Life at the Cell and Below-Cell Level. The Hidden History of a Fundamental Revolution in Biology
by
Gilbert N. Ling, Ph.D.
Pacific Press
2001
ISBN 0-9707322-0-1
"Dr. Ling is one of the most inventive biochemist I have ever met."
Prof. Albert Szent-Györgyi, Nobel Laureate
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A Super-Glossary
for Words, Terms and Basic Concepts Used in the Book
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f-, f+: fixed anion and fixed cation respectively FDNB: short for fluorodinitrobenzene F-effect: the combined direct electrostatic effect transmitted through space (D-effect) and electrostatic inductive effect transmitted through intervening atoms (I-effect), sometimes also called direct F-effect.
F1 soluble mitochondrial ATPase: a specific water-soluble ATPase isolated from mitochondria.
Federation Meetings: yearly meetings of the Federation of American Societies of Experimental Biology of the United States.
fermentation: an enzymatically controlled, anaerobic breakdown of energy-rich compounds like glucose into alcohol as that occurring in yeasts.
ferromagnetic cooperative transition: Iron, nickel and cobalt are described as ferromagnetic since they exhibit the properties of a magnet. This property originates from the existence of each atom of these metals as a magnetic dipole. And for that reason, the orientation of a particular atom depends on the orientation of its neighboring atoms—a fundamental characteristic of cooperative phenomenon. A ferromagnetic cooperative transition tends to be all-or-none, either all in the ordered magnetized state or the disordered random state.
fibrin: a white insoluble fibrous protein obtained from fibrinogen found in normal blood by the action of the proteolytic enzyme, thrombin in the clotting of blood.
fibrous protein: In contrast to globular proteins, fibrous proteins assume at least in part the fully-extended and other extended conformations. Examples include collagen and gelatin.
field overlapping enhances counterion association: A cation exchange resin bead, as a typical fixed charge system, contains only fixed anionic sites. Here each cation experiences not only the electrostatic attraction of a closely located fixed anion but also that of other fixed anions as well. A resting living cell or protoplasm, on the other hand, is as a rule an amphoteric fixed change system containing roughly equal number of fixed cations and fixed anions. Here the field experienced by a counter-cation is weakened by the fixed cations nearby. But even in a perfectly structured fixed system resembling the
NaCl crystal where each Na+ is surrounded by six Сl- and each Cl- is surrounded by six
Na+ the field experienced by each ion is more than that of one fixed ion of the opposite sign—as precisely described by the Madelung constant. Furthermore, the distribution of fixed anions and fixed cations in living cells are as a rule not uniform. Charge distribution along individual protein
molecules180 Fig. 3.5 and in different regions of the cell15
Fig. 15.5 tend to be segregated, thereby producing regions of fixed charges of one sign predominantly and in which the influence of field overlapping can be more pronounced in enhancing counterion association.
field theory: first introduced by Michael Faraday on the electric field produced by changing magnetic flux.
field strength: See electric field strength.
first order quadrupole broadening: When atoms whose nuclear charge distribution are not spherically symmetric are placed in an asymmetrical electric field, the NMR signal of these atoms may split into one center peak and two satellite peaks. For atoms with nuclear spin equal to 3/2, like
Na,23 the relative intensity of the center peak is 0.4. For cases in which, the size of the center peak does not differ significantly from the expected intensity (0.4), the quadrupole broadening is described as that of the first order.
fixed anion: a negatively-charged functional group that is a part of. and thus anchored on a protein or other macromolecule or a fixed charge system.
fixed cation: a positively-charged functional group that is a part of, and thus anchored on a protein, another macromolecule or a fixed charge system.
fixed charge: a chemical group that is spatially fixed and carries a net positive or negative charge.
fixed charge system: a three-dimensional system consisting of a fixed framework onto which are fixed a large number of charge-bearing groups.
fluid-mosaic model of cell membrane: a model offered by Singer and Nicolson for the cell membrane, consisting of a continuous phospholipid bilayer penetrated fully or partially by islets of protein molecules.
fluorescence: When a molecule absorbs a quantum of radiation, the molecule enters an excited state. If the molecule is stable enough, the excited molecule may return to its initial ground state by emitting radiation usually of a longer wave length. This type of emission is called fluorescence.
fluorescence yield: the ratio of the emitted radiation energy over that of the exciting radiation in fluorescence is called the fluorescence yield.
fluorodinitrobenzene, FDNB: a reagent which reacts with terminal amino groups of proteins It is also a specific inhibitor of the enzyme, adenylic kinase.
formic acid: HCOOH, a rather strong acid, first observed from distillates of ants (colonial insects belonging the family, Formicidae).
free energy, Gibbs free energy, F: also called useful energy by Guggenheim It represents the work, which a system is able to perform in a given isothermal process at constant pressure. The free energy F is related to the enthalpy or heat content H and the entropy S and absolute temperature Т by the
thermodynamic relation: F = H - TS. Now H = E + PV, where E is the energy (also called total energy, or internal energy), P and V are the pressure and volume respectively. Therefore,
F = E + PV - TS. (See also Helmholtz free energy.)
free energy of adsorption: See standard free energy of adsorption.
free energy of dimerization: the free energy change entailed in the association of two identical molecules (or monomers) into a double molecule or dimer.
free energy of solute distribution: See standard free energy of distribution.
freeze-drying: a procedure used in preparing microscopic sections for viewing under an electron microscope It involves the freezing of the specimen in liquid nitrogen followed by sublimation of the water in the frozen specimen before infiltrating it with an imbedding material.
freeze-substitution: a procedure used in electron microscopy, during which water in the frozen biological specimen is replaced at a very low temperature by acetone, which facilitates the infiltration of embedding material and minimize distortions of the original fine structure of the specimen.
freezing point depression: the lowering of the freezing point of a solvent like water.
frozen hydrated preparation: A biological specimen as a rule contains large amount of water. In the standard procedure in preparing sections for viewing under an electron microscope, this water is first removed by drying under vacuum and replaced directly or indirectly with an imbedding medium, which then can be polymerized into a solid form. In a frozen hydrated preparation, all these intermediary steps are eliminated and the specimen is viewed in its original frozen, hydrated state.
fucose: See D-fucose.
fully-extended conformation: According to the PM theory, the backbone NH and CO groups of a fully-extended protein molecule are not engaged in intra- or inter-macromolecular H-bonds but are directly exposed to and interact with the bulk-phase water.
"fully-satisfied state": a state of water molecules when all its H-bonding groups are fully engaged in forming H-bonds with H-bonding sites on macromolecules or with other polarized and oriented water molecules.
"fusing": joining as if by melting together.
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