H&I: TERMS IN MOLECULAR BIOLOGY

haplotype block

Combination of alleles and DNA markers that has been inherited in a large, linked block on one chromosome of a homologous pair—undisturbed by genetic recombination—across many generations.

Hedgehog protein

Secreted extracellular signal molecule that has many different roles controlling cell differentiation and gene expression in animal embryos and adult tissues.

helper T cell (TH cell)

Type of T cell that helps activate B cells to make antibodies, cytotoxic T cells to become effector cells, and macrophages to kill ingested pathogens.

heterochromatin

Chromatin that is highly condensed even in interphase; generally transcriptionally inactive. (Compare with euchromatin.)

heterochronic

Describes genes involved in developmental timing; mutation results in cells of a specific fate behaving as cells at a different stage of development.

high-mannose oligosaccharides

Broad class of N-linked oligosaccharides, attached to mammalian glycoproteins in the endoplasmic reticulum, containing two N acetylglucosamine residues and many mannose residues.

high-performance liquid chromatography (HPLC)

Type of chromatography that uses columns packed with tiny beads of matrix; the solution to be separated is pushed through under high pressure.

histone

One of a group of small abundant proteins, rich in
arginine and lysine, that combine to form the nucleosome cores around which DNA is wrapped in eukaryotic chromosomes.

histone chaperone (chromatin assembly factor)

Protein that binds free histones, releasing them once they have been incorporated into newly replicated chromatin.

histone H1

“Linker” (as opposed to “core”) histone protein that binds to DNA where it exits from a nucleosome and helps package nucleosomes into the 30-nm chromatin fiber.

Holliday junction (cross-strand exchange)

X-shaped structure observed in DNA undergoing recombination, in which the two DNA molecules are held together at the site of crossing-over, also called a cross-strand exchange.

homeotic selector gene

In Drosophila development, a gene that defines and preserves the differences between body segments.

homolog

One of two or more genes that are similar in sequence as a result of derivation from the same ancestral gene.

homologous

Genes, proteins, or body structures that are similar as a result of a shared evolutionary origin.

homologous chromosomes (homologs)

The maternal and paternal copies of a particular chromosome in a diploid cell.

homologous recombination (general recombination)

Genetic exchange between a pair of identical or very similar
DNA sequences, typically those located on two copies of the same chromosome.

homophilic

Binding between molecules of the same kind, especially those involved in cell–cell adhesion.

horizontal gene transfer

Gene transfer between bacteria via natural transformation by released naked DNA, transduction by bacteriophages, or sexual exchange by conjugation.

hormone

Signal molecule secreted by an endocrine cell into the bloodstream, which can then carry the signal to distant
target cells.

Hox complex

A gene complex consisting of a series of Hox genes

Hox genes

Genes coding for transcription regulators, each gene containing a homeodomain, and specifying body- region differences.

Hox proteins

Transcription regulator proteins encoded by Hox genes; possess a highly conserved, 60-amino-acid-long DNA-binding homeodomain.

HPV

Human papillomavirus; infects the cervical epithelium
and is important as a cause of carcinoma of the uterine cervix.

hyaluronan (hyaluronic acid)

Type of nonsulfated glycosaminoglycan with a regular repeating sequence of up to 25,000 identical disaccharide units, not linked to a core protein.

hybridization

In molecular biology, the process whereby two complementary nucleic acid strands form a base-paired duplex DNA-DNA, DNA-RNA, or RNA-RNA molecule.

hybridoma

Hybrid cell line generated by fusion of a tumor cell and another cell type.

hydrogen bond

Noncovalent bond in which an electropositive hydrogen atom is partially shared by two electronegative atoms.

hydronium ion (H3O+)

Water molecule associated with an additional proton.

hydrophilic

Dissolving readily in water. Literally, “water loving.”

hydrophobic

(lipophilic) Not dissolving readily in water. Literally, “water-fearing.”

hydrophobic force

Force exerted by the hydrogen-bonded network of water molecules that brings two nonpolar surfaces together by excluding water between them.

hypervariable region

In immunology: any of the three small parts of the variable region of an immunoglobulin or T cell receptor chain that show the highest variability from molecule to molecule and contribute to the antigen-binding site.

hypoxia-inducible factor 1α (HIF1α)

Transcription regulator, the intracellular levels of which increase in response to a shortage of oxygen, that stimulates transcription of the VEGF gene to promote angiogenesis.

Ig superfamily

Large and diverse family of proteins that contain immunoglobulin or immunoglobulin-like domains. Most are involved in cell–cell interactions or antigen recognition.

IgA

Immunoglobulin A; the principal class of antibody in
secretions, including saliva, tears, milk, and respiratory and
intestinal secretions.

IgD

Immunoglobulin D; produced by immature naïve B cells
after leaving the bone marrow.

IgE

Immunoglobulin E; binds with high affinity via its tail region
to a class of Fc receptors on the surface of mast cells (tissues) or basophils (blood), where it acts as an antigen receptor; antigen binding stimulates the secretion of cytokines and biologically active amines, which help attract white blood cells, antibodies, and complement proteins to the site of activation.

IgG

Immunoglobulin G; the major antibody class in the blood, produced in especially large quantities during secondary antibody responses.

IgM

Immunoglobulin M; the first class of immunoglobulin that a developing B cell in the bone marrow makes, forming B-cell receptors on its surface.

iHog

Protein with four or five immunoglobulin-like domains
and two or three fibronectin-type-III-like domains; located
on the cell surface and thought to serve as co-receptors for
Hedgehog proteins.

image processing

Computer based techniques in microscopy that process digital images in order to extract latent information.

imaginal disc

Group of cells that are set aside, apparently undifferentiated, in the Drosophila embryo and which will
develop into an adult structure, e.g., eye, leg, wing.

immunization

Method of inducing adaptive immune responses to pathogens or foreign molecules, usually involving the co-injection of an adjuvant, a molecule (often of microbial origin) that helps activate innate immune responses required for the adaptive responses.

immunoglobulin (Ig) superfamily

Large and diverse family of proteins that contain immunoglobulin domains or immunoglobulin-like domains. Most are involved in cell–cell interactions or antigen recognition.

immunoglobulin domain (Ig domain)

Characteristic protein domain of about 100 amino acids that is found in immunoglobulin light and heavy chains.

immunogold electron microscopy

Method to localize specific macromolecules using a primary antibody that binds to the molecule of interest and is then detected with a secondary antibody to which a colloidal gold particle has been attached.

immunological memory

Long-lived property of the adaptive immune system that follows a primary immune response to many antigens, such that a subsequent encounter with the same antigen will provoke a more rapid and stronger secondary immune response.

immunological self-tolerance

The lack of response of the adaptive immune system to an antigen.

immunological synapse

The highly organized interface that develops between a T cell and an antigen-presenting cell (APC) or target cell it is in contact with, formed by T-cell receptors binding to antigen–MHC complexes on the APC and cell-adhesion proteins binding to their counterparts on the APCs.

induced fit

A principle for increasing the specificity of substrate recognition by proteins and RNAs. In protein synthesis, a ribosome, or enzyme folds around a codon–anticodon interaction and only when the match is correct is the subsequent reaction allowed to proceed.

induced pluripotent stem cells (iPS cells)

Cells that are induced by artificial expression of specific transcription regulators to look and behave like the pluripotent embryonic stem cells that are derived from embryos.

induced regulatory T cell

A regulatory T cell (Treg cell) that develops from naive helper T cells when they are activated in the presence of TGFβ in the absence of IL6.

inflammasome

Intracellular protein complex formed after activation of cytoplasmic NOD-like receptors with adaptor proteins. It contains a caspase enzyme that cleaves pro-inflammatory cytokines from their precursor proteins.

inflammatory response

Local response of a tissue to injury or infection—characterized clinically by redness, swelling, heat,and pain.

inhibitors of apoptosis (IAPs)

Intracellular protein inhibitors of apoptosis.

inhibitory G protein (Gi)

Trimeric G protein that can regulate ion channels and inhibit the enzyme adenylyl cyclase in the plasma membrane.

inhibitory neurotransmitter

Neurotransmitter that opens transmitter-gated Cl– or K+ channels in the postsynaptic membrane of a nerve or muscle cell and thus tends to inhibit the generation of an action potential.

initial segment

Specialized membrane region at the base of a nerve axon (adjacent to the cell body) that is rich in voltage-gated Na+ channels plus other classes of ion channels that all contribute to the encoding of membrane depolarization into action potential frequency.

initiator caspases

Apoptotic caspases that begin the apoptotic process, activating the executioner caspases.

initiator tRNA

Special tRNA that intiates translation. It always carries the amino acid methionine, forming the complex Met-tRNAi.

innate immune response

An early immune response in all organisms to a pathogen, which includes the production of antimicrobial molecules and the activation of phagocytic cells. Such a response is not specific for the pathogen, in contrast to an adaptive immune response.

inner mitochondrial membrane

Mitochondrial membrane that encloses the matrix space and forms extensive invaginations called cristae.

inner nuclear membrane

One of two concentric membranes comprising the nuclear envelope; contnuous with the outer nuclear membrane; contains specific proteins as anchoring sites for chromatin and the nuclear lamina.

inositol phospholipid signaling pathway

Intracellular signaling pathway that starts with the activation of phospholipase C and the generation of IP3 and diacylglycerol (DAG) from inositol phospholipids in the plasma membrane.

integrin

Transmembrane adhesion protein that is involved in
the attachment of cells to the extracellular matrix and to each other.

interaction domain

Compact protein module, found in many intracellular signaling proteins, that binds to a particular structural motif (e.g., a short peptide sequence, a covalent modification, or another protein domain) in another protein or lipid.

intermembrane space

Compartment of mitochondrion between by the outer and inner mitochondrial membranes.

interphase

Long period of the cell cycle between one mitosis and the next.

interpolar microtubule

In the mitotic or meiotic spindle, a microtubule interdigitating at the equator with the microtubules emanating from the other pole.

intracellular pathogens

Pathogens, including all viruses and many bacteria and protozoa, that enter and replicate inside host cells to cause disease.

intrinsic pathway (mitochondrial pathway)

Pathway of apoptosis activated from inside the cell in response to stress or developmental signals; depends on the release into the cytosol of mitochondrial proteins normally resident in the mitochondrial intermembrane space.

intron

Noncoding region of a eukaryotic gene that is transcribed into an RNA molecule but is then excised by RNA splicing during production of the mRNA or other functional
RNA.

invadopodia

Actin-rich protrusions extending in three-dimensions that are important for cells to cross tissue barriers by degrading the extracellular matrix.

ion channel

Transmembrane protein complex that forms a water-filled channel across the lipid bilayer through which specific inorganic ions can diffuse down their electrochemical gradients.

ion-sensitive indicators

Molecules whose light emission reflects the local concentration of a particular ion; some are luminescent (emitting light spontaneously) while others are fluorescent (emitting light on exposure to light).

iron–sulfur cluster

Electron-transporting group consisting of either two or four iron atoms bound to an equal number of sulfur atoms, found in a class of electron-transport proteins.