Translation: tRNA, Ribosomes, and the Process

Transfer RNA (tRNA)

tRNAs are adapter molecules that ferry amino acids to the site of translation (ribosome).
Amino acids are linked to tRNA molecules in a specific manner.
tRNA then base pairs with mRNA, ensuring accuracy via codon-anticodon pairing.
Once the correct match is made, the amino acid is dropped off and added to the growing polypeptide chain.
Free tRNAs can then cycle back to pick up another amino acid of the same type, aided by an enzyme.

tRNA translates mRNA into a polypeptide.
Each tRNA enables the translation of a specific codon into a specific amino acid.
tRNAs serve as adapters because they can read the language of nucleotides and deliver the corresponding amino acid.

Each tRNA carries a specific amino acid on one end.
Each tRNA has an anticodon, a triplet sequence that binds to a complementary codon on the mRNA.
tRNA is a single-stranded molecule, about 80 nucleotides long, that folds into a distinctive shape.
It contains regions of hydrogen bonding within the chain, giving it a cloverleaf shape when flattened or an L-shape in three dimensions.
The anticodon loop is at one end, and the three prime end attaches to the amino acid.
Intramolecular bonds within the tRNA structure contribute to its stability.

Ensuring accuracy in translation is crucial to avoid incorrect amino acid insertion into the polypeptide chain.
Step 1: Correct match between tRNA and its amino acid:
- This is facilitated by aminoacyl tRNA synthetase enzymes, which read the amino acid and tRNA to ensure the correct pairing.
- tRNAs bound to their amino acids are called "charged" tRNAs.
Step 2: tRNA anticodon finds the appropriate codon on mRNA:
- This ensures that a codon always codes for the same amino acid.

There is some flexible pairing (wobble) at the third base of the codon.
The first and second positions of the anticodon have very strict binding requirements, but the third position can exhibit some flexibility.

The anticodon UCU can bind to both AGA and AGG codons.
Both AGA and AGG code for arginine, so the tRNA drops off arginine in both cases.
This explains why two different codons can code for the same amino acid, often differing in the third position.

Wobble explains why multiple codons can code for the same amino acid, often differing only in the third nucleotide position.
Example: the codons GCU, GCC, GCA, and GCG all code for alanine but differ in the third position.

Tyrosyl tRNA synthetase links tyrosine to tRNAs with anticodons that match tyrosine codons.
If the anticodon is AUA, the corresponding codon would be UAU.
UAU is indeed a codon for tyrosine.

The enzyme uses ATP to form a covalent bond between the amino acid and tRNA.
The enzyme reads both the amino acid and the anticodon of the tRNA to ensure specificity.
The charged tRNA is then released.
tRNAs can undergo multiple rounds of charging and amino acid delivery.

Ribosomes are the site of translation.
They are composed of many proteins and ribosomal RNA (rRNA) molecules.
mRNA is translated, while tRNA and rRNA function as nucleic acids and are not translated.

Ribosomes consist of two subunits: a large subunit and a small subunit.
Each subunit is made of proteins and rRNA.
Eukaryotic and bacterial ribosomes differ in structure, allowing some antibiotics to target bacterial ribosomes without affecting eukaryotic ribosomes.

Translation involves three main steps:
- Initiation
- Elongation (reading mRNA and adding amino acids to the growing polypeptide)
- Termination (release of the polypeptide)
Termination occurs when a stop codon is encountered; no tRNA recognizes stop codons.
Proteins and energy are required for the translation process.

The small and large ribosomal subunits come together when an mRNA binds.
The mRNA initially binds to the small subunit, followed by an initiator tRNA, and then the large subunit joins.
There are three tRNA binding sites within a ribosome: the A site, the P site, and the E site.

A Site (Aminoacyl-tRNA binding site): Binds to the tRNA carrying the next amino acid to be added to the chain.
P Site (Peptidyl-tRNA binding site): Binds to the tRNA holding the growing polypeptide chain.
E Site (Exit site): Where the tRNA that has released its amino acid exits the ribosome.

tRNAs, except for the initiator tRNA, enter through the A site.
They then move to the P site, where the polypeptide chain is transferred to the tRNA in this site.
Finally, the tRNA moves to the E site before exiting the ribosome.
mRNA is threaded through the ribosome, codon by codon.

Translation proceeds in the five prime to three prime direction along the mRNA.
The ribosome moves processively down the mRNA towards the three prime end.
The region of mRNA that has already been translated is on the five prime side of the ribosome.

The next codon to be read is the one currently in the A site.
The growing polypeptide chain is transferred from the tRNA in the P site to the amino acid on the tRNA in the A site.
The tRNA that was in the P site then moves to the E site and exits.
The mRNA is threaded through so that the next codon slides into the A site.
The amino end (N-terminus) of the polypeptide is synthesized first, followed by the carboxyl end (C-terminus).

The start codon is AUG, which codes for methionine.
The small ribosomal subunit binds to the mRNA and an initiator tRNA.
The complex then scans for the first start codon.
The large ribosomal subunit then joins, along with initiation factors, to form the complete ribosome.