BIO 3400: RNA, Transcription, and Splicing

I. The Structure of RNA

• RNA is a polymer of ribonucleotides.
• Differences from DNA:
  • Sugar is ribose (hydroxyl group at 2’ carbon).
  • Uses uracil (U) instead of thymine (T).
• RNA polynucleotides linked by phosphodiester bonds; have free 5’ phosphate and 3’ hydroxyl ends.
• Synthesized as single strand via transcription on a DNA template with RNA polymerase.

II. Coding vs. Noncoding RNA

• RNA categorized into coding (mRNA) and noncoding types.
• mRNA carries genetic code for protein synthesis (DNA → mRNA → protein).
• Noncoding RNA has various functions (e.g., tRNA, microRNA, rRNA).

III. Basic Gene Structure

• Genes consist of:
  • RNA-coding region (template for RNA synthesis).
  • Promoter (controls transcription start).
  • Terminator (ends transcription).
• Template strand: used by RNA polymerase (antisense). Nontemplate strand: not used (sense strand).

IV. The Process of Transcription in Bacteria

• Bacterial RNA polymerase (holoenzyme) initiates transcription with the sigma factor.
• Key regions of the promoter: -10 box, -35 box, UP element.
• Steps in transcription: initiation, elongation, termination.

V. Major Differences in Transcription Between Eukaryotes and Bacteria

• Eukaryotes have three RNA polymerases; bacteria have one.
• Eukaryotic promoters are more complex and require general transcription factors and mediator proteins.
• Eukaryotic transcription involves chromatin modulation and unique termination mechanisms.

VI. RNA Processing

• Includes three main events: 5’ cap addition, splicing of introns, and polyadenylation (3’ poly(A) tail).
• Splices out introns to produce mature mRNA from primary transcript.

VII. Methods for Detecting and Measuring RNA

• Techniques include cDNA cloning, rtPCR, real-time PCR, and RNA-Seq.
• cDNA is a stable form used for manipulation of RNA.
• RNA-Seq provides insights into transcriptome dynamics and gene expression profiles.