DNA AND RNA

Overview of DNA Replication

  • Double-Stranded DNA Sequences

    • Structure of DNA

    • Orientation: 5’ to 3’ and anti-parallel strands

  • DNA Synthesis Process

    • Role of DNA Polymerase

    • Needs to unwind the DNA before synthesizing new DNA

    • Requires helicase for unwinding

    • RNA Primer Requirement

    • DNA polymerase requires a double-stranded section to bind

    • Primase synthesizes an RNA primer to start the process

Steps in DNA Synthesis

  • Unwinding the DNA

    • Enzyme Involved: helicase unwinds the double-stranded DNA.

  • Synthesis of RNA Primer

    • Primase synthesizes an RNA primer, which is essential for DNA polymerase to initiate DNA synthesis.

    • Example of RNA primer synthesis:

    • 5’ to 3’ direction creating a sequence (e.g., UCGACUGU).

  • Elongation by DNA Polymerase

    • Enzyme Involved: DNA polymerase III elongates the RNA primer to form the complementary DNA strand.

    • Example elongation with DNA:

      • Pairs using T instead of U, following complementary base pairing.

Leading and Lagging Strands

  • Leading Strand

    • Continuous synthesis; DNA polymerase can add nucleotides, moving towards the fork.

    • Example Direction: Synthesizing continuously in 5’ to 3’ direction without interruptions.

  • Lagging Strand

    • Discontinuous synthesis; must create a new RNA primer for each Okazaki fragment.

    • Example: New primer synthesized as the strand unwinds, requiring multiple RNA primers to keep up with the continual unwinding.

Inhibition of DNA Replication in Viruses

  • Case Study: Herpes Simplex Virus

    • Complex Involved: helicase-primase complex required for viral DNA replication.

    • Drug: Criptelofir inhibits this complex.

  • Effects of Drug on DNA Replication:

    • Inhibition of Primase:

    • Replication cannot start; DNA polymerase has nothing to bind to.

    • Inhibition of Helicase:

    • Prevents unwinding of DNA; DNA polymerase is unable to progress due to lack of accessible template.

Transcription and Translation

  • Overview of Transcription

    • Occurs in the nucleus and involves creating an RNA copy of DNA.

    • RNA Polymerase helps in synthesizing RNA, transferring DNA information to mRNA.

  • Historical Anecdote: Mozart and the Vatican archives as a metaphor for transcription.

  • Translation process in ribosomes using mRNA for protein synthesis.

Gene Structure in Bacteria and Eukaryotes

  • Prokaryotic Gene Structure

    • Simple: promoter, coding region, terminator.

    • Stages:

    • Initiation: RNA polymerase binds to the promoter.

    • Elongation: Formation of RNA strand complementary to DNA.

    • Termination: RNA polymerase reaches terminator sequence and releases the new RNA strand.

  • Eukaryotic Gene Structure

    • Complex: includes introns (non-coding sequences) and exons (coding sequences).

    • Processing: Involves splicing of introns, adding a 5’ cap, and a 3’ poly-A tail to form mature mRNA.

Importance of Exons and Introns

  • Exons: Genes that are expressed and included in the final mRNA.

  • Introns: Genes not expressed that can be rearranged during splicing to allow for variability in protein coding.

  • Alternative Splicing: Enables a single gene to code for multiple proteins by mixing and matching exons and intron sequences.

Codons and Translation

  • Codons: Sequences of three nucleotides in mRNA that dictate specific amino acids.

  • Ribosome Interaction:

    • tRNA carries amino acids; recognizes codons via anticodon pairing.

    • Structure of Ribosomes: Composed of a small and large subunit, with three key sites:

    • A site: Accepts new tRNA

    • P site: Peptide bond formation

    • E site: Exit site for discharged tRNA

  • Translation Mechanism

    • Initiation with start codon (AUG), followed by tRNA recognition, peptide elongation, and termination with stop codons (UAA, UAG, UGA).

    • Release Factor: Binds at stop codons to terminate peptide synthesis and disassemble the ribosomal complex.

Summary of Molecular Biology Processes

  • DNA Replication: Involves unwinding, primer synthesis, elongation, and strand synthesis based on leading and lagging strand mechanisms.

  • Transcription: Conversion of DNA to a functional mRNA transcript, which requires processing in eukaryotes.

  • Translation: Interpretation of mRNA by ribosomes to synthesize polypeptides, guided by codon-anticodon pairing using tRNA.