ZOOHCC - 501: Molecular Biology (Theory)
Unit 3: Transcription and Regulatory RNAs
Prokaryotic Transcription
Although prokaryotes and eukaryotes perform basically the same transcription process, there are important differences in eukaryotic membrane-bound nuclei. For nuclear-bound genes, transcription occurs in the nucleus and the mRNA transcript must be transported to the cytoplasm. In prokaryotes, which lack membrane-bound nuclei and other organelles, transcription takes place in the cytoplasm of the cell.
RNA Polymerase
RNA polymerase is an enzyme that produces mRNA molecules (just as DNA polymerase produces new DNA molecules during DNA replication). Prokaryotes use the same RNA polymerase to transcribe all genes. In E. coli, the polymerase is composed of five polypeptide subunits. These subunits are assembled each time a gene is transcribed and disassembled when transcription is complete. Each subunit has a specific role (which you don't have to remember). Polymerases composed of all five subunits are called holoenzymes.
Protein involve
Prokaryotes use the same RNA polymerase to transcribe all genes. In E. coli, the polymerase consists of five polypeptide subunits, two of which are identical. Four of these subunits, called α, α, β and β', make up the core polymerase enzyme. These subunits are assembled each time a gene is transcribed and disassembled when transcription is complete. Each subunit has its own role. Two α subunits are required for the polymerase to assemble on DNA. The β subunit binds to ribonucleoside triphosphates and consequently becomes part of the 'newly born' mRNA molecule. β' binds to the DNA template. A fifth subunit, σ, is involved only in transcription initiation. It confers transcription specificity so that the polymerase initiates mRNA synthesis at a convenient initiation site. Without σ, the core enzyme transcribes from random sites to generate mRNA molecules that specify gibberish proteins. A polymerase composed of all five subunits is called a holoenzyme (a holoenzyme is a biochemically active compound composed of an enzyme and its coenzyme).
Initiation
Transcription in prokaryotes (and eukaryotes) requires partial unwinding of the DNA double helix at the mRNA synthesis region. The area of unwinding is called the transcription bubble. A DNA sequence to which a protein or enzyme involved in transcription binds to initiate the process is called a promoter. In most cases, promoters are upstream of the genes they control. Specific sequences in promoters are very important as they determine whether the corresponding gene is always transcribed, occasionally transcribed, or seldom transcribed. The structure and function of prokaryotic promoters are relatively simple (Figure 1). A critical sequence in prokaryotic promoters is located 10 bases before the transcription start site (-10) and is commonly referred to as the TATA box.
To initiate transcription, the RNA polymerase holoenzyme assembles at the promoter. The dissociation of σ allows the core enzyme to follow the DNA template and synthesize mRNA by adding RNA nucleotides following base-pairing rules, similar to how new DNA molecules are generated during DNA replication. Only one of the two strands of DNA is transcribed. The transcribed DNA strand is called the template strand because it is the template for mRNA production. The mRNA product is complementary to the template strand and nearly identical to the other DNA strand, called the non-template strand, except that RNA contains uracil (U) instead of thymine (T) found in DNA. The points are different. Like DNA polymerases, RNA polymerases add new nucleotides to the 3'-OH group of the previous nucleotide. This means that the growing strand of mRNA is synthesized in the 5'-3' direction. Since DNA is antiparallel, this means that RNA polymerase moves in the 3' to 5' direction along the template strand
Elongation.
As the elongation progresses, the hydrogen bonds connecting the complementary base pairs of the DNA double helix are broken, so the DNA is continuously unwound in front of the core enzyme (Figure 2). DNA is unwound behind the core enzyme while hydrogen bonds are reformed. The base pairs between DNA and RNA are not stable enough to maintain the stability of the mRNA synthetic components. Instead, RNA polymerase acts as a stable linker between the DNA template and the newly formed RNA strand, ensuring that elongation is not prematurely terminated.
Termination
When a gene is transcribed, RNA polymerase must be told to detach from the DNA template and release the newly made mRNA.There are two types of termination signals, depending on the gene being transcribed. One is protein-based and the other is RNA-based. Both termination signals are based on specific DNA sequences near the end of the gene that cause the polymerase to release the mRNA.
In prokaryotic cells, by the time transcription is finished, the processes of transcription and translation both occur in the cytoplasm, so they can occur simultaneously, so that transcription is already required to start making copies of the encoded protein. used (Fig. 3). In contrast, transcription and translation do not occur simultaneously in eukaryotic cells, as transcription occurs within the cell nucleus and translation occurs outside the cytoplasm.
