1. What is the difference in composition between the prokaryotic (E. coli) core polymerase and holoenzyme? How does the E. coli RNA polymerases find the correct place to start transcription from a gene
To understand the difference in composition between the prokaryotic core polymerase and holoenzyme, let's start with the basics. In prokaryotes, such as E. coli, RNA polymerase is the enzyme responsible for transcription, which is the process of synthesizing RNA from a DNA template.
The core polymerase consists of four subunits: α, β, β', and ω. The α subunit is assembled into two copies (α2), while the β and β' subunits form the catalytic center of the enzyme. The ω subunit is a small subunit that plays a regulatory role.
The holoenzyme, also known as RNA polymerase holoenzyme or RNA polymerase II holoenzyme, is formed by the addition of a fifth subunit called σ (sigma) to the core polymerase. The σ subunit is responsible for recognizing the promoter region in DNA and initiating transcription from the correct place.
Now, let's dive into how E. coli RNA polymerases find the correct place to start transcription from a gene. This process involves recognizing specific DNA sequences called promoters. Promoters are found upstream of the gene coding region and provide a site for RNA polymerase binding.
The σ subunit of the holoenzyme plays a crucial role in promoter recognition. It recognizes specific consensus sequences within the promoter region and helps initiate transcription. The consensus sequences include the -35 region and the -10 region, also called the Pribnow box.
When RNA polymerase encounters a promoter, the σ subunit binds to the consensus sequences, leading to the formation of a closed complex. This closed complex then transitions into an open complex, where the DNA strands separate, and transcription begins.
It's important to note that not all promoters are the same. The strength and specificity of the promoter sequences can vary, affecting the efficiency of transcription initiation. Additionally, regulatory proteins and other factors can influence the binding of RNA polymerase to promoters, allowing for tight control of gene expression.
In summary, the core polymerase of E. coli RNA polymerase consists of four subunits, while the holoenzyme includes an additional σ subunit. The σ subunit helps the holoenzyme recognize specific promoter sequences, thereby guiding the initiation of transcription from the correct position in a gene.