Protein Synthesis
- Transcription - Copying a sequence of DNA into mRNA
- Translation - Converting the information in rRNA to a sequence of amino acids
Transcription is similar to replication since a DNA strand is acting as a template to make a complementary mRNA strand.
The difference in transcription is that the copy is a mRNA molecule and only one DNA stand is copied.
The major enzyme catalyzing polymerization is named as RNA polymerase.
This is rRNA, because it transmits the message stored in the gene to the place where the polypeptide chain is actually being assembled.
Message in mRNA is translated to a sequence of amino acids.
This process occurs in association with ribosomes, which are present in the cytosol.
In addition to mRNA, other types of RNAs and enzymes are involved in the polypeptide synthesis.
The basic mechanism of the process of polypeptide synthesis is similar in prokaryotes and eukaryotes, with some important differences.
Transcription
Transcription is DNA directed RNA synthesis.
This is completed in three steps.
- Initiation
- Elongation
- Termination
Initiation:
The process of transcription is initiated at a specific site called promoter.
The promoter site includes a transcription initiation site and several other nucleotides.
Only one strand of the double stranded DNA acts as a template for transcription.
This is because only the template strand will have the promoter sequence in the correct orientation, which facilitates the binding of RNA polymerase.
The enzyme polymerizing the RNA is RNA polymerase.
This enzyme binds to the promoter site in correct orientation.
The RNA polymerase then unwinds the two DNA strands and begins the transcription at start point.
A component of RNA polymerase has the helicase activity, and hence DNA helicase is not involved in transcription.
Elongation:
RNA polymerase enzymes can start adding complementary ribonucleotides against the template DNA.
RNA polymerase continues to add nucleotides in 5’ to 3’ direction until it reaches the transcription termination site.
The DNA strands unwind as the RNA polymerase moves forward, exposing template DNA and allowing pairing with ribonucleotide.
The two stands rewind at the other end
Termination:
In prokaryotes, the polymerization continues passing the termination sequence of DNA and RNA polymerase enzyme falls off ending the transcription.
After termination, the newly synthesized pre mRNA in eukaryotes is subjected to RNA processing.
The mature RNA leaves the nucleus.
Translation
Once the mRNA is in the cytosol, translation process is initiated.
Ribosomes read the message written as a sequence of triplet codons in an mRNA and translate it into a sequence of amino acids in a polypeptide with the assistance of transfer RNAs(tRNA).
A tRNA attached to the correct amino acid from a pool in the cytosol, transports it to the ribosome which adds the amino acid to the growing end of the polypeptide chain by making a peptide bond.
The key players in translation are tRNAs.
A specific tRNA molecule binds a specific amino acid to its one end.
Its structure also carries, at a specific location, a triplet of nucleotides, which is complementary to the codon in the mRNA that code for the amino acid it carries.
This triplet is known as anti-codon and it can base-pair with the codon.
This is how tRNA does the translation, by acting as an adapter molecule between the triplet codon and the amino acid specified by it.
Structure of ribosome
- Initiation
- Elongation
- Termination
Initiation:
The first step in initiation is binding of small subunit of ribosome to mRNA and to the initiator tRNA which carries methionine as the first amino acid.
Then, the two subunits of the ribosome combine to form the functional ribosome.
This complex of ribosomal subunits, mRNA and initiator tRNA, is called translation initiation complex.
Then the mRNA moves until the AUG start codon, aligns with the P site of the large subunit.
Then, the anti-codon of the initiator tRNA forms hydrogen bonds with AUG start codon.
This signals the initiation of the translation.
Elongation:
ln this stage, amino acids are added to the C- terminus of the growing polypeptide chain by peptide bonds, one after the other governed by the triplet codons
Elongation is completed by a three-step cycle
At the end of the initiation stage P site is occupied with tRNA attached to methionine and A site is empty and is aligned with the next codon.
The second tRNA, charged with the corresponding amino acid is brought to the A site matching the codon and anticodon.
This first step in the cycle is the codon recognition.
As the second step a peptide bond is formed between the carboxyl group of the growing polypeptide chain in the P site with the amino group of the amino acid in the A site
An rRNA catalyses this reaction
The third step is the translocation of the mRNA
The mRNA moves codon by codon unidirectionally
In the process, the tRNA with the growing polypeptide chain in the A site is moved to the P site.
The released tRNA in the P site will move simultaneously to the E site, from where it is released to the cytosol.
The A site is now aligned with the next codon so that this cyclic process can continue.
ATP is used for the energy requirement of the elongation process
Termination:
When the mRNA moves, it finally aligns one of the stop codons: UAG, UAA or UGA with A site.
They do not code for any amino acid, hence there is no tRNA which comes into A site.
This releases the completed polypeptide chain to the cytosol.
The ribosome and the remainder of the translation assemble then fall apart
Polyribosomes/ Polysomes:
When the mRNA moves away for a sufficient distance, a second ribosome can bind to it.
Depending on the length of mRNA, a number of ribosomes can be attached to the mRNA simultaneously.
As such, mRNAs that are being translated actively are associated with multiple ribosomes attached to a string of mRNA, forming polyribosomes or polysomes.
Forming polyribosomes increases the rate of translation since they allow simultaneous translation by several ribosomes.
Fate of the proteins
The newly synthesized polypeptide is the primary structure of the polypeptide.
This is not functional as a protein as it is.
The polypeptide has to assume its functional form by folding and sometimes with post-translational modifications.
Certain polypeptides have additional segments than what is required for its function.
For example, a short segment of amino acids are present in certain polypeptides to act as signal peptide.
Signal peptide guides the polypeptide to a particular location in the cell or to be secreted.
This is referred to as protein trafficking.
Once the polypeptide is in place, the extra piece of the peptide chain is no longer needed and may be removed enzymatically.
The post-translational modifications include chemical modification of certain amino acids by attaching sugars (glycoproteins), lipids (lipoproteins), phosphate groups (phosphorylated proteins) and other additions.
The first amino acid, methionine, maybe removed enzymatically.
Enzymes may also cut the initial polypeptide into two or more pieces which forms a functional protein, by joining different combinations.
For example, the protein insulin is produced as a single polypeptide, but cut at two places to remove the central piece.
The other two polypeptide chains are joined together to form the functional insulin.
Selective Degradation of Proteins
The amount of a protein in a cell is determined on one hand by the rate of synthesis and on the other by the rate of degradation.
The selective degradation of proteins is an essential mechanism in regulation of cellular activities.
Certain proteins are degraded in response to specific signals.
Faulty or damaged proteins are recognized and rapidly degraded to avoid bad effects due to mistakes in polypeptide synthesis or errors in folding.
Some proteins for example regulatory proteins, need to be rapidly degraded after their function.
The structural proteins may remain for a longer period.