3520_S_GenesRNABiosynth_rev20240325-1

Genes & RNA Biosynthesis Notes

DNA Topology

  • Coiling in DNA is defined by the linking number (Lk).

  • Non-supercoiled (normal) DNA has a linking number based on its length.

    • For 10.5 base pairs per turn, add up base pairs to find the Lk of plasmids (Example: Lk for 2100 bp plasmid would be 2100/10.5).

  • Topoisomerases can change Lk by introduction or removal of supercoiling:

    • Type I: Changes Lk by 1 (Lk ± 1)

    • Type II: Changes Lk by 2 (Lk ± 2, energy required)

Supercoiling of DNA

  • Superhelical density (σ) describes the supercoiling of DNA and does not depend on DNA length.

  • Forms of supercoiling:

    • Negative supercoiling: Easier to unwind, occurs with decreased Lk.

    • Positive supercoiling: Harder to unwind, occurs with an increased Lk.

  • Example of Lk changes:

    • Relaxed Lk = 200.

    • If Lk changes to positive supercoil +2, Lk = 202.

RNA Synthesis

  • Central Dogma of Molecular Biology: DNA → RNA → Protein.

  • A gene is defined as the complete DNA encoding a final product (polypeptide or RNA).

Types of RNA

  • mRNA: Carries genetic info from DNA to ribosomes for protein synthesis.

  • rRNA: Structural components of ribosomes.

  • tRNA: Translates mRNA into amino acid sequence during translation.

Gene Structures

  • Prokaryotic mRNA:

    • Monocistronic: Contains one gene.

    • Polycistronic: Contains multiple genes, typically in bacteria.

  • Eukaryotic genes often contain introns:

    • Example: The human genome has ~20,000 genes and over 200,000 introns.

Transcription Process

  • Coding vs. Template Strand:

    • The coding strand has the same sequence as the RNA transcript (except T is replaced with U).

    • The template strand is used to synthesize RNA.

  • RNA Polymerase synthesizes RNA without requiring a primer.

  • Transcription Initiation: Begins at promoter sequences that specify where and when transcription occurs.

Promoters and Transcription Factors

  • Promoter sequences are crucial for RNA polymerase binding and transcription initiation.

  • The sigma factor in prokaryotic RNA polymerase determines the specificity of transcription.

Termination of Transcription

  • p-independent termination: Involves the formation of an RNA hairpin, causing RNA polymerase to detach from DNA.

  • p-dependent termination: Involves a helicase that separates the mRNA from the DNA template.

Importance of Introns and Splicing

  • Eukaryotic genes undergo splicing to remove introns and form mature mRNA.

    • Splicing process involves a lariat structure, formed via the 2’ OH of an adenosine.

RNA Structure and Functionality

  • RNA can adopt various structures for different functions, including catalysis and binding.

  • Examples include SELEX for identifying RNAs with specific functions.

RNA and Virus Replication

  • Retroviruses utilize reverse transcription to integrate RNA into the host genome.

  • Coronaviruses replicate RNA through RNA-dependent RNA synthesis and do not integrate into the host genome.

  • Single-stranded RNA genomes, like that of coronaviruses, can act directly as mRNA within the host cell upon entry without needing transcription.