chapter three section two: introduction to nucleic acid structure

What are phosphodiester bonds?

Phosphodiester bonds are the chemical linkages that connect nucleotide residues in DNA and RNA. They form when a phosphate group forms ester bonds with two ribose sugar molecules.

Where specifically do phosphodiester bonds connect in nucleic acids?

Phosphodiester bonds connect the 3′ position of one nucleotide to the 5′ position of the neighboring nucleotide, creating the sugar-phosphate backbone of nucleic acids.

What is the basic structure of the DNA double helix?

The DNA double helix consists of two polynucleotide strands wound around each other. The sugar-phosphate backbones run along the outside of the helix, while the nitrogenous bases face inward.

How do the two strands in DNA interact with each other?

The two strands in DNA interact via hydrogen bonding between complementary bases on opposite strands: adenine pairs with thymine, and guanine pairs with cytosine.

What does "antiparallel" mean in the context of DNA structure?

Antiparallel means the two strands of DNA run in opposite directions: one strand runs 5′ to 3′, while the complementary strand runs 3′ to 5′.

How does RNA structure typically differ from DNA?

RNA is usually single-stranded, while DNA is typically double-stranded.

How does RNA achieve structural complexity despite being single-stranded?

RNA forms intramolecular base pairs within the same strand, creating stem-loop structures or more complex folded conformations when loops interact with each other.

What is a nucleotide residue?

A nucleotide residue is an individual nucleotide that has been incorporated into a polynucleotide chain through phosphodiester bonds.

What defines the 5′ end of a nucleic acid?

The 5′ end is the terminal residue whose C5′ (carbon 5 of the ribose) is not linked to another nucleotide.

What defines the 3′ end of a nucleic acid?

The 3′ end is the terminal residue whose C3′ (carbon 3 of the ribose) is not linked to another nucleotide.

How are nucleic acid sequences conventionally written?

By convention, nucleic acid sequences are written from left to right, starting from the 5′ end and ending at the 3′ end.

What are Chargaff's rules?

Chargaff's rules state that DNA has equal numbers of adenine and thymine residues and equal numbers of guanine and cytosine residues.

Do RNA molecules follow rules similar to Chargaff's rules?

No, there appear to be no strict rules governing the nucleotide composition of typical RNA molecules, unlike DNA.

What are tautomers in the context of nucleic acids?

Tautomers are readily interconverted isomers of the purine and pyrimidine bases that differ only in hydrogen positions.

What is the charge state of nucleic acids at physiological pH?

At physiological pH, nucleic acids exist as polyanions (negatively charged polymers).

Why do nucleic acids carry negative charges?

The phosphate groups in the sugar-phosphate backbone are acidic and lose protons (H⁺) in solution, giving each phosphate group a negative charge.

How does the structure of DNA minimize repulsion between phosphate groups?

In DNA, the sugar-phosphate chains run along the periphery while the bases occupy the core, keeping the negatively charged phosphates as far apart as possible.

How is the length of DNA molecules typically described?

DNA molecules are described in terms of the number of base pairs (bp) due to their great lengths.

What is a stem-loop structure in RNA?

A stem-loop structure (also called a hairpin) forms when complementary sequences within a single RNA strand pair with each other, creating a double-stranded stem region and a single-stranded loop region.

How can RNA molecules form complex three-dimensional structures?

RNA molecules form complex structures when different loop regions interact with each other, creating tertiary interactions beyond the basic stem-loop structures.

Can DNA form tertiary structures?

Yes, DNA does have a tertiary structure, which refers to the higher-order folding and organization of the double helix within the cell. This structure involves the further twisting and coiling of the double helix, including supercoiling and interactions with proteins like histones.

What is the functional significance of RNA's ability to form complex structures?

RNA's ability to form complex structures allows it to perform diverse functions, including catalytic activities (as in ribozymes), structural roles (as in ribosomes), and specialized functions (as in tRNAs).

Why is the antiparallel arrangement of DNA strands important?

The antiparallel arrangement is essential for processes like DNA replication, where each strand serves as a template for the synthesis of a new complementary strand.

What is the significance of the major and minor grooves in DNA?

These grooves provide access points for proteins to interact with specific DNA sequences without unwinding the helix, allowing for processes like transcription factor binding and gene regulation.