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Biochemistry - Nucleic Acids and DNA Structure

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  • What are the two types of nitrogenous bases in nucleic acids?
    Purines (adenine, guanine) with a fused six- and five-member ring, and pyrimidines (cytosine, thymine, uracil) with a single six-member ring.
  • What sugar is found in RNA and DNA nucleotides?
    Ribose in RNA and 2’-deoxyribose in DNA; the difference is a hydroxyl group at the 2’ carbon in ribose.
  • Define a nucleoside.
    A molecule composed of a sugar (ribose or deoxyribose) and a nitrogenous base connected by a β-N-glycosidic bond.
  • How are nucleotides formed?
    By adding one or more phosphate groups to a nucleoside, forming a phosphoester bond with the 5’-OH of the sugar.
  • What is the backbone of DNA composed of?
    Alternating units of 2’-deoxyribose sugar and phosphate groups linked by 3’-5’ phosphodiester bonds.
  • Describe the base pairing rules in DNA.
    Adenine pairs with thymine via two hydrogen bonds, and cytosine pairs with guanine via three hydrogen bonds.
  • What is the structure of the DNA double helix?
    Two antiparallel strands forming a right-handed helix with a diameter of 2.0 nm and one turn every 3.4 nm (10 base pairs).
  • What forces stabilize the DNA double helix?
    Hydrogen bonding between base pairs and base stacking interactions involving van der Waals and dipole-dipole forces.
  • What is the difference between B-DNA, A-DNA, and Z-DNA?
    B-DNA is right-handed with 10 bps/turn; A-DNA is right-handed, wider, with 11 bps/turn; Z-DNA is left-handed with 12 bps/turn and a zigzag backbone.
  • What is a palindrome in DNA sequences?
    A sequence with twofold symmetry that reads the same forward and backward on complementary strands, capable of forming hairpin or cruciform structures.
  • What is the central dogma of molecular biology?
    The flow of genetic information: DNA → RNA → Protein via replication, transcription, and translation.
  • What is semiconservative DNA replication?
    Each daughter DNA molecule contains one parental strand and one newly synthesized strand.
  • In which direction does DNA polymerase synthesize DNA?
    In the 5’ to 3’ direction, adding nucleotides to the 3’-OH end of the growing strand.
  • What are Okazaki fragments?
    Short DNA fragments synthesized discontinuously on the lagging strand during DNA replication.
  • What is the role of DNA ligase in replication?
    It seals the phosphodiester bonds between Okazaki fragments to form a continuous DNA strand.
  • What is the function of RNA polymerase in transcription?
    To synthesize RNA from a DNA template by catalyzing phosphodiester bond formation between ribonucleotides.
  • What are the key promoter elements in prokaryotic transcription?
    The -10 (Pribnow box) and -35 regions upstream of the transcription start site, which bind RNA polymerase.
  • What is the wobble hypothesis in genetic code translation?
    The third base of a codon pairs loosely with the first base of the tRNA anticodon, allowing some tRNAs to recognize multiple codons.
  • What is the role of aminoacyl-tRNA synthetase?
    To attach the correct amino acid to its corresponding tRNA, forming aminoacyl-tRNA for protein synthesis.
  • What are the three stages of translation?
    Initiation: assembly of ribosome, mRNA, and initiator tRNA; Elongation: peptide chain extension; Termination: release of completed polypeptide.