Lecture 28: DNA Packaging and the Nucleus

Comprehensive vocabulary flashcards for Lecture 28, covering prokaryotic vs. eukaryotic genome structure, histone modifications, chromatin organization, nuclear pore complex architecture, and Ran GTPase-mediated nucleocytoplasmic transport.

Prokaryotic Genome

A singular, circular, negatively supercoiled bacterial chromosome found within the nucleoid.

Eukaryotic Genome

A genome containing approximately $3.2\text{ billion}$ base pairs across $23$ different DNA molecules ($\times 2\text{ pairs} = 46$ chromosomes) that wrap around histones to form chromatin.

Histones

A family of basic proteins ($\text{H1}$, $\text{H2A}$, $\text{H2B}$, $\text{H3}$, and $\text{H4}$) responsible for packaging DNA into structural units called nucleosomes.

Histone Octamer

A protein core consisting of two copies each of $\text{H2A}$, $\text{H2B}$, $\text{H3}$, and $\text{H4}$ around which DNA wraps twice to produce a nucleosome core.

Euchromatin

Decondensed, loosely packed chromatin that is accessible to transcription machinery and actively available for gene transcription.

Heterochromatin

Highly condensed, tightly packed chromatin that is inaccessible and not available for gene transcription.

Histone Methyltransferase

An enzyme that adds a methyl group to specific lysine residues on histones, regulating chromatin compaction and gene expression.

Histone Demethylase

An enzyme that removes a methyl group from modified lysine residues on histones.

Histone Acetyltransferase

An enzyme that transfers an acetyl group onto histone lysine residues, typically promoting chromatin opening and gene accessibility.

Histone Deacetylase

An enzyme that removes acetyl groups from lysine residues on histones, allowing chromatin to recondense.

Chromatin Remodeling Proteins

Specialized proteins that reposition nucleosomes along the DNA strand to expose specific sequences and make DNA more accessible.

Nuclear Structure

The eukaryotic nuclear compartment consisting of a double-membrane nuclear envelope, nuclear lamina, nucleolus, chromatin, nucleoplasm, and nuclear pores.

Nuclear Pores

Channels spanning the nuclear envelope that control the bidirectional traffic of macromolecules between the nucleus and the cytoplasm.

Nucleoporins

Proteins that line the nuclear pore; segments extending into the channel contain repeats of phenylalanine ($\text{F}$) and glycine ($\text{G}$) known as $\text{FG}$ repeats.

Nuclear Localization Signal (NLS)

A peptide sequence rich in basic amino acids (lysine and/or arginine) that marks a protein for nuclear import; mutating a lysine to threonine via site-directed mutagenesis abolishes entry.

Importin

A soluble transport receptor protein that binds the $\text{NLS}$ on cargo proteins and facilitates passage through nucleoporin $\text{FG}$ repeats into the nucleus.

Ran-Dependent Nuclear Import Cycle

A pathway in which importin brings cargo inside, binds $\text{Ran-GTP}$ to release cargo, exits to the cytosol, and is freed when cytosolic $\text{GAP}$ hydrolyzes $\text{Ran-GTP}$ to $\text{Ran-GDP}$.

GAP (GTPase-Activating Protein)

A cytosolic factor that stimulates $\text{Ran-GTP}$ to hydrolyze its bound $\text{GTP}$ into $\text{Ran-GDP}$, releasing importin or exportin cargo in the cytosol.

GEF (Guanine Nucleotide Exchange Factor)

A nuclear factor that stimulates $\text{Ran-GDP}$ to release $\text{GDP}$ and bind $\text{GTP}$, maintaining a steep concentration gradient of high $\text{Ran-GTP}$ in the nucleus.

Nuclear Export Signal (NES)

A peptide sequence on nuclear adapter proteins (bound to RNAs like rRNA and miRNA) recognized by exportin to trigger export from the nucleus.

Exportin

A nuclear transport receptor that binds an $\text{NES}$-bearing protein complex simultaneously with $\text{Ran-GTP}$ to mediate nuclear egress.

Central Dogma

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

Gene

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

Coupled Transcription and Translation

A process characteristic of prokaryotes where polyribosomes bind and translate mRNA molecules while they are still being synthesized by RNA polymerase.