliminary phase takes place in the  cytoplasm.
  • Translation initiation.
    • The mRNA binds, at its 5` end, to the minor subunit of  ribosomes  thanks to an initial sequence called the leader region.
    • The mRNA moves until it reaches the initiation codon: AUG.
    • The major subunit of the ribosome binds.
    • Parts of the ribosome:
      • Peptidyl site or P site.
      • Aminoacyl site or A site.
  • Elongation  or elongation  of the polypeptide chain.
    • An aminoacyl-tRNA, with  anticodon  complementary to the  codon  of the  mRNA  that follows the start codon, AUG, occupies the A (aminoacyl) site  of the  ribosome  that was free.
    • A peptide bond occurs.
    • The formed peptide passes to the P site.
  • Termination.
    • Termination codons: UAA, UAG and UGA.
    • Polyribosomes or polysomes: mRNA chains are translated by more than one ribosome at a time.
  • Association of several polypeptide chains and, sometimes, prosthetic groups, to constitute proteins.