Key Concepts of Nucleic Acid Structures to Know for Biological Chemistry II

Nucleic acid structures, including DNA and RNA, are fundamental to understanding biological chemistry and biophysics. Their unique shapes and interactions play crucial roles in genetic information storage, expression, and regulation, impacting cellular functions and processes.

1. DNA double helix structure

   • Composed of two antiparallel strands of nucleotides twisted around each other.
   • The sugar-phosphate backbone forms the outer structure, while nitrogenous bases pair in the interior.
   • Stabilized by hydrogen bonds between complementary base pairs (A-T and G-C).

2. RNA single-stranded structure

   • Typically single-stranded, allowing for diverse shapes and functions.
   • Contains ribose sugar, which has an additional hydroxyl group compared to DNA.
   • Can form secondary structures through intramolecular base pairing.

3. A-form, B-form, and Z-form DNA

   • A-form: Right-handed helix, shorter and wider than B-form, often found in dehydrated conditions.
   • B-form: Most common form in physiological conditions, right-handed helix with a smooth backbone.
   • Z-form: Left-handed helix, zigzagged structure, may play a role in gene regulation.

4. Base pairing (Watson-Crick and Hoogsteen)

   • Watson-Crick pairing: A pairs with T (or U in RNA) and G pairs with C, forming stable hydrogen bonds.
   • Hoogsteen pairing: Alternative pairing that allows for different structural conformations, often seen in triple-stranded DNA.

5. Major and minor grooves

   • Major groove: Wider space between the two DNA strands, accessible for protein binding and recognition.
   • Minor groove: Narrower space, less accessible, but still important for interactions with small molecules and proteins.

6. Phosphodiester backbone

   • Composed of alternating sugar and phosphate groups, providing structural integrity to nucleic acids.
   • The phosphodiester bond links the 5' phosphate of one nucleotide to the 3' hydroxyl of another.

7. Nucleotide composition (sugar, phosphate, base)

   • Each nucleotide consists of a nitrogenous base (A, T, C, G in DNA; A, U, C, G in RNA), a sugar (deoxyribose in DNA, ribose in RNA), and a phosphate group.
   • The specific sequence of nucleotides encodes genetic information.

8. DNA supercoiling

   • Refers to the over- or under-winding of the DNA double helix, affecting its compactness and accessibility.
   • Supercoiling is important for DNA packaging in cells and plays a role in replication and transcription.

9. Hairpin loops and stem-loop structures

   • Hairpin loops: Formed when a single strand of nucleic acid folds back on itself, creating a double-stranded region.
   • Stem-loop structures: Common in RNA, consisting of a stem (double-stranded) and a loop (unpaired bases), important for function and stability.

10. G-quadruplex structures

    • Formed by guanine-rich sequences that can stack into a four-stranded structure.
    • Associated with telomeres and regulatory regions, potentially influencing gene expression and stability.

11. Triple-stranded DNA

    • Consists of three strands, often formed by Hoogsteen base pairing.
    • Can play roles in genetic regulation and stability, and is involved in certain biological processes.

12. Holliday junctions

    • Crucial intermediates in genetic recombination, formed during the exchange of DNA strands.
    • Characterized by a cross-shaped structure, allowing for the resolution of genetic material.

13. tRNA cloverleaf structure

    • A specific secondary structure of transfer RNA (tRNA) that resembles a cloverleaf.
    • Contains an anticodon region for amino acid recognition and acceptor stem for amino acid attachment.

14. Ribozyme structures

    • RNA molecules with catalytic activity, capable of performing biochemical reactions.
    • Their three-dimensional structures are critical for their function, often involving complex folding.

15. DNA-RNA hybrids

    • Formed during transcription when RNA is synthesized from a DNA template.
    • Important for various cellular processes, including gene expression and regulation.