Molecular Biology: DNA Structure, Replication, and Transcription

Vocabulary practice flashcards covering nucleic acid biochemistry, eukaryotic and prokaryotic DNA organization, replication machinery, and transcription mechanisms.

Nucleotide

A nucleic acid monomer formed by the addition of a phosphate group to a nucleoside component.

Purine-Pyrimidine Base Pairing

Hydrogen bonding between complementary purine and pyrimidine bases occurring in standard pairs of either $2$ or $3$ bonds, determining GC and AT content ratios.

$2'\text{-OH}$ Position

The specific carbon location on the ribose pentose sugar where RNA carries a hydroxyl group that is missing in DNA.

Pentose Sugar Differences

The structural distinction between the sugars of DNA and RNA, where DNA is missing one hydroxyl group compared to RNA.

$5'$ and $3'$ Ends

Terminal orientations of DNA and RNA strands that define strand directionality based on phosphate group linkage.

Prokaryotic Origin of Organelles

The evolutionary theory supported by the observation that mitochondria and chloroplasts maintain their genomes as circular DNA molecules.

Polytene Chromosomes

Specialized chromosomes characterized under microscopy by having regions of loosely bound DNA adjacent to tightly bound regions.

Histones

Proteins that aid in folding and compacting DNA to allow it to fit within the cell.

Heterochromatin

Chromosomal regions that consistently maintain a high degree of coiling and compaction.

Repetitive DNA

Repeated nucleotide sequences that are found distributed throughout the entire genome.

DNA Ligase

The enzyme used during lagging strand extension to join Okazaki fragments by sealing them with a phosphodiester bond.

Bacterial vs. Eukaryotic DNA Structure

The primary structural divergence between bacterial and eukaryotic genomes, defined by circular versus linear genomic architecture.

Single-Stranded Binding Proteins

Proteins whose primary replication function is to protect exposed single-stranded genetic information from degradation or re-annealing.

Polymerase Directionality

The directional activity of polymerases in adding or removing nucleotides, defined by the carbon position and functional groups (hydroxyl or phosphate).

DNA Gyrase (Topoisomerase)

The enzyme responsible for maintaining the structural integrity of the DNA double helix by resolving twists and knots during replication.

Non-Template Strand

The coding DNA strand whose sequence is nearly identical to the transcribed RNA, differing only because thymine (T) nucleotides are interchanged with uracil (U).

TATA Box

A conserved promoter DNA sequence recognized during transcription initiation in eukaryotes.

Rho-Independent Transcription Termination

A bacterial termination mechanism that utilizes GC-rich stem-loop structures to destabilize AU base pairing and release the nascent RNA transcript.

Central Dogma of Molecular Biology

The foundational principle stating that genetic information flows from DNA to RNA to protein via transcription and translation.

Sigma Factor

A bacterial transcription protein that associates with RNA polymerase to enable specific promoter recognition and the initiation of transcription.

Phosphodiester Bond

The covalent chemical bond linking nucleotides together into a continuous polymer strand.

Telomerase

An enzyme required to maintain telomeres because linear DNA molecules shrink due to the end-replication problem of linear chromosomes.

DNA Polymerase Holoenzyme Recognition Sites

Primed regions with double-stranded sequences recognized as start points for replication synthesis.

RNA Polymerase II

The eukaryotic enzyme primarily responsible for the synthesis of messenger RNA (mRNA).

Acentric Chromosome Fragments

Chromosome pieces lacking centromeres that fail to segregate properly, resulting in the loss of genetic information during cell division.

Negative Charge of Nucleic Acids

The electrostatic property of the DNA and RNA phosphate backbone that facilitates histone binding in DNA packaging and allows separation in gel electrophoresis.