Chapter 4 Nucleic Acids, Sections 4.1-4.3

Flashcards covering the structure of nucleic acids (DNA and RNA), their components (bases, sugars, phosphates), historical discoveries, properties like supercoiling, and different conformational forms.

Nucleic Acids (NAs)

Polymers of nucleotides.

Nucleotides

Comprised of three main components: a base (purine or pyrimidine), a sugar molecule (deoxyribose or ribose), and a phosphate group.

Bases

Aromatic heterocyclic molecules that vary between nucleotides, classified into Purines and Pyrimidines based on their ring structure.

Purines

One of the two primary classes of nitrogenous bases found in nucleotides, characterized by a double-ring structure (e.g., Adenine, Guanine).

Pyrimidines

One of the two primary classes of nitrogenous bases found in nucleotides, characterized by a single-ring structure (e.g., Cytosine, Thymine, Uracil).

Tautomerization (of bases)

The process where purine and pyrimidine bases can exist in different isomeric forms, such as Keto-Enol or Imino-Amino.

Nucleosides

A molecule consisting of a nitrogenous base covalently linked to a pentose sugar (ribose for RNA, deoxyribose for DNA).

Phosphodiester Linkage

The covalent bond that links nucleotides together to form nucleic acid polymers, connecting the 3' carbon of one sugar to the 5' carbon of another via a phosphate group.

Nucleotide Residue

An individual nucleotide unit within a nucleic acid polymer (DNA or RNA).

Dinucleotide

A molecule composed of two nucleotides linked together by a phosphodiester bond.

Oligonucleotide

A short polymer consisting of a few nucleotides linked together.

RNA Stability

RNA is readily hydrolyzed in basic conditions due to the presence of the 2' hydroxyl group on its ribose sugar.

Avery's Experiment (1944)

A landmark experiment demonstrating that DNA, not protein, was the genetic material responsible for transforming nonpathogenic bacteria into pathogenic ones.

Hershey-Chase Experiment (1952)

An experiment using radioactive sulfur and phosphorus to confirm that DNA, not protein, carries the genetic information in bacteriophages.

Chargaff's Rules

Observations that in DNA, the amount of adenine equals thymine (%A = %T), and the amount of guanine equals cytosine (%G = %C), implying that the total purines equal total pyrimidines (%A + %G = %T + %C).

B-form DNA

The most common structural form of DNA in cells, characterized by a right-handed double helix where bases occupy the core and the sugar-phosphate chains are on the outside.

Watson-Crick Pairing

Specific hydrogen bonding between complementary bases in DNA: Adenine pairs with Thymine (two H-bonds), and Guanine pairs with Cytosine (three H-bonds).

Major Groove

The wider and deeper groove on the surface of the DNA double helix, providing a site for protein binding and specific recognition of base sequences.

Minor Groove

The narrower and shallower groove on the surface of the DNA double helix, also involved in protein interactions but typically less specific.

Antiparallel Strands (DNA)

The characteristic where the two strands of the DNA double helix run in opposite 5' to 3' directions.

DNA Double Helix Diameter

Approximately 20 Å.

Rise per turn (DNA)

The axial distance covered by one complete turn of the DNA double helix, which is approximately 34 Å and contains 10 base pairs.

Melting Temperature (Tm)

The temperature at which half of a double-stranded DNA sample denatures or unwinds into single strands; higher GC content leads to a higher Tm.

Hydrophobic Effect (DNA)

The primary force driving the hydrophobic bases to stack in the interior of the DNA double helix, excluded from water, while the hydrophilic sugar-phosphate backbone interacts with water on the outside.

Base Stacking

The arrangement of bases in the DNA double helix where they stack on top of each other, stabilized by π-π van der Waals interactions, with a distance of 3.4 Å between bases.

A-form DNA

An alternative helical form of DNA, wider and shorter than B-form, often seen in double-stranded RNA or DNA-RNA hybrids under dehydrating conditions.

Z-DNA

A left-handed double helical form of DNA, characterized by a zigzag backbone, where pyrimidines are in anti-conformation and purines are in syn-conformation, less common in vivo than B-DNA.

Syn/Anti Conformation

Refers to the spatial orientation of the nitrogenous base relative to the sugar in a nucleoside; 'anti' is more common in B-DNA, while 'syn' can occur in Z-DNA purines.

Supercoiled DNA

A compact, highly coiled form of circular DNA, essential for packaging long DNA molecules within cells.

Relaxed DNA

A less coiled and extended form of DNA compared to supercoiled DNA.

Plasmid

A small, circular, extrachromosomal DNA molecule found in bacteria and some eukaryotes, capable of autonomous replication.

Linking Number (L)

A topological property of closed circular DNA, representing the total number of times one DNA strand crosses the other.

Twist (T)

The number of helical turns of one DNA strand around the duplex axis.

Writhe (W)

The number of superhelical turns or crossovers of the DNA duplex axis upon itself.

Topoisomerases

Enzymes that regulate the state of DNA supercoiling by breaking and rejoining DNA strands; they often require ATP hydrolysis as energy input to introduce or remove supercoils.

Gel Electrophoresis (DNA)

A laboratory technique used to separate DNA molecules based on their size and conformation (e.g., supercoiled, relaxed); smaller or more compact DNA molecules migrate faster through the gel.

Ethidium Bromide

A fluorescent dye used in gel electrophoresis to visualize DNA by intercalating into the double helix.

Single-stranded RNA

Most naturally occurring RNA molecules are single-stranded, often forming complex secondary and tertiary structures through internal base pairing (self-complementarity).

Transfer RNA (tRNA)

A type of RNA molecule that carries specific amino acids to the ribosome during protein synthesis, characterized by extensive intramolecular complementarity that folds into a distinct tertiary structure (e.g., cloverleaf).