D&E TERMS: Biology

dark-field microscopy

Type of light microscopy in which oblique rays of light focused on the specimen do not enter the objective lens, but light that is scattered by components in the living cell can be collected to produce a bright image on a dark background.

death receptor

Transmembrane receptor protein that can signal the cell to undergo apoptosis when it binds its extracellular ligand.

death-inducing signaling complex (DISC)

Activation complex in which initiator caspases interact and are activated following binding of extracellular ligands to cell-surface death receptors in the extrinsic pathway of apoptosis.

default pathway

The transport pathway of proteins directly to the cell surface via the nonselective constitutive secretory pathway, entry into which does not require a particular signal.

defensin

Positively charged, amphipathic, antimicrobial peptide—secreted by epithelial cells—that binds to and disrupts the membranes of many pathogens.

delayed K+ channel

Neuronal voltage-gated K+ channel that opens following membrane depolarization but during the falling phase of an action potential due to slower activation kinetics than Na+ channels; opening permits K+ efflux, driving the membrane potential back toward its original negative value, ready to transmit a second impulse.

Delta

Single-pass transmembrane signal protein displayed
on the surface of cells that binds to the Notch receptor protein on a neighboring cell, activating a contact-dependent signaling mechanism.

dendrite

Extension of a nerve cell, often elaborately branched, that receives stimuli from other nerve cells.

dendritic cell

The most potent type of antigen-presenting cell, which takes up antigen and processes it for presentation to T cells. It is required for activating naïve T cells.

deoxyribonucleic acid (DNA)

Polynucleotide formed from covalently linked deoxyribonucleotide units. The store of hereditary information within a cell and the carrier of this
information from generation to generation.

depolarization

Deviation in the electric potential across the plasma membrane towards a positive value. A depolarized cell has a potential that is positive outside and negative inside.

desmosome

Anchoring cell–cell junction, usually formed
between two epithelial cells.

detergent

Small amphiphilic molecule, more soluble in water
than lipids, that disrupts hydrophobic associations and destroys the lipid bilayer thereby solubilizing membrane proteins.

D gene segment

A short DNA sequence that encodes a part of the variable region of an immunoglobulin heavy chain or the β chain of a T cell receptor (TCR).

diacylglycerol (DAG)

Lipid produced by the cleavage of inositol phospholipids in response to extracellular signals.

dideoxy sequencing

The standard enzymatic method of DNA sequencing.

differential-interference-contrast microscope

Type of light microscope that exploits the interference effects that occur when light passes through parts of a cell of different refractive indices. Used to view unstained living cells.

differentiation

Process by which a cell undergoes a change to an overtly specialized cell type.

diffusion

The net drift of molecules through space due to random thermal movements.

Dishevelled

Scaffold protein recruited to the Frizzled family of cell-surface receptors upon their activation by Wnt binding that helps relay the signal to other signaling molecules.

DNA helicase

Enzyme that is involved in opening the DNA helix into its single strands for DNA replication.

DNA library

Collection of cloned DNA molecules, representing either an entire genome (genomic library) or complementary DNA copies of the mRNA produced by a cell (cDNA library).

DNA ligase

Enzyme that joins the ends of two strands of DNA together with a covalent bond to make a continuous DNA strand.

DNA methylation

Addition of methyl groups to DNA.

DNA microarray

A large array of short DNA molecules (each of known sequence) bound to a glass microscope slide or other suitable support.

DNA polymerase

Enzyme that synthesizes DNA by joining nucleotides together using a DNA template as a guide.

DNA primase

Enzyme that synthesizes a short strand of RNA on a DNA template, producing a primer for DNA synthesis.

DNA repair

A set of processes for repairing the many accidental lesions that occur continually in DNA.

DNA replication

Process by which a copy of a DNA molecule is made.

DNA supercoiling

A conformation with loops or coils that DNA adopts in response to superhelical tension; conversely, creating various loops or coils in the helix can create such
tension.

DNA topoisomerase (topoisomerase)

Enzyme that binds to DNA and reversibly breaks a phosphodiester bond in one or both strands.

DNA tumor virus

General term for a variety of different DNA viruses that can cause tumors.

DNA-only transposon

Transposable element that exists as DNA throughout its life cycle. Many move by cut-and-paste transposition.

dolichol

Isoprenoid lipid molecule that anchors the precursor oligosaccharide in the endoplasmic reticulum membrane during protein glycosylation.

domain (protein domain)

Portion of a protein that has a tertiary structure of its own.

Dorsal protein

Transcription regulator of the NFκB family regulating gene expression and involved in establishing the dorsoventral axis in the embryo.

double helix

The three-dimensional structure of DNA, in which two antiparallel DNA chains, held together by hydrogen-
bonding between the bases, are wound into a helix.

drivers

Mutations that are causal factors in the development of cancer.

dynamic instability

Sudden conversion from growth to shrinkage, and vice versa, in a protein filament such as a microtubule or actin filament.

dynamin

Cytosolic GTPase that binds to the neck of a clathrin-coated vesicle in the process of budding from the membrane, and which is involved in completing vesicle formation.

dynein

Large motor protein that undergoes ATP-dependent movement along microtubules.

E2F protein

Transcription regulatory protein that switches on many genes that encode proteins required for entry into the S phase of the cell cycle.

early endosome

Common receiving compartment with which most endocytic vesicles fuse and where internalized cargo is sorted either for return to the plasma membrane or for degradation by inclusion in a late endosome.

ectoderm

Embryonic epithelial tissue that is the precursor of the epidermis and nervous system.

edema factor

One of the two A subunits of anthrax toxin; an adenylyl cyclase that catalyzes production of cAMP, leading to ion imbalance and consequent edema in the skin or lung.

effector Bcl2 family proteins

Pro-apoptotic proteins of the intrinsic pathway of apoptosis that in response to an apoptotic stimulus become activated and aggregate to form oligomers in the mitochondrial outer membrane, inducing the release of cytochrome c and other intermembrane proteins.

effector cell

Cell that carries out the final response or function in a particular process.

egg-polarity genes

Genes in the Drosophila egg that define the anteroposterior and dorsoventral axes of the future embryo through the creation of landmarks (mRNA or protein) in the egg that provide signals organizing the developmental process.

elastic fiber

Extensible fiber formed by the protein elastin in many animal connective tissues, such as in skin, blood vessels, and lungs, which gives them their stretchability and resilience.

elastin

Extracellular protein that forms extensible fibers (elastic fibers) in connective tissues.

electrochemical gradient

Combined influence of a difference in the concentration of an ion on two sides of a membrane and the electrical charge difference across the membrane (membrane potential).

electron microscope

Microscope that uses a beam of electrons to create the image.

electron microscope (EM) tomography

Technique for viewing three-dimensional specimens in the electron microscope in which multiple views are taken from different directions by tilting the specimen holder.

electron-transport chain

Series of reactions in which electron carrier molecules pass electrons “down the chain” from higher to successively lower energy levels.

electrostatic attraction

A noncovalent, ionic bond between two molecules carrying groups of opposite charge.

embryonic stem cells (ES cells)

Cells derived from the inner cell mass of the early mammalian embryo.

endocrine cell

Specialized animal cell that secretes a hormone into the blood. Usually part of a gland, such as the thyroid or pituitary gland.

endocytic vesicle

Vesicle formed as material ingested by the cell during endocytosis is progressively enclosed by a small portion of the plasma membrane, which first invaginates and then pinches off to form the vesicle.

endocytosis

Uptake of material into a cell by an invagination of the plasma membrane and its internalization in a membrane-
enclosed vesicle.

endoderm

Embryonic tissue that is the precursor of the gut and associated organs.

endoplasmic reticulum (ER)

Labyrinthine membrane-bounded compartment in the cytoplasm of eukaryotic cells, where lipids are synthesized and membrane-bound proteins and secretory proteins are made.

endosome maturation

Process by which early endosomes mature to late endosomes and endolysosomes; in the conversion process, the endosome membrane protein composition changes, the endosome moves from the cell periphery to close to the nucleus, and the endosome ceases to recycle material to the plasma membrane and irreversibly commits its remaining contents to degradation.

endothelial cell

Flattened cell type that forms a sheet (the endothelium) lining all blood and lymphatic vessels.

entropy (S)

Thermodynamic quantity that measures the degree of disorder or randomness in a system; the higher the entropy, the greater the disorder.

enveloped virus

Virus with a capsid surrounded by a lipid bilayer membrane (the envelope), which is often derived from the host-cell plasma membrane when the virus buds from the cell.

enzyme

Protein that catalyzes a specific chemical reaction.

enzyme-coupled receptor

A major type of cell-surface receptor that has a cytoplasmic domain that either has enzymatic activity or is associated with an intracellular enzyme. In either case, the enzymatic activity is stimulated by an extracellular ligand binding to the receptor.

ephrin

One of a family of membrane-bound protein ligands
for the Eph receptor tyrosine kinases (RTKs) that, among many other functions, stimulate repulsion or attraction responses that guide the migration of cells and nerve cell axons during animal development.

epidermis

Epithelial layer covering the outer surface of the body. Has different structures in different animal groups.

epigenetic inheritance

Inheritance of phenotypic changes in a cell or organism that do not result from changes in the nucleotide sequence of DNA.

epistasis analysis

Analysis to discover the order in which the genes act, by investigating if a mutation in one gene can mask the effect of a mutation in another gene when both mutations are present in the same organism or cell.

epithelium (plural epithelia)

Sheet of cells covering the outer surface of a structure or lining a cavity.

equilibrium

State in a chemical reaction where there is no net change in free energy to drive the reaction in either direction.

equilibrium constant (K)

The ratio of forward and reverse rate constants for a reaction.

ER lumen Space

enclosed by the membrane of the endoplasmic reticulum (ER).

ER resident protein

Protein that remains in the endoplasmic reticulum (ER) or its membranes and carries out its function there, as opposed to proteins that are present in the ER only in transit.

ER retention signal

Short amino acid sequence on a protein that prevents it from moving out of the endoplasmic reticulum (ER).

ER signal sequence

N-terminal signal sequence that directs proteins to enter the endoplasmic reticulum (ER). Cleaved off by signal peptidase after entry.

ER tail-anchored proteins

Membrane proteins anchored in the endoplasmic reticulum (ER) membrane by a single transmembrane α helix contained at their C-terminus.

erythrocyte

Small hemoglobin-containing blood cell of vertebrates that transports oxygen to, and carbon dioxide from, tissues. Also called a red blood cell.

erythropoietin

A hormone produced by the kidney that stimulates the production of red blood cells in bone marrow.

ethylene

Small gas molecule that is a plant growth regulator influencing plant development in various ways including
promoting fruit ripening, leaf abscission, and plant senescence and functioning as a stress signal in response to wounding, infection, and flooding.

euchromatin

Region of an interphase chromosome that stains diffusely; “normal” chromatin, as opposed to the more condensed heterochromatin.

eukaryote

Organism composed of one or more cells that have a distinct nucleus.

eukaryotic initiation factor (eIF)

Protein that helps load initiator tRNA on to the ribosome, thus initiating translation.

excitatory neurotransmitter

Neurotransmitter that opens cation channels in the postsynaptic membrane, causing an influx of Na+, and in many cases Ca2+, that depolarizes the postsynaptic membrane toward the threshold potential for firing an action potential.

executioner caspases

Apoptotic caspases that catalyze the widespread cleavage events during apoptosis that kill the cell.

exocytosis

Excretion of material from the cell by vesicle fusion with the plasma membrane; can occur constitutively or be regulated.

exon

Segment of a eukaryotic gene that consists of a sequence of nucleotides that will be represented in mRNA or in a final transfer, ribosomal, or other mature RNA molecule.

exosome

Large protein complex with an interior rich in 3′-to-5′ RNA exonucleases; degrades RNA molecules to produce ribonucleotides.

extracellular pathogens

Pathogens that disturb host cells and can cause serious disease without replicating in host cells.

extracellular signal molecule

Any secreted or cell-surface chemical signal that binds to receptors and regulates the activity of the cell expressing the receptor.

extrinsic pathway

Pathway of apoptosis triggered by extracellular signal proteins binding to cell-surface death receptors.