Nucleotides and Nucleic Acids (5D) - Chem & Physics

1. What base is found in DNA but not in RNA?

   Thymine. DNA incorporates thymine for greater stability against cytosine deamination compared to uracil.

2. How many hydrogen bonds are in a $G$-$C$ base pair in DNA?

   $3$ hydrogen bonds. Three hydrogen bonds between guanine and cytosine provide stronger pairing in DNA.

3. Which atoms are connected by the N-glycosidic bond in nucleotides?

   Sugar $1'$ carbon to base $N$ (purine $N^9$, pyrimidine $N^1$). The glycosidic bond connects the anomeric carbon of the sugar to the nitrogen of the base.

4. Which nitrogenous bases are aromatic and therefore absorb UV light near $260\,\text{nm}$?

   All nucleobases (purines and pyrimidines) are aromatic. Aromaticity confers planarity and UV absorbance, useful for quantifying nucleic acids.

5. Which end of a nucleic acid strand typically has the free hydroxyl group?

   The $3'$ end. The 3' end hydroxyl is the site for chain elongation during nucleic acid synthesis.

6. Which functional groups are joined to form a $3'$-$5'$ phosphodiester bond?

   $3'$-$OH$ of one sugar to $5'$ phosphate of the next nucleotide. This linkage ensures the 5' to 3' polarity in nucleic acid strands.

7. Which DNA base pair is expected to increase duplex melting temperature ($T_m$)?

   Higher $G$-$C$ content. G-C pairs form three hydrogen bonds, increasing stability and thus raising the melting temperature.

8. What is the standard base-pairing rule in RNA?

   $A$ pairs with $U$; $G$ pairs with $C$. RNA uses uracil to pair with adenine, enabling specific interactions in RNA structures.

9. Which bases are purines in nucleic acids?

   Adenine and guanine. Purines are double-ringed bases essential for DNA and RNA structure and function.

10. Which end of a nucleic acid strand typically has the free phosphate group?

    The $5'$ end. The 5' end phosphate is where synthesis begins and caps or modifications often occur.

11. What is the standard base-pairing rule in DNA?

    $A$ pairs with $T$; $G$ pairs with $C$. Complementary base pairing via hydrogen bonds stabilizes the DNA double helix.

12. How many hydrogen bonds are in an $A$-$T$ base pair in DNA?

    $2$ hydrogen bonds. Two hydrogen bonds form between adenine and thymine, contributing to DNA stability.

13. What are the three components of a nucleotide?

    Nitrogenous base + pentose sugar + phosphate group. Nucleotides form the building blocks of nucleic acids, combining these components via covalent bonds.

14. What is the structural difference between a nucleoside and a nucleotide?

    Nucleoside lacks phosphate; nucleotide includes phosphate. Nucleosides are precursors to nucleotides, with the phosphate addition enabling polymerization into nucleic acids.

15. Which bases are pyrimidines in nucleic acids?

    Cytosine, thymine, and uracil. Pyrimidines are single-ringed bases that pair with purines in nucleic acid duplexes.

16. Which bond forms the nucleic acid sugar-phosphate backbone?

    $3'$-$5'$ phosphodiester bond. Phosphodiester bonds link nucleotides, creating the directional backbone of DNA and RNA.

17. What is the key structural difference between purines and pyrimidines?

    Purines have two rings; pyrimidines have one ring. The ring structure affects base pairing and stacking interactions in nucleic acids.

18. What base is found in RNA but not in DNA?

    Uracil. RNA uses uracil instead of thymine to pair with adenine during transcription and translation.

19. What is the major chemical reason RNA is less stable than DNA in base?

    RNA has a $2'$-$OH$ that promotes backbone hydrolysis. The 2'-OH in RNA enables nucleophilic attack on the phosphodiester bond in alkaline conditions.

20. What is the chemical difference between ribose and deoxyribose?

    Deoxyribose has $H$ at $2'$; ribose has $OH$ at $2'$. The absence of the 2'-OH in deoxyribose enhances DNA stability by preventing hydrolysis.

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