Cell Biology: DNA Packaging and the Nucleus

Comprehensive vocabulary flashcards covering DNA packaging, chromatin structure and modification, nuclear structure, nuclear transport mechanisms, and the Central Dogma.

Nucleoid

The region containing the bacterial chromosome, which is a circular DNA molecule that is negatively supercoiled, extensively folded, and complexed to a few proteins.

Chromatin

The structural complex of eukaryotic DNA wrapped around histone proteins.

Histones

A family of basic proteins consisting of five types ($H1$, $H2A$, $H2B$, $H3$, and $H4$) that facilitate DNA packaging in eukaryotic cells.

Histone Octamer

The protein core of a nucleosome formed by two copies each of histones $H2A$, $H2B$, $H3$, and $H4$.

Nucleosome Core Particle

The structural unit consisting of DNA wrapped twice ($146\text{ base pairs}$) around a histone octamer, appearing as 'beads on a string.'

Linker DNA

The stretch of DNA ($> 50\text{ bp}$) that connects adjacent nucleosome core particles, yielding a total nucleosome repeat length of approximately $200\text{ bp}$.

Euchromatin

Decondensed, loosely packed chromatin that is actively available for transcription.

Heterochromatin

Highly condensed, tightly packed chromatin that is transcriptionally inactive and inaccessible to transcription machinery.

Histone Acetylation

A reversible post-translational modification catalyzed by histone acetyltransferases (and reversed by histone deacetylases) on specific lysine residues that leads to looser chromatin packing.

Histone Methylation

A post-translational modification catalyzed by histone methyltransferases (and reversed by histone demethylases) on specific lysine residues that leads to tighter chromatin packing.

Chromatin Remodeling Complex

A protein complex that repositions nucleosomes by sliding DNA around the histone core to make specific DNA sequences more accessible.

Nuclear Lamina

A meshwork of protein filaments lining the inner surface of the inner nuclear membrane that provides mechanical support and shape to the nucleus.

Nuclear Pore Complex (NPC)

A large cylindrical structure spanning the nuclear envelope (with an overall diameter of approximately $120\text{ nm}$) that regulates bidirectional transport of macromolecules between the nucleoplasm and cytosol.

Nucleoporins

The protein components that make up the nuclear pore complex, possessing unstructured regions extending into the channel enriched with FG repeats.

FG Repeats

Phenylalanine-glycine repeat motifs found in nucleoporins that create a flexible diffusion barrier preventing the passage of proteins larger than approximately $40\text{ kD}$.

Nuclear Localization Signal (NLS)

A specific sequence enriched with basic amino acid residues (lysine and/or arginine) that directs synthesized proteins into the nucleus.

Importin

A nuclear transport receptor protein that binds an NLS-bearing cargo protein in the cytosol and navigates through the FG repeats of the nuclear pore complex into the nucleus.

Nuclear Export Signal (NES)

A short amino acid sequence on cargo or RNA-binding proteins that targets them for export from the nucleus to the cytosol.

Exportin

A nuclear transport receptor protein that binds NES-containing cargo in a ternary complex with Ran-GTP to mediate export into the cytosol.

Ran-GEF (Guanine Nucleotide Exchange Factor)

An enzyme exclusively located in the nucleus that catalyzes the exchange of GDP for GTP on Ran, establishing a high nuclear concentration of Ran-GTP.

Ran-GAP (GTPase-Activating Protein)

An enzyme exclusively located in the cytosol that stimulates Ran to hydrolyze its bound GTP into GDP and inorganic phosphate ($\text{P}_i$), triggering cargo release.

Central Dogma of Molecular Biology

The framework describing the flow of genetic information: DNA sequence is transcribed into RNA sequence, which is then translated into an amino acid sequence to form a protein.

Gene

The functional unit of heredity, defined as a sequence of DNA that directs the synthesis of a specific polypeptide.

Polyribosome

A cluster of multiple ribosomes simultaneously translating a single mRNA molecule in a linear sequence.

Coupled Transcription and Translation

The simultaneous transcription of DNA and translation of the resulting mRNA occurring in prokaryotes due to the absence of a nuclear envelope separating the two processes.