Translation: mRNA and Genetic Code

• Translation is the process where the nucleotide sequence of mRNA is used to order and join amino acids into a polypeptide chain.
• In eukaryotic cells, protein synthesis takes place in the cytoplasm, involving three types of RNA working together.

Messenger RNA (mRNA)

• Carries genetic information transcribed from DNA as a series of three-nucleotide sequences called codons.
• Each codon specifies a particular amino acid.
• Cells use a triplet code, where every three-nucleotide sequence, or codon, is "read" from a specific starting point in the mRNA.
• There are 64 possible codons, 61 specify individual amino acids, and 3 are stop codons.
• Most amino acids are encoded by more than one codon, only methionine and tryptophan each have a single codon.
• Leucine, serine, and arginine are each specified by six different codons.
• Different codons for a given amino acid are synonymous.
• The genetic code is degenerate, meaning more than one codon can specify the same amino acid.
• Synthesis of all polypeptide chains in prokaryotic and eukaryotic cells begins with the amino acid methionine.
• In most mRNAs, the start (initiator) codon specifying the aminoterminal methionine is AUG.
• GUG is used as the initiator codon in a few bacterial mRNAs.
• CUG occasionally is used as an initiator codon for methionine in eukaryotes.
• The three codons UAA, UGA, and UAG do not specify amino acids but are stop (termination) codons marking the carboxyl terminus of polypeptide chains.
• The reading frame is from the start codon to a stop codon.
• A linear array of ribonucleotides in groups of three in mRNA specifies the sequence of amino acids in a polypeptide chain and signals where synthesis starts and stops.

Transfer RNA (tRNA)

• Deciphers codons in mRNA, with each amino acid having its own subset of tRNAs.
• tRNAs bind to their specific amino acid and carry it to the growing end of a polypeptide chain according to the mRNA codon.
• Each tRNA molecule contains a three-nucleotide sequence, an anticodon, that base-pairs with the complementary codon in the mRNA.

Aminoacyl-tRNA Synthetases

• Are part of a two-step decoding process for translating nucleic acid sequences in mRNA into amino acid sequences in proteins.
• An aminoacyl-tRNA synthetase first couples a specific amino acid, via a high-energy ester bond, to either the 2' or 3' hydroxyl of the terminal adenosine in the corresponding tRNA.
• A three-base sequence in the tRNA (the anticodon) then base-pairs with a codon in the mRNA specifying the attached amino acid.
• If an error occurs in either charging step, the wrong amino acid may be incorporated into a polypeptide chain.

Ribosomal RNA (rRNA)

• Associates with a set of proteins to form ribosomes.
• Ribosomes physically move along an mRNA molecule, catalyzing the assembly of amino acids into polypeptide chains.
• Ribosomes also bind tRNAs and accessory proteins necessary for protein synthesis.
• Ribosomes are composed of a large and a small subunit, each containing its own rRNA molecule(s).

Steps in Translation

• Like transcription, translation is broken into initiation, elongation, and termination phases.
• All three phases involve the ribosome, which directs the translation process.
• Multiple ribosomes can translate a single mRNA molecule simultaneously, starting at the first codon and moving one codon at a time.
• A group of ribosomes, also known as a polysome, allows for the simultaneous production of multiple strings of amino acids, called polypeptides, from one mRNA.
• When released, polypeptides may be complete or require further processing to become mature proteins.

Initiation Phase

• The 40S subunit of the ribosome attaches to the mRNA strand and finds the start codon, almost always AUG, which corresponds to the amino acid methionine.
• The specific tRNA molecule carrying methionine recognizes this codon and binds to it.
• The 60S subunit then joins the 40S subunit to form the 80S initiation complex.

Elongation Phase

• Begins when the ribosome shifts to the next codon on the mRNA.
• The tRNA corresponding to this codon binds, resulting in two tRNA molecules on the mRNA strand for a short time.
• The amino acids carried by these tRNAs bind together.
• The ribosome shifts again, releasing the first tRNA/
• The third codon in the mRNA strand is ready to bind the appropriate tRNA/
• The process repeats along the entire length of the mRNA to elongate the polypeptide chain.

Termination Phase

• The ribosome reaches a stop codon, signaling the end of the genetic message.
• The ribosome detaches from the mRNA and releases the amino acid chain, marking the final phase of translation.

Post-Translational Modification (PTM)

• For many proteins, moderate to extensive PTM is necessary before the protein is complete.
• PTM refers to chemical changes that occur after a protein is produced, impacting its structure, electrophilicity, and interactions.
• Common PTMs are based on the addition of chemical groups like phosphorylation, acetylation, hydroxylation, and methylation.
• Other PTMs are based on the addition of complex groups (glycosylation, AMPylation, lipidation), the addition of polypeptides (ubiquitination), the cleavage of proteins (proteolysis), or modification of amino acids (deamidation).