Nucleus and Chromosomes

The nucleus of a non-dividing cell, encompassing the $\text{G}1$, $\text{S}$, and $\text{G}2$ phases of the cell cycle.

Interphase Cell Nucleus

The pathological dissolution or degradation of the nucleus, significant in tumor diagnosis.

Karyolysis

The pathological condensation and shrinkage of the nucleus, significant in tumor diagnosis.

Pyknosis

The pathological fragmentation of the nucleus, significant in tumor diagnosis.

Karyorrhexis

The nuclear material composed of DNA and proteins (histones) organized as euchromatin or heterochromatin.

Chromatin

The non-membranous nuclear region and primary site of $\mathbf{rRNA}$ synthesis and initial ribosomal assembly.

Nucleolus

The double-membrane system (inner and outer membranes) perforated by nuclear pores that surrounds the nucleus.

Nuclear Envelope

The amorphous material enclosed by the nuclear envelope, exclusive of the chromatin and the nucleolus.

Nucleoplasm

The characteristic staining of the nucleus (e.g., with hematoxylin) primarily due to the phosphate groups of the $\text{DNA}$ in chromatin.

Basophilic Nucleus

The biochemical classification of chromatin, consisting of $\text{DNA}$ and associated proteins.

Nucleoprotein Complex

The unique feature that condenses $\text{DNA}$ while still permitting the transcriptional machinery to access specific gene regions.

Chromatin Packaging

The five basic proteins ($\text{H1}, \text{H2A}, \text{H2B}, \text{H3}, \text{H4}$) with high lysine and arginine content that are highly conserved across species.

Histone Proteins

The highly condensed, densely staining form of chromatin that is generally transcriptionally inactive.

Heterochromatin

The dispersed, light-staining form of chromatin that contains the genes actively undergoing transcription.

Euchromatin

Cell types (e.g., neurons, hepatocytes) where euchromatin is the predominant form.

Metabolically Active Cells

Cell types (e.g., circulating lymphocytes, sperm, plasma cells) where heterochromatin predominates.

Metabolically Inactive Cells

Heterochromatin located at the periphery of the nucleus, closely associated with the inner nuclear membrane.

Marginal Chromatin

Discrete, irregular bodies of heterochromatin found throughout the nucleoplasm.

Karyosomes

Heterochromatin that physically associates with the nucleolus.

Nucleolar-Associated Chromatin

A histochemical stain that reacts with the deoxyribose of $\text{DNA}$ and effectively stains heterochromatin.

Feulgen Stain

Examples include $\text{Hoechst dyes}$ and $\text{Propidium iodide}$, used to stain $\text{DNA}$.

Fluorescent Vital Dyes

The discrete, non-random location occupied by the chromatin of each chromosome within the interphase nucleus.

Chromosome Territories

The highly condensed form of chromatin (e.g., at $\text{telomeres and centromeres}$) made of short $\text{DNA}$ tandems that are virtually never transcribed.

Constitutive Heterochromatin

Chromosomal regions that are specifically inactivated in a particular cell type (e.g., during embryonic development) as a means of gene control.

Facultative Heterochromatin

The smallest unit of chromatin structure, represented by $\mathbf{10\text{-nm}\text{-diameter}}$ particles.

Nucleosomes

The formation of nucleosomes (coiling of the $\text{DNA}$ around the protein core), visualized as "beads on a string."

First Level of Chromatin Folding

The protein core of the nucleosome, formed by joining two $\text{H2A–H2B}$ dimers and two $\text{H3–H4}$ dimers.

Histone Octamer

Approximately $\mathbf{146}$ nucleotide pairs wrapped around the histone octamer.

DNA Wrapping in Nucleosome

The extended configuration of nucleosomes, representing the "beads on a string" structure.

11 nm Fiber

The result of tight packing and coiling of nucleosomes.

30 nm Chromatin Fiber

The configuration ($\mathbf{300 \text{ nm} \text{ fiber}}$) of the $\mathbf{30 \text{ nm}}$ chromatin fiber seen when mitotic chromosomes are experimentally unraveled.

Looped Domains

Quantifies chromosome compaction: $\text{Total extended DNA length} \div \text{length of the packaged chromatin fiber}$.

DNA Packing Ratio

The $\text{DNA}$ coiling state that is generally relaxed and allows for gene synthesis (transcription/replication).

Negative Supercoiling

The tight $\text{DNA}$ coiling state that strictly inhibits access to $\text{DNA}$.

Positive Supercoiling

Enzymes that catalyze the winding and unwinding reactions necessary to regulate $\text{DNA}$ supercoiling.

Topoisomerases I and II

The mechanism by which the nuclear envelope helps organize chromatin by binding heterochromatin near nuclear pores.

Chromatin Loop Binding

The chemical description of a chromosome formed from $\text{DNA}$ coiled around histone proteins.

Nucleoprotein

The fifth histone that helps link nucleosomes together to facilitate the formation of the $\mathbf{30 \text{ nm}}$ chromatin fiber.

Histone $\text{H1}$

The classification of non-histone chromosomal proteins (in contrast to the basic histones).

Acidic Proteins

The specific $\text{DNA}$ form found in the nucleolus, which is transcriptionally active.

$\text{rRNA}$ Genes

Proteins located within the nucleolus that help control the progression of the cell cycle.

Regulatory Cell-Cycle Proteins

A $\text{p}53$ binding protein located in the nucleolus that regulates the cell cycle and decreases as cellular differentiation progresses.

Nucleostemin

The role of the nucleolus, as viruses can target and use its components to favor their own transcription and translation.

Viral Replication Target

Abolishes the basophilia and metachromasia staining of the nucleolus, confirming the staining is due to $\text{RNA}$ phosphate groups.

Ribonuclease ($\text{RNAse}$) effect

The characteristic staining result of the nucleolus due to the very low concentration of its $\text{DNA}$.

Feulgen-Negative Nucleolus

Nuclear bodies involved in the maturation and processing of $\text{small nucleolar RNA}$ ($\text{snoRNA}$) and $\text{small nuclear RNA}$ ($\text{snRNA}$).

Cajal Bodies ($\text{CBs}$)

$\text{RNA}$- and protein-rich nuclear bodies (interchromatin granule clusters) necessary for splicing of $\text{mRNA}$ precursors into mature $\text{mRNAs}$.

Speckles

Nuclear bodies involved in programmed cell death, genomic stability, antiviral effects, and cell division control.

$\text{PML}$ Bodies

Tubular invaginations of the nuclear envelope that project into the internal nuclear space, increasing the contact area with the inner nuclear membrane.

Nucleoplasmic Reticulum

The experimental observation suggesting the nuclear matrix is involved in anchoring chromatin fibers at $\text{DNA/RNA}$ synthesis sites.

$\text{H}^3$-thymidine association

The nucleolar region containing $\text{DNA}$ loops of $\text{rRNA}$ genes, $\text{RNA}$ polymerase I, and transcription factors (on chromosomes $\mathbf{13, 14, 15, 21, 22}$).

Fibrillar Centers

The nucleolar region containing ribosomal genes that are actively undergoing $\text{RNA}$ transcription.

Fibrillar Material ($\text{Pars Fibrosa}$)

The nucleolar region that represents the site of initial ribosomal assembly and contains densely packed, pre-ribosomal particles.

Granular Material ($\text{Pars Granulosa}$)

A stretch of $\text{DNA}$ carrying multiple copies of $\text{rRNA}$ genes, essential for nucleolus function.

Nucleolus Organizer Region ($\text{NOR}$)

The space separating the inner and outer nuclear membranes, which is continuous with the $\text{rER}$ lumen.

Perinuclear Cisternal Space

The $\mathbf{70\text{-}80 \text{ nm}}$ openings in the nuclear envelope that mediate active transport between the nucleus and cytoplasm.

Nuclear Pores

The nuclear membrane component that is continuous with the $\text{rER}$ and often has polyribosomes attached to its cytoplasmic side.

Outer Nuclear Membrane

The nuclear membrane component adjacent to the nuclear lamina and containing specific lamin receptors and lamina-associated proteins.

Inner Nuclear Membrane

A rigid network of Intermediate Filaments ($\text{Lamins A, C}$) attached to the inner nuclear membrane that serves as scaffolding.

Nuclear Lamina

The specific intermediate filament proteins that construct the nuclear lamina.

Lamins A and C

The lamin protein that is crosslinked to the inner nuclear membrane via its interactions with lamin receptors.

Lamin B Protein

The process that occurs during mitosis, allowing the nuclear envelope to break down and reform.

Lamins Disassembly/Reassembly

Specific examples of lamin receptors found on the inner nuclear membrane.

Emerin, Nurim, LBR

Clinical condition caused by a single base mutation in a lamin gene, leading to premature aging symptoms and severe nuclear shape abnormalities.

Hutchinson–Gilford Progeria

Muscle wasting disease associated with mutations in lamins ($\text{A/C}$) or lamin receptors ($\text{Emerin}$).

Emery-Dreifuss Muscular Dystrophy

The collective term for the approximately 30 different proteins that form the structure of the Nuclear Pore Complex ($\text{NPC}$).

Nucleoporins

The structure within the center of the nuclear pore that facilitates nuclear translocation (importation/exportation).

Central Plug/Transporter

The molecular energy requirement for the active, regulated transport of large molecules through the $\text{NPC}$.

$\text{GTP}$-Energy Dependent

The attached signal sequence required on large proteins produced in the cytoplasm (e.g., histones) for their passage into the nucleus.

Nuclear Localization Signal ($\text{NLS}$)

A soluble cytosolic receptor that binds to $\text{NLS}$-proteins, directing them from the cytoplasm to the $\text{NPC}$ for nuclear import.

Importin

The attached signal sequence on $\text{RNA}$ proteins that binds to $\text{exportin}$ and $\text{Ran-GTP}$ for movement out of the nucleus.

Nuclear Export Sequence ($\text{NES}$)

A protein that moves molecules (e.g., ribosomal subunits, $\text{NES}$-proteins) from the nucleus into the cytoplasm through the $\text{NPC}$.

Exportin

The structure anchored by the nucleoplasmic ring of the $\text{NPC}$, assembled from eight thin filaments joined distally by a terminal ring.

Nuclear Basket/Cage

The approximate length of the entire $\text{DNA}$ structure in a human cell, requiring high coiling and packaging.

DNA $\mathbf{1.8 \text{ meters}}$ length

The total number of chromosomes found in a typical human cell.

$\mathbf{46}$ Chromosomes

The scientific endeavor completed in 2003 that sequenced the human genome ($\mathbf{2.85\text{B}}$ base pair consensus sequence).

Human Genome Project

A union of genomic sequences encoding a coherent set of potentially overlapping functional products.

New Gene Definition

The implication of the new gene definition, where a gene for a product may exist in $\mathbf{1, 3}$ or more copies, not always two.

Copy Number Variations ($\text{CNVs}$)

The histone combinations that form tight dimers, essential for assembling the nucleosome octamer.

$\text{H3–H4}$ and $\text{H2A–H2B}$ Complexes

The observation that histone sequences are highly conserved, exemplified by minimal difference between pea and cow Histone $\text{H4}$.

Amino Acid Conservation

The process where the $\text{DNA}$ double helix separates into two single strands (e.g., by heat).

$\text{DNA}$ Denaturation

The process where separated $\text{DNA}$ single strands spontaneously re-associate to reform the double helix (reannealing).

$\text{DNA}$ Renaturation

The area located at each end of the chromosome, which shortens with each cell division.

Telomere

The primary constriction where sister chromatids are joined, and the kinetochore is assembled.

Centromere

The protein structure assembled at the centromere that serves as the attachment site for spindle fibers during mitosis.

Kinetochore

The short tandem repeated $\text{DNA}$ sequences that make up the constitutive heterochromatin of the centromere (e.g., human alphoid satellite repeat).

$\text{CENs}$ (Centromere Repeats)

A specific centromere-specific histone (histone $\text{H3}$) involved in centromere function and structure.

$\text{CenH3}$

An enzyme (present in malignant cells) that adds repeated nucleotide sequences to chromosomal ends, counteracting shortening and potentially causing cell "immortalization."

Telomerase

Short fluorescent $\text{DNA}$ sequences used to visualize specific regions of metaphase chromosomes ($\text{Fluorescence in situ hybridization}$).

$\text{FISH}$ Probes

The characteristic $\text{DNA}$ structure found in $\text{prokaryotes}$ (plus plasmids).

Circular Chromosome

The composition of the chromosome found in $\text{prokaryotes}$ (as opposed to $\text{DNA} + \text{histone}$ in eukaryotes).

$\text{DNA}$ only composition

The region in the cytoplasm of prokaryotes where the circular $\text{DNA}$ is complexed with protein and attached to the plasma membrane.

Bacterial Nucleoid

Small, circular, supercoiled $\text{DNA}$ molecules in bacteria that carry genes for nonessential functions (e.g., drug resistance, virulence).

Plasmids

Plasmids specifically involved in bacterial conjugation (genetic transformation).

$\text{F}$ Factors

Plasmids that carry genes conferring drug resistance in bacteria.

$\text{R}$ Factors

The scientist credited with isolating the chemistry of the nucleus, naming the substance nuclein.

Johann Friedrich Miescher

The scientist credited with the identification of chromosomes.

Walther Flemming

The scientist who discovered that a factor in diseased bacteria could transform harmless bacteria into deadly bacteria.

Frederick Griffith

The team that demonstrated DNA was the agent responsible for genetic transformation in bacteria.

Avery, MacLeod, McCarty

The landmark experiment using phage $\text{T2}$ that confirmed $\text{DNA}$, not protein, was the genetic material or "transforming principle."

Hershey and Chase Experiment