Gene Expression in Prokaryotes: Transcription

Gene Expression in Prokaryotes: Transcription

• RNA molecules are synthesized from DNA during transcription
• Transcription copies only specific parts of DNA, such as a gene or a few genes, into RNA
• Transcription is a selective process: individual genes only get transcribed when needed
• Transcription requires DNA template, raw materials (substrates), and a transcription apparatus.
• The template used for transcription is a single strand of the DNA double helix
• The nucleotide strand used is called the template strand. The opposite strand is called the non-template or coding strand.
• RNA synthesis is complementary and antiparallel to the template DNA strand.
• RNA is usually single-stranded, unlike DNA which consists of two polynucleotide strands.
• RNA synthesis always proceeds in the 5' to 3' direction.

RNA Structure

• Ribosomes are catalytic RNA molecules (ribozymes) and might have been the first carriers of genetic information
• RNA is a polymer of nucleotides bound together with phosphodiester bonds
• RNA has ribose sugar
• RNA contains uracil instead of thymine
• RNA usually consists of one strand; under specific conditions, RNA segments can be paired, creating a secondary structure and forming regions that can be paired.

Classes of RNA

• Ribosomal RNA (rRNA): combines with ribosomal proteins to form ribosomes.
• Messenger RNA (mRNA): carries the genetic code from the DNA to the ribosome, specifying the order of amino acids to synthesize proteins.
• Transfer RNA(tRNA): acts as a link between the genetic code in mRNA and the amino acid sequence in the protein.
• rRNA, tRNA and mRNA molecules perform specific functions inside the cell
• Pre-mRNAs or primary transcripts are modified before becoming mRNA and exiting the nucleus for translation into protein
• Additional RNA classes exist in eukaryotic cells: small nuclear RNA (snRNA); small nucleolar RNA (snoRNA), microRNA (miRNA) and small interfering RNA (siRNA)

The Transcription Unit

• A transcription unit is a segment of DNA that encodes an RNA molecule.
• It typically consists of three regions: promoter, RNA-coding region, and terminator.
• Promoter: a DNA sequence where the transcription apparatus binds. It indicates which strand is the template for transcription and the direction.
• RNA-coding region: segment of DNA that contains the sequence of nucleotides that is copied into an RNA molecule.
• Terminator: a sequence of nucleotides that signals the end of transcription.
• Transcription apparatus, including RNA polymerase, plays a critical role

The Transcription Apparatus

• RNA polymerase: the enzyme that catalyzes the transcription process, synthesizing RNA using a DNA template.
• Bacterial RNA polymerase usually consist of one type that synthesizes all kinds of bacterial RNA, mRNA, tRNA, rRNA.
• Eukaryotic cells have three different types of RNA polymerase
• RNA polymerase I: synthesizes rRNA
• RNA polymerase II: synthesizes mRNAs and some snRNAs, snoRNAs, and miRNAs
• RNA polymerase III: synthesizes tRNAs, the small rRNAs, some snRNAs, and some other small RNAs
• The sigma factor is involved in binding with bacterial RNA polymerase to the promoter

The Process of Bacterial Transcription

• Transcription, including initiation, elongation, and termination stages
• Initiation: the process of assembling the transcription apparatus at the promoter and initiating RNA synthesis
• Elongation: the process of adding nucleotides to the 3' end of the elongating RNA.
• Termination: the recognition of and separation of RNA from the DNA template

Initiation of Transcription

• Consensus sequences are short stretches of nucleotides and play role in initiation of transcription sequences within the DNA.
• Promoters in bacterial DNA contain short consensus sequences, which are important in initiation of transcription.
• The sigma factor plays a role in binding RNA polymerase with promoter
• Sigma factor leaves after transcription initiated.

Elongation of Transcription

• RNA polymerase undergoes conformational changes in elongation.
• The sigma subunit is released.
• The RNA transcripts are synthesized from the DNA template.

Termination of Transcription

• Transcription stops when the polymerase transcribes a terminator.
• Bacterial cells: utilize either rho-dependent or Rho-independent terminators.
• Rho-dependent terminators require specific proteins called rho factor.