What Are Start Codons And Stop Codons

Decoding the genetic blueprint within our DNA relies on specific signals that instruct the cellular machinery where to start and stop reading the code, and these signals are known as start codons and stop codons. These codons play a vital role in protein synthesis, ensuring that the correct amino acid sequence is assembled to form functional proteins.

The Central Dogma: From DNA to Protein

The central dogma of molecular biology outlines the flow of genetic information within a biological system, starting with DNA, then RNA, and finally protein. This process involves two major steps: transcription and translation.

• Transcription: DNA serves as a template for synthesizing RNA molecules, specifically messenger RNA (mRNA). This process occurs in the nucleus, where the genetic information encoded in DNA is transcribed into a complementary RNA sequence.
• Translation: The mRNA molecule then carries this genetic information from the nucleus to the ribosomes in the cytoplasm. Here, the mRNA sequence is translated into a protein, with each three-nucleotide codon in the mRNA specifying a particular amino acid.

Start Codons: Initiating the Synthesis of Proteins

A start codon is a specific nucleotide triplet within an mRNA molecule that signals the ribosome to begin protein synthesis. It acts as a "start" signal, indicating the precise location on the mRNA where translation should commence.

The Universal Start Codon: AUG

The most common and widely recognized start codon is AUG, which encodes for the amino acid methionine in eukaryotes and N-formylmethionine in prokaryotes. This codon is highly conserved across different species, highlighting its fundamental role in initiating protein synthesis.

• Eukaryotes: In eukaryotic organisms, AUG typically codes for methionine. However, the methionine residue may be removed from the protein during post-translational modification.
• Prokaryotes: In prokaryotic organisms, AUG codes for N-formylmethionine (fMet), a modified form of methionine. This modification helps in the initiation of translation in prokaryotes.

Mechanism of Start Codon Recognition

The initiation of protein synthesis is a complex process that involves the coordinated action of various initiation factors and the ribosome.

1. Ribosome Assembly: The small ribosomal subunit (30S in prokaryotes, 40S in eukaryotes) binds to the mRNA molecule near the 5' end.

2. Scanning: The small ribosomal subunit scans the mRNA in the 5' to 3' direction until it encounters the start codon AUG. This scanning process is facilitated by initiation factors, which help the ribosome locate the start codon.

3. Initiator tRNA Binding: A special transfer RNA (tRNA) molecule, called the initiator tRNA, carries methionine (or N-formylmethionine in prokaryotes). The initiator tRNA recognizes and binds to the AUG start codon through complementary base pairing.

4. Large Subunit Recruitment: Once the initiator tRNA is bound to the start codon, the large ribosomal subunit (50S in prokaryotes, 60S in eukaryotes) joins the complex. This completes the formation of the functional ribosome, which is now ready to begin protein synthesis.

Context Matters: Kozak Sequence and Shine-Dalgarno Sequence

The efficiency of start codon recognition is influenced by the surrounding nucleotide sequence, known as the context sequence. This context sequence helps the ribosome to correctly identify the start codon and initiate translation efficiently.

• Kozak Sequence (Eukaryotes): In eukaryotes, the Kozak sequence is a consensus sequence that precedes the AUG start codon. The consensus sequence is GCCRCCAUGG, where R represents a purine (A or G). This sequence enhances the efficiency of translation initiation.
• Shine-Dalgarno Sequence (Prokaryotes): In prokaryotes, the Shine-Dalgarno sequence is a purine-rich sequence located upstream of the AUG start codon. The consensus sequence is AGGAGG. This sequence base-pairs with a complementary sequence on the small ribosomal subunit, helping to position the ribosome correctly for translation initiation.

Alternative Start Codons

While AUG is the most common start codon, alternative start codons can also initiate protein synthesis in certain organisms and under specific conditions. These alternative start codons include:

• GUG (Valine): In some cases, GUG can function as a start codon, encoding for valine. However, translation initiation from GUG is generally less efficient than from AUG.

• UUG (Leucine): UUG can also serve as a start codon, encoding for leucine. Similar to GUG, translation initiation from UUG is less efficient than from AUG.

• CUG (Leucine): Rarely, CUG can initiate translation, coding for leucine.

The use of alternative start codons can result in the production of protein isoforms with different N-terminal sequences. These isoforms may have distinct functions or localization within the cell.

Stop Codons: Terminating Protein Synthesis

A stop codon is a nucleotide triplet within an mRNA molecule that signals the ribosome to stop protein synthesis. It acts as a "stop" signal, indicating the precise location on the mRNA where translation should terminate. Unlike start codons, stop codons do not code for an amino acid.

The Three Stop Codons: UAG, UGA, and UAA

There are three stop codons: UAG (amber), UGA (opal), and UAA (ochre). These codons are recognized by release factors rather than tRNA molecules.

• UAG (Amber): This stop codon is one of the three signals that terminate translation.
• UGA (Opal): Another stop codon that signals the end of protein synthesis.
• UAA (Ochre): The third stop codon that terminates translation.

Mechanism of Stop Codon Recognition

The termination of protein synthesis is a crucial step that ensures the correct length and sequence of the protein.

1. Ribosome Stalling: When the ribosome encounters a stop codon (UAG, UGA, or UAA) on the mRNA, it stalls, as there is no tRNA molecule that can recognize these codons.

2. Release Factor Binding: Release factors (RFs) are proteins that recognize stop codons and bind to the ribosome. In eukaryotes, there are two release factors: eRF1 and eRF3. In prokaryotes, there are three release factors: RF1, RF2, and RF3.

   • eRF1/RF1 and RF2: These release factors recognize the stop codons. eRF1 recognizes all three stop codons in eukaryotes, while RF1 recognizes UAG and UAA in prokaryotes, and RF2 recognizes UGA and UAA.

   • eRF3/RF3: This release factor is a GTPase that helps facilitate the termination process.

3. Peptide Chain Release: Upon binding of the release factor, the peptidyltransferase activity of the ribosome is altered, leading to the hydrolysis of the bond between the tRNA and the polypeptide chain. This releases the newly synthesized polypeptide chain from the ribosome.

4. Ribosome Dissociation: After the polypeptide chain is released, the ribosome dissociates into its large and small subunits, along with the mRNA and release factors. This allows the ribosome subunits to be recycled and used for further rounds of protein synthesis.

Termination Efficiency and Readthrough

The efficiency of translation termination can be influenced by the surrounding nucleotide sequence, similar to start codon recognition. A strong termination context can enhance the efficiency of stop codon recognition, while a weak context can lead to readthrough.

• Readthrough: Readthrough occurs when the ribosome fails to recognize a stop codon and continues translation into the 3' untranslated region (UTR) of the mRNA. This can result in the production of elongated proteins with altered functions.

Recoding Events

In some cases, stop codons can be recoded to specify an amino acid, leading to the incorporation of non-standard amino acids into the protein.

• Selenocysteine: In both prokaryotes and eukaryotes, UGA can be recoded to specify selenocysteine, a rare amino acid containing selenium. This recoding event requires specific cis-acting elements in the mRNA and a specialized tRNA molecule.

• Pyrrolysine: In some archaea and bacteria, UAG can be recoded to specify pyrrolysine, another non-standard amino acid. This recoding event also requires specific mRNA elements and a specialized tRNA molecule.

Significance of Start and Stop Codons

Start and stop codons are essential for accurate and efficient protein synthesis. They ensure that the correct amino acid sequence is assembled to form functional proteins.

• Defining the Open Reading Frame (ORF): Start and stop codons define the boundaries of the open reading frame (ORF), which is the region of the mRNA that is translated into protein. The start codon marks the beginning of the ORF, and the stop codon marks the end.

• Preventing Truncated or Elongated Proteins: By accurately initiating and terminating translation, start and stop codons prevent the production of truncated or elongated proteins that may be non-functional or even harmful to the cell.

• Regulation of Gene Expression: Start and stop codons can also play a role in the regulation of gene expression. The efficiency of start codon recognition can be influenced by various factors, such as the context sequence and the availability of initiation factors. Similarly, the efficiency of stop codon recognition can be affected by the termination context and the presence of release factors.

Mutations in Start and Stop Codons

Mutations in start and stop codons can have significant consequences for protein synthesis and cellular function.

Start Codon Mutations

• Loss-of-Start Codon: A mutation that eliminates the start codon can prevent translation initiation, resulting in the complete absence of the protein.

• Creation of New Start Codons: A mutation that creates a new start codon upstream of the original start codon can result in the production of a truncated protein. Alternatively, a new start codon downstream of the original start codon can lead to the production of an N-terminally extended protein.

Stop Codon Mutations

• Nonsense Mutations: A mutation that changes a codon to a stop codon is called a nonsense mutation. This results in premature termination of translation, leading to the production of a truncated protein.

• Readthrough Mutations: A mutation that eliminates a stop codon can result in readthrough, where the ribosome continues translation into the 3' UTR of the mRNA. This can lead to the production of an elongated protein with altered function.

Conclusion

Start and stop codons are essential signals that define the boundaries of protein-coding regions in mRNA and regulate the initiation and termination of protein synthesis. The start codon AUG signals the ribosome to begin translation, while the stop codons UAG, UGA, and UAA signal the ribosome to stop translation. The efficiency of start and stop codon recognition is influenced by various factors, including the context sequence and the availability of initiation and release factors. Mutations in start and stop codons can have significant consequences for protein synthesis and cellular function, leading to the production of truncated, elongated, or non-functional proteins. Understanding the role of start and stop codons is crucial for comprehending the mechanisms of gene expression and the impact of mutations on protein synthesis.