Properties of DNA and Catalytic RNAs Flashcards

Vocabulary practice flashcards generated from Lecture 3 covering DNA stability, denaturation, RNA structures, catalytic ribozymes, and functional non-coding RNAs.

Base Stacking

The primary interaction driving double-stranded DNA thermodynamic stability, resulting from hydrophobic interactions and cumulative van der Waals forces between stacked nitrogenous bases in aqueous solution.

Hydrophobic Effect

The thermodynamic tendency of non-polar nitrogenous base molecules to aggregate together in aqueous solution, minimizing exposure to water and facilitating base stacking.

DNA Complementarity

The molecular base-pairing specificity governed by hydrogen bonding between nitrogenous bases, where adenine pairs with thymine via $2$ hydrogen bonds and guanine pairs with cytosine via $3$ hydrogen bonds.

DNA Denaturation

The reversible process where thermal energy (temperatures above physiological range, e.g., $100^\text{o}\text{C}$) or alkaline pH conditions disrupt hydrogen bonds, causing double-stranded DNA to separate into single strands without breaking covalent phosphodiester bonds.

DNA Renaturation

The reversible process, also known as annealing, where complementary single strands of denatured DNA come together upon slow cooling to reform the double helix.

DNA Hybridization

The process where denatured single strands of DNA or RNA from two different source molecules pair and anneal together upon cooling to form a hybrid double-stranded molecule.

Hyperchromic Shift

The sharp increase in UV light absorption at $260\text{ nm}$ observed when double-stranded DNA denatures into single-stranded DNA due to reduced base stacking and increased conformational flexibility.

Melting Temperature ($T_m$)

The midpoint temperature of the hyperchromic shift curve at which $500\%$ of a DNA sample is double-stranded and $50\%$ is single-stranded.

2-Deoxyribose

The pentose sugar present in DNA nucleotides that lacks a hydroxyl group ($\text{-OH}$) at carbon position $\text{C2'}$, having a hydrogen atom instead.

Ribose

The pentose sugar present in RNA nucleotides containing an ionizable hydroxyl group ($\text{-OH}$) at carbon position $\text{C2'}$, making RNA chemically active and susceptible to intramolecular cleavage.

Stem-Loop

An RNA secondary structure formed when two nearby complementary sequences within the same molecule base-pair to form a double-stranded stem with an unpaired single-stranded loop region.

Pseudoknot

A complex RNA secondary structure created when unpaired bases within a stem-loop loop region base-pair with a non-contiguous complementary sequence elsewhere on the RNA molecule.

G:U Wobble Base Pair

A non-Watson-Crick base pair formed between guanine and uracil in RNA that possesses thermostability comparable to A:T pairs and aids in forming complex RNA secondary and tertiary structures.

Transesterification Reaction (RNA Cleavage)

An intramolecular RNA cleavage reaction initiated when the deprotonated $2'\text{-OH}$ oxyanion ($\text{O}^-$) executes a nucleophilic attack on the adjacent $3'$ phosphate group, breaking the phosphodiester backbone and yielding a $2',3'\text{-cyclic}$ phosphate.

RNase P

A eukaryotic ribonucleoprotein ribozyme that exclusively uses its catalytic RNA subunit to cleave the extra $5'$ precursor sequence from pre-tRNA to produce mature tRNA.

Group I Self-Splicing Introns

Self-splicing RNA introns that initiate self-excision using an external free guanosine ($\text{G}$) nucleotide that performs a nucleophilic attack on the $5'$ splice junction.

Group II Self-Splicing Introns

Self-splicing RNA introns that initiate self-excision using the $2'\text{-OH}$ group of an internal adenosine ($\text{A}$) nucleotide within the intron to attack the $5'$ splice junction, forming a lariat structure.

Lariat Structure

A circular branched intron intermediate released during Group II self-splicing, wherein an internal adenine nucleotide is covalently bound to three phosphodiester linkages at its $\text{5'}$, $\text{3'}$, and $\text{2'}$ hydroxyl positions.

Rolling Circle Transcription

A replication process used by viroids wherein host RNA polymerase repeatedly transcribes a small circular RNA template without stopping, producing long concatemers that are subsequently cleaved into functional monomers by embedded ribozyme domains.

Hammerhead Ribozyme

A catalytic RNA domain consisting of three stem-loops that facilitates specific phosphodiester cleavage between stem I and stem III via nucleophilic attack of a $2'\text{-OH}$ group on a target $3'$ phosphate.

siRNA (Short Interfering RNA)

Functional non-coding RNAs that bind target mRNAs with perfect sequence complementarity and recruit host cellular complexes to cleave and degrade target mRNA, blocking protein expression.

miRNA (Micro Interfering RNA)

Functional non-coding RNAs that pair with target mRNAs via perfect or partial complementarity to repress translation or induce mRNA degradation at the post-transcriptional level.

XIST

A long non-coding RNA (lncRNA) transcribed from the XIST locus that induces heterochromatin formation over an entire X chromosome, silencing gene expression during mammalian dosage compensation.

TSIX

A long non-coding RNA transcribed in the antisense direction from the XIST locus that functions as a direct transcriptional repressor of XIST, preventing X-inactivation and maintaining chromosome activity.

HOTAIR

A long non-coding RNA encoded in intergenic regions between HOX genes that acts as a scaffold to assemble chromatin-modifying complexes that repress target gene transcription.

Long Non-Coding RNA (lncRNA)

Functional non-coding RNA transcripts longer than 200 nucleotides that are not translated into proteins but regulate expression, chromatin structure, and molecular scaffolding.