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Nucleic Acid Structure and Base Pairing (1B) - Bio & Biochem

  1. If double-stranded DNA is 40%40\% guanine, what percentage is cytosine?
    40%40\%. In double-stranded DNA, guanine pairs equally with cytosine, so their percentages match due to base pairing rules.
  2. Which atoms are connected by a 3′3'-5′5' phosphodiester linkage in nucleic acids?
    3′-OH3'\text{-OH} of one sugar to 5′5' phosphate of the next. The linkage forms between the 3' carbon of one nucleotide's sugar and the 5' phosphate of the adjacent one, creating the backbone.
  3. Identify the complementary RNA strand to 5′-AUGC-3′5'\text{-AUGC-}3' (write 5′→3′5' \rightarrow 3').
    5′-GCAU-3′5'\text{-GCAU-}3'. RNA complementarity uses A-U and G-C pairing, with the strand written in the conventional 5' to 3' orientation.
  4. Which bases are pyrimidines in nucleic acids?
    Cytosine, thymine, and uracil. Pyrimidines feature a single-ring structure, contrasting with the double-ring purines in nucleic acids.
  5. What is the correct directionality for writing a nucleic acid sequence by convention?
    5′→3′5' \rightarrow 3'. Sequences are conventionally written from 5' to 3' to reflect the direction of synthesis and transcription.
  6. What is the standard Watson–Crick base-pairing rule in DNA?
    A-T\text{A-T} and G-C\text{G-C}. Watson-Crick pairing in DNA follows complementary rules where A pairs with T and G with C via hydrogen bonds.
  7. How many hydrogen bonds form in a guanine–cytosine base pair?
    3 hydrogen bonds. G-C pairs involve three hydrogen bonds, providing greater stability compared to A-T pairs in nucleic acids.
  8. What type of bond links a base to the 1′1' carbon of the sugar in a nucleotide?
    β\beta-N-glycosidic bond. This bond connects the nitrogen of the base to the anomeric carbon of the sugar, forming nucleosides and nucleotides.
  9. Which base is present in DNA but not RNA under standard cellular conditions?
    Thymine. DNA incorporates thymine for pairing with adenine, unlike RNA which uses uracil in standard cellular processes.
  10. How many hydrogen bonds form in an adenine–thymine (or adenine–uracil) base pair?
    2 hydrogen bonds. A-T or A-U pairs form two hydrogen bonds, contributing to the stability of the double helix structure.
  11. What is meant by antiparallel strands in double-stranded DNA?
    One strand is 5′→3′5' \rightarrow 3' and the other is 3′→5′3' \rightarrow 5'. Antiparallel orientation allows complementary base pairing and maintains the double helix structure in DNA.
  12. What three components make up a nucleotide?
    Nitrogenous base + pentose sugar + phosphate. Nucleotides form from these components, with the base linked to sugar via glycosidic bond and phosphate attached to sugar.
  13. What is the sugar in DNA, and what key functional group difference distinguishes it from RNA sugar?
    Deoxyribose; lacks the 2′-OH2'\text{-OH} (has 2′-H2'\text{-H}). Deoxyribose in DNA lacks the hydroxyl at C2', making it more stable than ribose against hydrolysis.
  14. What defines the 5′5' end of a nucleic acid strand in terms of functional groups?
    Free 5′5' phosphate (or 5′-OH5'\text{-OH} if unphosphorylated). The 5' end features an exposed phosphate or hydroxyl on the 5' carbon, marking the start of the polynucleotide chain.
  15. Identify the complementary DNA strand to 5′-AGTC-3′5'\text{-AGTC-}3' (write 5′→3′5' \rightarrow 3').
    5′-GACT-3′5'\text{-GACT-}3'. Complementary strands follow Watson-Crick rules: A pairs with T, G with C, written in antiparallel 5' to 3' direction.
  16. What is the defining structural difference between a nucleoside and a nucleotide?
    Nucleotide = nucleoside + phosphate group(s). Nucleosides consist of a base and sugar, while nucleotides include an additional phosphate, defining their structural distinction.
  17. Which DNA groove (major or minor) provides more base-specific information for protein binding?
    Major groove. The major groove exposes more of the base edges, enabling specific interactions with proteins like transcription factors.
  18. What type of covalent bond forms the nucleic acid backbone between nucleotides?
    3′3'-5′5' phosphodiester bond. Phosphodiester bonds link nucleotides via sugar-phosphate backbone, providing structural integrity to DNA and RNA.
  19. Which bases are purines in nucleic acids?
    Adenine and guanine. Purines have a double-ring structure, distinguishing them from single-ring pyrimidines in nucleic acids.
  20. What is the standard Watson–Crick base-pairing rule in RNA (including RNA duplexes)?
    A-U\text{A-U} and G-C\text{G-C}. In RNA, uracil replaces thymine to pair with adenine, while guanine-cytosine pairing remains consistent.
  21. What is the sugar in RNA, and what functional group at the 2′2' position distinguishes it from DNA sugar?
    Ribose; has the 2′-OH2'\text{-OH} group. Ribose in RNA includes a hydroxyl at C2', enabling unique reactivity compared to deoxyribose in DNA.
  22. What defines the 3′3' end of a nucleic acid strand in terms of functional groups?
    Free 3′-OH3'\text{-OH} group. The 3' end has an exposed hydroxyl on the 3' carbon, allowing for chain extension during synthesis.
  23. If double-stranded DNA is 30%30\% adenine, what percentage is guanine?
    20%20\%. Adenine pairs with thymine, leaving the remaining percentage split equally between guanine and cytosine.
  24. Which base is present in RNA but not DNA under standard cellular conditions?
    Uracil. RNA uses uracil instead of thymine to pair with adenine, a key difference from DNA under normal conditions.

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