Lesson 4: Transcription and mRNA Maturation

1. RNA Structure

• RNA has a primary structure that is a polynucleotide chain.

• RNA can form secondary structures like hairpins and loops due to complementary base pairing.

• The proportion of rare bases in RNA is higher than in DNA.

2. Location of RNA and DNA in the Cell

• RNA is found in both the nucleus and cytoplasm.

• DNA is found in the nucleus, mitochondria, and chloroplasts.

3. Transcription

• Transcription is the process of transferring genetic information from DNA to RNA.

• The transcription process requires:

• A DNA template strand.

• The transcription machinery, including RNA polymerase and transcription factors.

• rNTPs (ribonucleotide triphosphates) as building blocks for the RNA molecule.

• rNTPs are added to the 3′-OH end of the growing RNA molecule.

4. Role of the Promoter Region in Transcription

• The promoter region plays a role in:

• Allowing the transcription machinery to recognize and bind to DNA.

• Determining which strand is the template strand.

• Directing the transcription process.

• Determining the transcription start site.

5. Transcription Initiation

• Transcription begins when the RNA polymerase enzyme binds to the promoter region at the transcription start site.

• The transition from initiation to elongation requires a conformational change in RNA polymerase.

6. Transcription in Prokaryotes

• Prokaryotes generally have a single RNA polymerase that catalyzes RNA synthesis.

• The TATA box is located at position -10 relative to the transcription start site.

• Consensus sequence refers to a sequence that is conserved and similar across most individuals within a species.

• The -10 region sequence in bacterial promoters is typically 5′-TATAAT-3′.

• The -35 region sequence in bacterial promoters is typically 5′-TTGACA-3′.

• Transcription in prokaryotes begins when the first rNTP binds to the RNA polymerase complex.

• The first rNTP added to the RNA polymerase complex is usually ATP or GTP.

• Transcription initiation in prokaryotes ends when the RNA sequence reaches about 10 ribonucleotides, the RNA polymerase structure changes, and the sigma subunit is usually released.

• The structure of RNA polymerase in prokaryotes consists of 6 subunits: 2 alpha, 1 beta, 1 beta’, 1 omega, 1 sigma. The first 5 subunits form the core enzyme which binds to the sigma subunit to form the holoenzyme.

• The rate of ribonucleotide addition to RNA at 37°C is about 40 ribonucleotides/s.

• The transcription bubble is a region of unwound DNA, about 18 nucleotides long, where transcription occurs.

• The DNA-RNA hybrid region has a length of about 8-9 bp.

7. Transcription Termination in Prokaryotes

• Prokaryotes have two types of transcription termination signals: rho-dependent and rho-independent.

• Rho is a protein consisting of 6 identical subunits and a region with ATPase activity.

• Rho binds to RNA at the rut site.

8. Transcription in Eukaryotes

• Eukaryotes have 3 types of RNA polymerases: I, II, III.

• Plants also have RNA polymerases IV and V.

• RNA polymerase I participates in the transcription of rRNA.

• RNA polymerase II participates in the transcription of pre-mRNA, some snRNAs, snoRNAs, and some miRNAs.

• RNA polymerase III participates in the transcription of tRNA, some snRNAs, small rRNAs, and some miRNAs.

• RNA polymerase IV participates in the transcription of some siRNAs.

• RNA polymerase V participates in the transcription of RNAs that have roles in DNA methylation and chromosome structure.

9. mRNA Maturation

• mRNA maturation goes through these steps:

• 5′ capping.

• Polyadenylation at the 3′ end.

• Pre-mRNA splicing.

10. 5′ Capping of mRNA

• The 5′ cap is a methylated guanosine (m7G) attached to the 5′ end of mRNA.

• The bond between the methyl group and guanosine in the m7G cap is a 5′-triphosphate-5′ bond.

• The cap has the following functions:

• Facilitates the transport of pre-mRNA from the nucleus to the cytoplasm.

• Protects mRNA from exonucleases.

• RNA methyltransferase is the enzyme involved in the process of adding the methyl group to guanosine.

11. Functions of RNA Types

• mRNA: Encodes the amino acid sequence of a polypeptide chain.

• rRNA: Forms the basic structure of ribosomes and catalyzes protein synthesis.

• tRNA: Participates in protein synthesis.

• snRNA: Functions in nuclear processes, including pre-mRNA splicing.

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