Allostery In biochemistry, an enzyme or other protein is allosteric if its activity or efficiency changes in
response to the binding of an effector molecule at a so-called allosteric site. Changes that enhance
activity are referred to as allosteric activation, while the opposite is called allosteric inhibition.
”Allostery” is derived from the Greek ”other site”, referring to the typical scenario in which an enzyme’s
allosteric and active sites are distinct.
Anabolism the energy-requiring building phase of metabolism in which simpler substances are
combined to form more complex substances.
Apoptosis A normal series of events in a cell that leads to its death.
ATP (Adenosine TriPhosphate) A molecule consisting of adenosine (adenine plus a ribose sugar) and
three phosphate groups. The last two phosphates are joined by high energy bonds which provide energy
used in chemical reactions such as respiration and glycolysis. In plants, ATP is formed in the chlorplasts
during photosynthesis.
Autocatalysis A single chemical reaction is said to have undergone autocatalysis, or be autocatalytic, if
the reaction product is itself the catalyst for that reaction.
Autopoiesis Autopoiesis literally means ”self-production” (from the Greek: auto for self- and poiesis for
creation or production) and expresses a fundamental complementarity between structure and
function. The term was originally introduced by Chilean biologists Francisco Varela and
Humberto Maturana in the early 1970s: The canonical example of an autopoietic system, and one
of the entities that motivated Varela and Maturana to define autopoiesis, is the biological
cell.
CAS/Crk signalling Molecular coupling of p130CAS and Crk occurs in response to integrin activation
and plays a pivotal role in signalling pathways, culminating in cell proliferation, survival and migration
[Chodniewicz and Klemke 2004].
Deregulated CAS/Crk signalling mechanisms are involved in the pathogenesis of malignant metasases
[Chodniewicz and Klemke 2004]. The Abl protein is a negative regulator of CAS/Crk coupling, serving
to suppress the CAS/Crk-mediated signalling cascade. CAS/Crk-mediated cell invasion and survival
requires activation of the small GTPase Rac, while uncoupling CAS from Crk prevents migration and
induces apoptosis of the invasive tumour cells.
Catabolism The metabolic breakdown of large molecules in living organism, with accompanying
release of energy.
Catalysis An increase in the velocity of a chemical reaction or process produced by the presence of a
substance that is not consumed in the net chemical reaction or process; negative catalysis
denotes the slowing down or inhibition of a reaction or process by the presence of such a
substance.
Catalyst A chemical substance that increases the rate of a reaction without being consumed; after the
reaction it can potentially be recovered from the reaction mixture chemically unchanged. The
catalyst lowers the activation energy required, allowing the reaction to proceed more quickly
or at a lower temperature. In a fuel cell, the catalyst facilitates the reaction of oxygen and
hydrogen. It is usually made of platinum powder very thinly coated onto carbon paper or
cloth.
Cell Smallest unit of life (single cell organism or bacteria) or unit of higher organisms, i.e.,
multicellular organisms. Cells are surrounded by a cell membrane (and cell wall in bacteria and
plants = a membrane plus some chemically more stable structures, often mixtures of proteins
and polysaccharides) and contain all necessary elements to sustain life; proteins, nucleic
acids, lipids, minerals, and a diverse class of metabolites. Cells of higher organisms (known
as eukaryotes) are subdivided into subcellular compartments called organelles such as the
mitochondrion, the cell nucleus, the endoplasmatic reticulum, the Golgi apparatus and many smaller
organelles with highly specialized functions. While all these organelles are found in animal
cells, plant cells in addition contain a central vacuole that controls pressure to stabilize the
cell and chloroplasts, the site of photosynthesis or light depended biosynthesis of sugars
(carbohydrates).
Cell-cell signaling Any process that mediates the transfer of information from one cell to
another.
cell-cell signaling involved in cell fate commitment Signaling between cells that results in the
commitment of a cell to a certain fate. This is often done by secretion of proteins by one cell which
affects the neighboring cells and causes them to adopt a certain fate.
Chemotaxis Directional movement (migration) of biological cells or organisms in response to
concentration gradients of chemicals, whereby the cells are attracted or repelled by substances exhibiting
chemical properties.
Chemoton The chemoton model was introduced by Gnti in 1971 (see review Gnti 2002) as a
fundamental unit model of living systems. It consists in three functionally dependent autocatalytic
subsystems: the metabolic chemical network, the template polymerization and the membrane subsystem
enclosing them all. The correct functioning of the chemoton lies in the precise stoichiometric coupling
of the three subunits. It ensures that both the surface and the inner components evolve into doubling their
initial value, leading to the subsequent division into two identical chemotons. Besides the detailed
introductory papers of G nti, only a few studies of this model exist in the literature, presentinh however
contradictory conlusions. The present study aims toward a thorough survey of the chemoton’s
characteristics, such as replication period or optimal template length, in the parameters’ space.
Additionally, a comparative study between the deterministic approach and the stochastic one is
performed.
CSNDB (Cell Signaling Networks Database) A database for cell signaling networks.
http://geo.nihs.go.jp/csndb.html. Doesnt seem to be running anymore
Crosstalk The undesirable addition of one signal to another in a circuit usually caused by coupling
through parasitic elements. An example would be inductive or capacitive coupling between adjacent
conductors.
Cytokine Proteins manufactured by cells of various lineages that, when secreted, drive specific
responses (eg, proliferation, growth, or maturation) in other susceptible cells.
Cytoplasm the protoplasm of a cell excluding the nucleus, The material between the nuclear and cell
membranes; includes fluid (cytosol) organelles, and various membranes.
Cytosolic The cytosol (as opposed to cytoplasm, which also includes the organelles) is the internal fluid
of the cell, and a large part of cell metabolism occurs here. Proteins within the cytosol play an important
role in signal transduction pathways, glycolysis, and they act as intracellular receptors and form part of
the ribosomes, enabling further protein synthesis. In prokaryotes, all chemical reactions take place in the
cytosol.
Dimerization Dimerization is the formation of a polymer from two similar chemical structures.
Eukaryote Living organism composed of one or more cells with a distinct nucleus and cytoplasm.
Includes all forms of life except viruses and bacteria (prokaryotes).
G protein
Synonym: GTP binding protein
A heterotrimeric guanine nucleotide binding protein that transduces a signal derived from a
transmembrane receptor; also, small cytoplasmic proteins that regulate intracellular process.
Gap junction A specialized area of apposed plasma membranes containing connexons, proteins that
bridge the extracellular space and that allow the cytoplasm of one cell to communicate with that of the
other cell.
Genetic regulatory network A gene regulatory network (also called a GRN or genetic regulatory
network) is a collection of DNA segments in a cell which interact with each other and with other
substances in the cell, thereby governing the rates at which genes in the network are transcribed into
mRNA.
Homeostasis In biology used to describe a condition where an organism maintains a stable structure
where in fact a constant flux of molecules occurs. Although many organisms can live for years, all
cellular components like proteins, membranes, sugars, and nucleic acids are constantly recycled while
never compromising the integrity of the organism as a whole. This turnover processes can be
characterized by specific half-life values that for most proteins, membranes, and RNA (but not DNA
structures) are measured in hours. In a more narrow sense homeostasis refers to the maintenance of
water and salt concentration in cells
Kinase
Synonyms: Phosphokinase, Phosphotransferases, Transphosphorylases
An enzyme that catalyzes the transfer of phosphate groups from a high-energy phosphate-containing
molecule (as ATP or ADP) to a substrate.
Ligand A small molecule that binds specifically to a larger one; for example, a hormone is the ligand for
its specific protein receptor.
Lysis In biology, lysis refers to the breakdown of a cell caused by damage to its plasma (outer)
membrane. Lysis can be caused by chemical or physical means (for example, strong detergents or
high-energy sound waves) or by an infection.
Mesoscopic In physics and chemistry, the mesoscopic scale refers to the length scale at which
one can reasonably discuss the properties of a material or phenomenon without having to
discuss the behavior of individual atoms. For solids and liquids this is typically a few to ten
nanometers, and involves averaging over a few thousand atoms or molecules. Hence, the
mesoscopic scale is roughly identical to the nanoscopic or nanotechnology scale for most
solids.
Metabolism Sum of the physical and chemical changes that take place in living organisms. These
changes include both synthesis (anabolism) and breakdown (catabolism) of body constituents. In a
narrower sense, the physical and chemical changes that take place in a given chemical substance within
an organism. It includes the uptake and distribution within the body of chemical compounds, the
changes (biotransformations) undergone by such substances, and the elimination of the compounds and
their metabolites.
Metabolic control analysis (MCA)
Synonym: Metabolic control theory
Metabolic control analysis is a phenomenological quantitative sensitivity analysis of fluxes and
metabolite concentrations. In MCA one studies the relative control exerted by each step (enzyme) on the
system’s variables (fluxes and metabolite concentrations). This control is measured by applying a
perturbation to the step being studied and measuring the effect on the variable of interest after the system
has settled to a new steady state.
Monomer (Chemistry) Any molecule that can be chemically bound as a unit of a polymer. Neutron Star:
A collapsed star of extremely high density. Generally these objects have slightly more mass than the
Sun, but are only about 10 km in radius. A neutron star has intense gravity, and may also have an intense
magnetic field and fast rotational component. Oort Cloud: The spherical region around the Sun thought
to contain a large number of cometary bodies.
Osmosis Osmosis is the diffusion of a solvent through a semipermeable membrane from a region of low
solute concentration to a region of high solute concentration. The semipermeable membrane is
permeable to the solvent, but not to the solute, resulting in a chemical potential difference across the
membrane which drives the diffusion.
Organelle A subcellular structure having a specialized function for example the mitochondrion, the
chloroplast, or the spindle apparatus.
Phosphorylation The addition of a phosphate group to a compound by an enzyme (eg, thymidine
kinase, tyrosine kinase). Phosphorylation is an essential step in many cellular processes.
Polymer Large organic molecule formed by combining many smaller molecules (monomers) in a
regular pattern.
Polymerization A chemical reaction in which two or more small molecules combine to form larger
molecules that contain repeating structural units of the original molecules. A hazardous polymerization
is the above reaction with an uncontrolled release of energy.
Prokaryote Organism made of simple cells that lack a well-defined, membrane-enclosed nucleus: a
bacterium.
Protein A molecule made up of amino acids that are needed for the body to function properly. Proteins
are the basis of body structures such as skin and hair and of substances such as enzymes, cytokines, and
antibodies.
Regulatory sequences
Synonyms: Genetic regulatory element, Regulator regions, nucleic acid, Regulatory regions
Nucleic acid sequences involved in regulating the expression of genes.
Ribozyme A ribozyme, or RNA enzyme, is an RNA molecule that can catalyze a chemical reaction.
Many natural ribozymes catalyze either their own cleavage or the cleavage of other RNAs, but they have
also been found to catalyze the aminotransferase activity of the ribosome. Investigators studying the
origin of life have produced ribozymes in the laboratory that are capable of catalyzing their own
synthesis under very specific conditions.
Second messenger In biology, second messengers are low-weight diffusible molecules that are used in
signal transduction to relay a signal within a cell. They are synthesized or released by specific enzymatic
reactions, usually as a result of an external signal that was received by a transmembrane receptor and
pre-processed by other membrane-associated proteins. There are three basic types of second messenger
molecules:
These intracellular messengers have some properties in common:
http://www.nationmaster.com/encyclopedia/Second-messenger
SPAD (Signaling Pathway Database) The Signaling PAthway Database is an integrated database for
genetic information and signal transduction systems.
http://www.grt.kyushu-u.ac.jp/spad/
Signal transduction The cascade of processes by which an extracellular signal (typically a hormone or
neurotransmitter) interacts with a receptor at the cell surface, causing a change in the level of a second
messenger (for example calcium or cyclic AMP) and ultimately effects a change in the cell’s functioning
(for example, triggering glucose uptake, or initiating cell division). Can also be applied to sensory signal
transduction, eg. of light at photoreceptors.
Stoichiometric Calculation of the quantities of chemical elements or compounds involved in a chemical
reaction.