Question

In an operon for synthesis of an amino acid that is controlled wholly or in part by attenuation, why does the presence of the amino acid prevent transcription of the whole operon while the absence of the amino acid permits it?

Short answer

Answer: The presence or absence of an amino acid regulates the transcription of an operon through attenuation by controlling the formation of either a transcription termination structure or an antiterminator structure in the mRNA. When the amino acid is present, it leads to the formation of a transcription termination structure that prevents the expression of the entire operon. In the absence of the amino acid, the formation of an antiterminator structure allows the transcription of the entire operon, resulting in the synthesis of the amino acid.

Step-by-step solution

Understand the operon model of gene regulation

Operons are functional units of DNA that contain a group of genes under the control of a single promoter. The genes in an operon are usually related to a particular metabolic pathway, such as the synthesis of an amino acid. In bacteria, transcription of the genes in an operon is regulated by the presence or absence of specific molecules, such as the amino acid being synthesized.

Define attenuation

Attenuation is a regulatory mechanism in which transcription of an operon is controlled by premature termination of the RNA transcript. This occurs when there is a formation of a transcription termination structure in the 5' untranslated region of the mRNA, which acts as a molecular switch.

Describe the role of the amino acid in attenuation

In the synthesis of an amino acid, the presence or absence of the amino acid determines whether the whole operon is transcribed or not. When the amino acid is present at high levels, it binds to a specific regulatory protein or is incorporated directly into tRNA. The binding of the amino acid to the regulatory protein or its presence in the tRNA affects the ribosome's movement and leads to the formation of the transcription termination structure in the mRNA. This causes the premature termination of transcription, preventing the expression of the entire operon.

Explain the effect of the absence of the amino acid

In the absence of the amino acid, the regulatory protein remains inactive or the tRNA is not charged with the amino acid. As a result, the ribosome does not stall, which allows the formation of an alternative RNA secondary structure, the antiterminator structure. This structure prevents the transcription termination, allowing the transcription of the entire operon and consequently the synthesis of the amino acid.

Recap

In summary, the presence of an amino acid prevents the transcription of the whole operon through the formation of a transcription termination structure via attenuation, while the absence of the amino acid permits transcription by allowing the formation of the antiterminator structure. This regulatory mechanism ensures that the operon is only transcribed when there is a need to synthesize the amino acid.

Key concepts

Attenuation in Gene Regulation

Attenuation is a sophisticated method used by bacteria to regulate gene expression, particularly in operons related to amino acid biosynthesis. Understanding attenuation is like following a clever dance that the cell performs to conserve resources; think of it as an on-the-fly decision about whether to continue a production line or to shut it down based on the end product's availability.

In essence, it couples transcription and translation - two major processes in gene expression. When an amino acid is plentiful, the need to produce more of it diminishes. In this scenario, a specific sequence in the RNA transcript, often at the beginning, forms a hairpin-like structure. This loop, called a transcription termination structure, signals the machinery to stop transcribing the DNA into RNA; it's like a 'stop' sign for the polymerase.

Conversely, when the amino acid is scarce, the cell needs to manufacture more for survival. To ensure production continues, another RNA structure called an antiterminator forms instead, which allows the transcription process to proceed. This simple yet effective mechanism helps the cell efficiently allocate resources, implementing a go/no-go decision at the stage of RNA synthesis.

Transcription Termination Structure

At the heart of attenuation lies the transcription termination structure, a fascinating RNA element that acts as a molecular switch. Picture a train (the RNA polymerase) chugging along the tracks (the DNA) and the formation of this structure as a sign that the bridge ahead (further transcription) is out. In the presence of adequate amounts of amino acid, this loop forms and halts the polymerase in its tracks.

The formation of this structure is a clever interplay involving the newly synthesized RNA, the ribosome that's starting translation, and the charged tRNAs. Normally, the ribosome tails the polymerase closely during translation. However, if there are enough charged tRNAs - indicating plenty of amino acids - the ribosome can swiftly add amino acids to the growing peptide chain. This rapid action influences the RNA to fold into the terminator structure, which effectively cuts the transcription process short.

This auto-regulation ensures that energy and resources are not wasted in making enzymes when their end product - the amino acid - is already available. The structure itself is typically a stem-loop followed by a sequence of uracil bases, a formation that signals the end of the RNA transcript.

Amino Acid Biosynthesis

The operon model brilliantly intertwines with the cell's need to make its own amino acids, the building blocks of proteins. Amino acid biosynthesis operons are essentially groups of genes that encode the enzymes necessary to construct an amino acid from simpler starting materials. Imagine amino acid biosynthesis as a multi-step recipe, where each step is catalyzed by a specific enzyme produced by the operon's genes.

When a cell senses a low internal supply of a particular amino acid, the biosynthesis operon kicks into gear, transcribing the genes into mRNA, which is then translated into enzymes. These enzymes work sequentially, like factory workers on an assembly line, each adding a piece to form the final amino acid product. This process is not just a critical part of survival for bacteria but is a target for antibiotic design, as disrupting amino acid biosynthesis can halt the growth of bacterial cells.

This process, when not controlled by attenuation, is meticulously regulated at multiple levels to ensure balance within the cell. Produced on demand, these amino acids can then be used to make proteins, helping the cell to adapt to varying nutritional conditions.