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lec 13 GOB Chemistry: Nucleic Acid Synthesis and Transcription

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Terms in this set (20)

  • What provides the energy for nucleic acid synthesis?
    Hydrolysis of phosphoanhydride bonds in nucleotides (NTPs or dNTPs) provides the energy, releasing pyrophosphate (PPi) which is further hydrolyzed to 2 Pi, making the reaction irreversible.
  • What is the DNA polymerase reaction?
    DNA polymerase catalyzes the addition of dNMPs from dNTPs to the 3' OH end of a DNA strand, releasing PPi and using energy from hydrolysis of 2 phosphoanhydride bonds.
  • How many ATP equivalents are used to add one base during DNA synthesis?
    Two ATP equivalents are hydrolyzed per base added, corresponding to the cleavage of two phosphoanhydride bonds in dNTP.
  • What determines which base DNA polymerase adds?
    Complementarity to the template strand determines the base added; DNA polymerase adds nucleotides only to the 3' OH of the primer strand.
  • What proteins are important for replication initiation?
    Helicase (unwinds DNA), topoisomerase (relieves supercoiling), single-stranded binding proteins (prevent reannealing), and primase (synthesizes RNA primer).
  • Why are origins of replication rich in A-T base pairs?
    A-T base pairs have weaker interactions (2 hydrogen bonds) than G-C pairs (3 hydrogen bonds), making the DNA easier to unwind at origins.
  • What is the role of primase in DNA replication?
    Primase synthesizes a short RNA primer that provides a 3' OH for DNA polymerase to extend during replication.
  • Why is one strand of DNA replicated discontinuously?
    Because DNA polymerase can only synthesize 5' to 3', the lagging strand is synthesized discontinuously as Okazaki fragments moving opposite the replication fork.
  • What is the function of the DNA clamp?
    The DNA clamp increases DNA polymerase processivity by holding it onto the DNA template, allowing synthesis of thousands of nucleotides without dissociation.
  • How does DNA polymerase proofread during replication?
    DNA polymerase has 3' to 5' exonuclease activity that removes incorrectly paired nucleotides, checking base size and hydrogen bonding in the minor groove.
  • How are Okazaki fragments joined into a continuous strand?
    DNA ligase seals nicks between Okazaki fragments by forming phosphodiester bonds, using energy from ATP hydrolysis.
  • What are telomeres and why are they important?
    Telomeres are repetitive DNA sequences at chromosome ends that protect against loss of genetic information during replication; extended by telomerase.
  • What is the central dogma of molecular biology?
    Information flows from DNA to RNA (transcription) and from RNA to protein (translation).
  • What are the three main types of RNA in the central dogma?
    Messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).
  • Which DNA strand is used as the template for mRNA synthesis?
    The noncoding (antisense or template) strand is used by RNA polymerase to synthesize mRNA, which is complementary to it and identical to the coding (sense) strand except for U replacing T.
  • What is required for transcription initiation?
    Transcription factors bind promoter sequences (e.g., TATA box), recruit helicase to unwind DNA, and RNA polymerase binds to start RNA synthesis.
  • How does RNA polymerase elongate the RNA transcript?
    RNA polymerase adds nucleotides to the 3' end of the growing RNA strand using energy from hydrolysis of 2 phosphoanhydride bonds per nucleotide.
  • How is transcription elongation regulated?
    Phosphorylation of RNA polymerase disrupts its interaction with transcription factors, allowing elongation to proceed.
  • How does transcription termination occur?
    Termination can be RNA-dependent (RNA forms a helix disrupting RNA polymerase) or protein-dependent (Rho protein binds RNA and disrupts polymerase).
  • What modifications occur to eukaryotic mRNA after transcription?
    mRNA is processed by adding 5' cap and 3' poly-A tail, and introns are removed by splicing to produce mature mRNA ready for translation.