Histology and The Cell Nucleus: Key Terms and Concepts (Histology 101, Chapter 3)

A comprehensive set of vocabulary flashcards covering key histology concepts from tissue fixation and staining to organelles, nucleus structure, cell cycle regulation, and cell death mechanisms as presented in the lecture notes.

Histology

The scientific study of the microscopic structure of cells, tissues, and organs (microscopic anatomy) and how structure relates to function.

Fixation

The process of preserving tissue structure and preventing enzymatic degradation, typically using chemicals as soon as the tissue is removed from the body.

Formalin

A 37% aqueous solution of formaldehyde used as a fixative; preserves general cellular architecture by cross-linking proteins but does not fix lipids well.

Paraffin embedding

Infiltration and embedding of fixed tissue in paraffin so it can be thinly sectioned (typically 5–15 μm) for microtomy.

Hematoxylin and Eosin (H&E) staining

The routine stain in histology; hematoxylin stains basophilic (nucleic acids, acidic components) blue, eosin stains acidophilic (proteins, cytoplasm) pink/red.

Hematoxylin

A basic-like dye that binds acidic components (basophilia) such as nucleic acids in the nucleus.

Eosin

An acidic dye that stains basic components (acidophilia), such as most cytoplasmic proteins, pink/red.

H&E staining in paraffin sections

Process of staining paraffin-embedded tissue after deparaffinization and rehydration to visualize structure under light microscopy.

Histochemistry

Chemical procedures that localize specific chemical components in tissues, often using dyes or enzymes.

Cytochemistry

Chemical methods that localize specific cellular components, including enzymatic activity and immunochemical techniques.

PAS (Periodic Acid–Schiff) reaction

Stains carbohydrates and carbohydrate-rich macromolecules magenta; used to demonstrate glycogen, basement membranes, mucus, and reticular fibers.

Schiff reagent

Reagent used in PAS and Feulgen reactions that reacts with aldehyde groups to give a magenta color.

Feulgen reaction

A stain for DNA based on acid hydrolysis creating aldehyde groups that react with Schiff reagent; quantitative for DNA (not RNA).

Mordant

A fixing/bridging agent that helps a dye bind to tissue (e.g., hematoxylin–mordant–tissue complex).

Acidic dyes (acidophilia)

Dyes with net negative charge that bind cationic tissue components, staining structures like cytoplasm and extracellular fibers.

Basophilia

Affinity of tissue to basic dyes (e.g., hematoxylin) due to binding to anionic groups like nucleic acids.

Metachromasia

Color shift to a different color when basic dyes bind to tissue polyanions (e.g., toluidine blue staining metachromatically).

Immunocytochemistry

Localization of specific antigens in cells/tissues using antibodies; can be visualized with fluorescence or electron-dense labels.

Direct immunofluorescence

Immunocytochemical method where a fluorescent dye is attached directly to the primary antibody.

Indirect immunofluorescence

Immunocytochemical method where a fluorescently labeled secondary antibody binds to a primary antibody; amplifies signal.

Horseradish peroxidase (HRP)

An enzyme used in immunocytochemistry; produces a colored product (often with DAB) at the site of antigen–antibody binding.

DAB (diaminobenzidine)

A chromogen substrate for HRP that yields a brown precipitate in situ, allowing light-microscopy visualization of antigen location.

Fluorescein

A common fluorophore used to label antibodies for fluorescence imaging in immunocytochemistry.

Monoclonal antibodies

Antibodies derived from a single B-lymphocyte clone; highly specific to a single epitope.

Polyclonal antibodies

Mixtures of antibodies produced by multiple B-cell clones; recognize multiple epitopes on an antigen.

Hybridoma

Immortalized cell line produced by fusing an antibody-producing B cell with a myeloma cell; used to produce monoclonal antibodies.

FISH (Fluorescence In Situ Hybridization)

Hybridization technique using fluorescent DNA/RNA probes to localize specific sequences on chromosomes or within cells.

Autoradiography

Localization of radioactive material in tissue sections using photographic emulsions to visualize radioactivity.

Hybridization

Process by which single-stranded nucleic acids anneal to complementary sequences; used to localize specific DNA or RNA.

Monoclonal antibodies in medicine

Clinical applications include tumor detection/metastasis, tumor subtype differentiation, infectious disease testing, and targeted therapies when conjugated with toxins or isotopes.

frozen sections

Rapid tissue freezing and sectioning (5–10 μm in cryostat) for quick intraoperative diagnosis; often stained with H&E, methylene blue, or PAS.

Cryostat

A refrigerated instrument used to cut frozen tissue sections for rapid diagnostic microscopy.

Feulgen microspectrophotometry

Measurement of DNA content in cells using Feulgen-stained sections and spectrophotometry or flow cytometry.

Köhler illumination

A method for achieving even, optimal illumination in a light microscope by aligning the light path and diaphragms.

Ultraviolet (UV) microscopy

Microscopy using UV light (≈200 nm) to excite UV-absorbing molecules; requires quartz optics; enables detection of nucleic acids and certain proteins.

Confocal microscopy

A microscopy technique that uses a pinhole to reject out-of-focus light, enabling high-resolution 3D reconstruction of specimens.

Atomic Force Microscope (AFM)

Nonoptical microscope using a sharp cantilever tip to scan surfaces at molecular/atomic resolution; can image in liquid.

Virtual microscopy

Digital scanning of glass slides to create high-resolution virtual slides viewable remotely; includes annotation and wide accessibility.

Freeze fracture

Electron-mmicroscopy technique that cleaves membranes along the hydrophobic plane to reveal E-face and P-face, exposing integral membrane proteins.

E-face / P-face

Surfaces revealed after freeze-fracture; E-face corresponds to the extracellular side, P-face to the cytoplasmic side of the membrane.

Lipid rafts

Microdomains in the plasma membrane rich in cholesterol and glycosphingolipids, acting as signaling platforms for protein organization.

Caveolae

Small, flask-shaped invaginations of the plasma membrane enriched with caveolins; involved in signaling and endocytosis.

COP-I / COP-II

Coat protein complexes that mediate retrograde (COP-I) and anterograde (COP-II) vesicular transport between ER and Golgi.

Clathrin-coated pits

Specialized membrane regions where clathrin forms a cage to invaginate and bud vesicles during receptor-mediated endocytosis.

SNAREs (v-SNARE / t-SNARE)

Membrane proteins that mediate vesicle docking and fusion; v-SNAREs on vesicles pair with t-SNAREs on target membranes.

Endocytosis

Process by which cells take up material from the exterior via vesicle formation; includes pinocytosis, phagocytosis, and receptor-mediated endocytosis.

Exocytosis

Process by which vesicles fuse with the plasma membrane to secrete contents; can be constitutive or regulated.

Lysosome

Membrane-bound organelle containing hydrolytic enzymes for digestion of macromolecules; maintains acidic pH to protect its contents.

Lysosome-associated membranes (LAMPs/LIMPs/LGPs)

Major lysosomal membrane proteins that are highly glycosylated and protect the lysosomal lumen from its enzymes.

Autophagy

Lysosome-mediated degradation of cytoplasmic components; macroautophagy, microautophagy, and chaperone-mediated autophagy.

Mitochondria

Double-membrane-bound organelles that generate ATP via the electron transport chain; contain own DNA and ribosomes; regulate apoptosis.

Cristae

Infoldings of the inner mitochondrial membrane that increase surface area for oxidative phosphorylation.

Apoptosis

Programmed cell death; orderly, noninflammatory cellular demolition mediated by caspases and mitochondrial signals.

Caspases

Cysteine proteases activated in a proteolytic cascade that dismantle cellular components during apoptosis.

Cytochrome c / SMAC/DIABLO

Mitochondrial proteins released during apoptosis that activate caspases (cytochrome c) and inhibit inhibitors (SMAC/DIABLO).

Bcl-2 family

Family of proteins regulating mitochondrial permeability and apoptosis; includes anti- and pro-apoptotic members.

Anoikis

Apoptosis triggered by loss of cell–extracellular matrix interactions, often mediated by integrins.

Necrosis

Uncontrolled cell death due to injury; membrane rupture, inflammatory response, and release of lysosomal enzymes.

Nucleolus

Nuclear substructure where ribosomal RNA (rRNA) synthesis and initial ribosomal assembly occur; composed of fibrillar centers, fibrillar material, and granular material.

Chromatin

DNA-histone complex within the nucleus; exists as euchromatin (transcriptionally active, lighter staining) and heterochromatin (condensed, darker).

Nucleosome

Basic unit of chromatin; DNA wrapped around a histone octamer, about 146 base pairs of DNA.

Barr body

Inactivated X chromosome in female somatic cells; facultative heterochromatin visible as a dense, condensed body in interphase nuclei.

Nuclear envelope

Double membrane surrounding the nucleus (inner and outer membranes with perinuclear space); continuous with endoplasmic reticulum on the outer face.

Nuclear pores / Nuclear pore complex (NPC)

Rings of proteins forming openings in the nuclear envelope that regulate bidirectional transport of proteins, RNA, and ribonucleoproteins.

Nuclear lamina / Lamins

A dense network of intermediate filaments (lamins) beneath the inner nuclear membrane supporting the nuclear envelope and organizing chromatin.

Nucleoplasm

Fluid interior of the nucleus excluding chromatin and nucleolus; contains nuclear matrix and other components.

Karyotype

ordered picture of chromosomes from a dividing cell, used to analyze chromosomal number and structure.

Telomere

Protective DNA-protein caps at chromosome ends; shorten with cell division and relate to cellular lifespan; maintained by telomerase in some cells.

DNA vs RNA in nucleus

DNA contains the genetic blueprint; RNA (including rRNA and mRNA) is transcribed/processed in the nucleus and then transported to the cytoplasm.

MPF (cyclin–Cdk complex)

Maturation-promoting factor; a cyclin–Cdk complex (e.g., Cyclin B–Cdk1) that drives cells into mitosis by phosphorylating key targets.

Cell cycle checkpoints

Quality-control points (G1, S, G2, M) that halt progression if DNA is damaged or replication is incomplete; regulate cell-cycle progression.

G1 restriction point (R-point)

Point at which a cell commits to DNA synthesis and S phase progression; controlled by pRb–E2F interactions.

Mitosis vs Meiosis

Mitosis: nuclear division producing two genetically identical diploid daughter cells; Meiosis: two sequential divisions producing haploid gametes with genetic diversity.

Barr body

Inactivated X chromosome in female somatic cells; a visible marker of X-chromosome inactivation.