Gene Expression and Translation

From RNA to Protein: Translation

Translation is the process of making protein from RNA.
It is the second phase of gene expression.
Messenger RNA (mRNA) information is converted into a protein sequence.
Proteins give cells their particular function or phenotype.
The function of cells at a cellular level dictates how the whole organism functions.

The genetic code encodes information for protein synthesis, fundamentally residing in the DNA sequence.
The DNA sequence is split into three nucleotide chunks called codons.
One codon encodes for one amino acid in the protein.
There are four bases, implying 4^3 = 64 possible different sequences of DNA.

One start codon: AUG encodes methionine.
Three termination codons: these signal the end of translation.
60 codons for 20 amino acids.
The genetic code is redundant: most amino acids have more than one codon that can encode them.

The genetic code is almost universal for most forms of life, although there are some variations in codon usage.
Most amino acids have four codon options, some have a couple, and the start codon has only one.
Having more options allows for mutations in the DNA sequence that don't impact the amino acid encoded.

In prokaryotic cells: translation begins before transcription is finished.
In eukaryotes: transcription occurs in the nucleus; translation occurs in the cytoplasm.
Eukaryotic compartmentalization allows for differential regulation.
Prokaryotes lack a nucleus, so transcription and translation happen in the same space.

tRNA acts as an adapter, linking the codon in the mRNA sequence to the amino acid.
The three nucleotides of complementary RNA in the tRNA is called an anticodon.
tRNAs recognize codons and bind to specific amino acids, acting as the intermediary.
Aminoacyl tRNA synthetases attach the specific amino acid to the correct tRNA, creating a charged tRNA.

tRNAs have a similar structure and the base paired regions twist like a DNA molecule.
At the bottom is the RNA sequence that is complementary to the messenger RNA codon (anticodon).
One end attaches to a specific amino acid.

Produces charged tRNA in a cycle that requires ATP.
For every tRNA and amino acid combination, there is a specific aminoacyl tRNA synthetase enzyme.
This ensures that the correct tRNA is bound to the correct amino acid.
Example:
- Alanine binds to the active site of the enzyme.
- Alanine-specific tRNA binds, a reaction occurs, and alanine is attached to the tRNA molecule.
- The charged tRNA floats off to take part in translation and the process continues with another alanine and ATP.

Messenger RNA is brought into the active site of the ribosome.
The ribosome has two subunits: small and large, that clamp around the mRNA molecule.
Once they do that, there are three active sites that are formed: A, P, and E.

Ribosome looks like a hand grabbing around the RNA molecule.
The active sites are adjacent to each other.
Part of the structure of the ribosome is RNA itself called ribosomal RNA.
Removing the ribosomal RNA prevents it from working.
Hypothesis that life actually developed from an RNA world initially before proteins came along.

A complex of proteins/enzymes comes in at the start codon (AUG) with methionine (fMet in prokaryotes) attached to tRNA.
Small ribosomal subunit is bound to the mRNA and begins the process.
The start sequence is called the Shine-Dalgarno sequence (anti-SD).
Positions the small subunit so that the first codon is the first thing it sees.
The large subunit comes in and the whole thing is set up as a complex around that specific start codon.

Ribosome moves along the RNA in a five to three prime direction.
Polypeptides grow and are generated within the ribosome and then spill out of the active site once they get long enough.
Polypeptide is just all the amino acids joined together and are polymerized together with an N and C terminus.

N and C termini refer to the amino group (amine) and carboxylic acid group on either end of the amino acid chain.
Charged tRNAs bring in amino acids one at a time to be stitched onto the growing polypeptide chain.
Specificity comes from the anticodon and codon base pairing and the aminoacyl tRNA synthetase enzymes.
A release factor binds at the stop codon acting as a roadblock.
The ribosome works its way along the RNA and gets to the point where there's a stop codon, and the release factor blocks the whole process.
The whole complex falls apart, and the small and large subunits are released from the RNA, and the polypeptide is released.
The peptide chain is then folded up into a fully functioning protein.

Multiple ribosomes run the whole length of the RNA molecule.
Creates almost like a traffic jam of ribosomes.
Ribosomes cover an RNA molecule.
Allows regulation from the RNA production (transcription) and allows the making of lots of copies of a protein from a single RNA molecule.
Stability of the RNA is dictated by its function.
Developmental processes may have unstable RNA, while other processes have stable RNA.
Translation occurs at 12 amino acids a second.