Glossary of Terms

Molecular Biology, Genetics and Clinical Neurology

Laura Liscum, Stephen L. Sturley and Marc Patterson (Compiled and edited by Cate Walsh Vockley)

Included here is a glossary of terms frequently used in molecular biology and neurobiology. Much of it is jargon and will probably not be encountered in daily life, but nevertheless it will be found in the literature. It is by no means complete, however it should help in finding explanations for most puzzling terms!

Alleles: Alternate forms of a gene at a specific location or locus; a single allele for each locus is inherited separately from each parent ( e.g., at the location for eye color genes, the inherited allele might result in blue or brown eyes). A significant number of different alleles (forms) may exist for a single gene, with many alleles representing mutations that disrupt gene function and cause disease.

Ataxia: Failure of muscular coordination; irregularity of muscle action.

Base Sequence: The order of nucleotide bases in a DNA molecule.

Brainstem: The ‘stalk’ of brain tissue that connects the spinal cord, cerebellum and cerebral hemispheres. Control of eye movements, breathing, heart rate, blood pressure and the nerves of the head and neck reside in the brainstem. Brain death is defined by irreversible loss of the brainstem function.

Cataplexy: A sudden loss of muscle tone, usually evoked by a strong stimulus such as laughter or anger. Cataplexy is believed to represent a fragment of rapid eye movement (REM) sleep that intrudes into otherwise normal consciousness. It correlates with dysfunction of the upper brainstem.

Cell: The basic unite of all organisms. Can be of several different types depending on function [e.g. macrophages (a type of blood cell), neuron (nerve cell), hepatocyte (liver cell) erythrocyte (red blood cell)]. The cell is separated from the external environment by the plasma membrane and within the cell is subdivided into organelles such as the nucleus, the endoplasmic reticulum, the golgi or the lysosome.

Cholesterol: The most abundant sterol in mammalian cells.

Chromosomes: The self-copying genetic structures of cells containing the cellular DNA that bears in its nucleotide sequence the genes or blueprints for cell function. In prokaryotes (cells that do not have a nucleus), chromosomal DNA is circular, and the entire genome (all the genes in an organism) is carried on one chromosome. Eukaryotic cell (with a nucleus) genomes consist of a number of chromosomes whose DNA is associated with different kinds of proteins.

Cloning: The process of producing a group of cells (clones), all genetically identical, from a single ancestor cell. In recombinant DNA technology, the use of DNA manipulation procedures to produce multiple copies of a single gene or segment of DNA is referred to as cloning DNA. More recently “cloning” has been used to describe the asexual production of whole organisms from a single somatic diploid cell (i.e. not a sperm or ovum but a cell that has a complete set of chromosome) e.g. “Dolly the sheep”.

Coat Protein: Proteins that coat vesicles and direct their trafficking or movement in cells.

Cortex: The outer layer of any organ, as in the cerebral and cerebellar cortex. In the brain, the cortex consists of neurons (grey matter).

DNA (Deoxyribonucleic Acid): The molecule that encodes genetic information. The four nucleotides in DNA contain the bases: adenine (A), guanine (G), cytosine (C), and thiamine (T) held together by weak bonds between base pairs of nucleotides. In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its paired or complimentary strand (like a mirror image).

DNA Sequence: The relative order of base pairs, whether in a fragment of DNA, a gene, a chromosome, or an entire genome.

Dystonia: Disordered muscle tone.

Early Endosome: A vesicle that has just pinched off of the plasma membrane.

Endogenous: Developing or coming from within an organism.

Endoplasmic Reticulum: A network (reticulum) of membranes inside (endo) the cell soup (plasm). The assembly line for protein and lipid synthesis.

Endosome: A vesicle (soma = body) that has pinched or budded off of the plasma membrane into (endo) the cell.

Enzyme: A protein that acts as a catalyst, speeding the rate at which a biochemical reaction proceeds (helps it happen more quickly and efficiently) but not altering the direction or nature of the reaction. Example, sphingomyelinase.

Eukaryote: Cell or organism with membrane bound, structurally discrete nucleus and other well-developed subcellular compartments. Eukaryotes include all organisms except viruses, bacteria, and blue-green algae. Compare to prokaryote below.

Exogenous: Developed or originating outside the organism.

Fatty Acid: A major building block of cellular lipids. It is a long carbon chain that ends in a carboxylic acid (a chemical structure = -COOH).

Ganglioside: A sphingolipid with sugars attached.

Gene: The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product (i.e., a protein or RNA molecule). See gene expression. Example NPC1, NPC2.

Gene Expression: The process by which a gene’s coded information is converted into the structures present and operating in the cell. Expressed genes include those that are transcribed (copied) into mRNA and then translated into protein and those that are transcribed into RNA but not translated into protein (e.g. transfer and ribosomal RNAs)

Gene Knockout: Specific targeting of a gene by homologous recombination (pairing and rearrangement of 2 copies or alleles of a gene) commonly performed in mice. Frequently, this is designed to produce a complete and specific loss of function of the gene. (See transgenic mice).

Genotype: The genetic makeup of an individual; usually refers to the gene structure of a particular gene being analyzed.

Gene Product: The biochemical material, either RNA or protein, resulting from expression of a gene. The amount of gene product is used to measure how active a gene is; abnormal amounts can be correlated with disease-causing alleles.

Genetic Code: The sequence of nucleotides, coded in triplets (codons) along the mRNA that determines that sequence of amino acids in protein synthesis. The DNA sequence of a gene can be used to predict the mRna sequence, and the genetic code can in turn be used to predict the amino acid sequence.

Glycolipid: A lipid with sugar attached.

Glycoprotein: A protein with sugar attached.

GM2 and GM3: Simple gangliosides that serve as building blocks for complex ones.

Golgi Apparatus: An organelle that looks like a stack of membranes, containing enzymes that add sugars to proteins and lipids. Also contains other protein modification enzymes. The cell’s dessert buffet.

Homologies: Similarities in DNA or protein sequences between individuals of the same species or among different species.

Hydrophilic: Loves water.

Hydrophobic: Hates water.

Late Endosome: A vesicle that pinched off of the plasma membrane a while ago.

Lipid: Molecules that prefer to be in chloroform rather than water (hydrophobic, or won’t dissolve in water).

Lysosome: An organelle (soma = body) that contains enzymes that lyse (cut up) proteins, lipids, nucleic acids, and sugars. The cell’s recycling center.

Membranes: A planar (flat) bilayer (two layers) of lipids. Looks like an Oreo cookie, with hydrophilic heads facing out (the cookie part) and hydrophobic legs in the middle (the filling). All eukaryotic (i.e. higher) cells are separated from the external environment and subdivided by membranes. This serves to protect or insulate the cells from extremes of pH (acidity/alkalinity), drying/desiccation, or salinity and to isolate toxic components into protected or non-lethal compartments within the cell. Membranes are made up of phospholipid bilayers, which contain cholesterol and proteins.

Metabolite: The product of a metabolic (enzymatic) reaction.

Mitochondrion: An organelle that uses glucose and fatty acids to make energy. The cell’s Power plant.

Nucleus: An organelle that contains most of the cells genetic material (nucleic acid). The cell’s cookbook.

Null: Completely missing.

Organelle: Little organ. A compartment within the cell that contains proteins (i.e. enzymes) that work together for a common purpose.

Permease: A protein pump that permits efficient movement of molecules through membranes (see transporter). A protein that helps molecules permeate (cross) the membrane.

pH: A measurement of how acidic (like lemon juice) or basic (like baking soda) a solution is.

Phenotype: the outward appearance or physical symptoms of an individual.

Phospholipid: Another building block of membranes which, along with cholesterol, that forms a barrier for the cell from the outside and also for sub-compartments of the cell. Has hydrophilic head and hydrophobic legs (the fatty acids). An important type of phospholipid is sphingomyelin. Gangliosides are also types of phospholipids.

Plasma Membrane: The outermost membrane of the cell which insulates or protects it from the environment. It is made up of phospholipid, cholesterol and membrane protein (often pumps to allow passage of molecules through the barrier).

Protein: A large molecule composed of one or more chains of amino acids in a specific order; the order is determined by the base sequence of nucleotides in the gene coding for the protein. Proteins are required for the structure, function, and regulation of the body’s cells, tissues, and organs, and each protein has unique functions. Examples are hormones, enzymes, and antibodies.

Rabs: A family of coat proteins. Mammalian cells have at least 60 different Rab proteins.

Sequencing: Determination of the order of nucleotides (base sequences) in a DNA or RNA molecule or the order of amino acids in a protein.

Sphingolipid: A lipid that contains sphingosine. Enriched in the brain. Named after the Sphinx because of their enigmatic nature.

Sphingomyelin: A specific type of phospholipid and an important component of membranes, particularly the plasma membrane. Sphingomyelin is acted on by the enzyme Sphingomyelinase, which is defective in NP A and B disease. Cholesterol binds to Sphingomyelin in the plasma membrane.

Systemic: pertaining to or affecting the body as a whole.

Transporter: A protein that permits or promotes movement within the cell or across membranes. Can act as a permease or as a mediator of transport vesicle fusion events.

Vesicle: A small membrane-delimited sac that buds off of one membrane, carrying cargo, and fuses with another.